KaPPA-View 4
The Kazusa Plant Pathway Viewer, Version 4.0

Advanced Manualver. 1.0

Kazusa DNA Research InstituteLegal Notices
We have done our best to ensure that the material contained within this document is both useful and accurate.
However, please be aware that errors may exist in this document and that the information contained in thismanual is subject to change without notice. We make no warranty of any kind with regard to this material.
We shall not be held liable for errors contained herein and/or for direct or indirect damage that might beincurred as a consequence of using of KaPPA-View4.
This document and KaPPA-View contain proprietary information that is protected by copyright. All rightare reserved.
KaPPA-View Copyright © 2004-2011, Kazusa DNA Research Institute. All rights reserved.
Adobe® and Acrobat® are trademarks of Adobe Systems Incorporated. All rights reserved.
Microsoft®, Windows®, and other Microsoft products referenced herein are trademarks of Microsoft
Corporation.
Apple®, Macintosh®, and Mac OS®, and other Apple Computer products referenced herein are
trademarks of Apple Computer, Inc.
All other trademarks are the property of their respective owners. All rights reserved.

KaPPA-View4 Advanced Manual

Table of Contents
1. Introduction .................................................................................................... 1
1-1. Background and History ........................................................................................... 1
What is "KaPPA"? ..................................................................................................................... 1

1-2. Overview of KaPPA-View4 ....................................................................................... 1
1-3. User Setup ............................................................................................................... 4
1-4. Other Manuals .......................................................................................................... 5

2. Login, Logoff and User Privileges ................................................................ 6
2-1. Access to KaPPA-View4 .......................................................................................... 6
2-2. Login as a Guest User ............................................................................................. 6
2-3. Main Menu................................................................................................................ 7
2-4. User privileges.......................................................................................................... 8
2-4-1. Guest and Power Users .................................................................................................. 8
2-4-2. Create User Account....................................................................................................... 8
2-4-3. Expiration of Power User ................................................................................................ 8

2-5. Login as a Power User ............................................................................................. 9
2-5-1. Power User Menu (Side Menu) ....................................................................................... 9
2-5-2. Changing the Password ................................................................................................ 10
2-5-3. Editing Power User Information .................................................................................... 10

2-6. Logoff ..................................................................................................................... 11
2-6-1. Automatic Logoff ........................................................................................................... 11

3. Uploading and Management of Data........................................................... 12
3-1. Temporary and Permanent Uploading ................................................................... 12
3-2. Uploading Experiment Data ................................................................................... 12
3-3. Uploading User Maps ............................................................................................. 13
3-4. Uploading Correlation Data .................................................................................... 14
3-5. Management of Uploaded Data (for Power Users) ................................................ 15
3-5-1. Editing of Data Information............................................................................................ 15
3-5-2. Removing Data ............................................................................................................. 16

3-6. Sending User Maps to the KaPPA-VIew4 Administrator (for Power Users) .......... 16

4. Data Analysis ............................................................................................... 18
4-1. Data Selection for Browsing ................................................................................... 18
4-1-1. Creation of a "Compared Experiment Pair" ................................................................... 18i

Contents

4-1-2. Selection of Compared Experiment Pairs for Browsing ................................................ 23

4-2. Data Browsing on the Maps ................................................................................... 25
4-2-1. The Data Browsing Window .......................................................................................... 25
4-2-2. Metabolic Pathway Tree ............................................................................................... 27
4-2-3. Map Mode ..................................................................................................................... 28
4-2-4. Metabolic Pathway Map ................................................................................................ 30
4-2-5. Pop-up Information Window .......................................................................................... 36
4-2-6. Bird's Eye Map .............................................................................................................. 38
4-2-7. Thumbnails of the Maps ................................................................................................ 43

4-3. Data Analysis Functions ......................................................................................... 43
4-3-1. Simple Map ................................................................................................................... 43
4-3-2. Multiple Map Mode ........................................................................................................ 45
4-3-3. Overlay of Correlation Data........................................................................................... 47
4-3-4. Comparison of Two Experiments in One Species ......................................................... 52
4-3-5. Data Comparison between the Species ........................................................................ 53
4-3-6. Displaying All Experiment Data ..................................................................................... 55

5. Map Browsing Functions............................................................................. 56
6. Searching ..................................................................................................... 57
6-1. Gene, Compound and Enzymatic Reactions ......................................................... 57
6-2. Blast Searching ...................................................................................................... 58

7. Download...................................................................................................... 60
8. Utilization from External Systems .............................................................. 62
8-1. Data Uploading APIs .............................................................................................. 62
8-1-1. Data Transferring Procedure......................................................................................... 62
8-1-2. Sample Codes .............................................................................................................. 63
8-1-3. Behavior of KaPPA-View4 after the Transferring .......................................................... 64

8-2. Direct Access by IDs of Gene, Compound, Reaction, and Map ............................ 64
8-2-1. URL Format .................................................................................................................. 64
8-2-2. Specifying Species........................................................................................................ 67

9. File Format.................................................................................................... 69
9-1. General Notices...................................................................................................... 69
9-2. Experiment Data for Uploading .............................................................................. 69
9-2-1. Data Part....................................................................................................................... 69
9-2-2. Header Part................................................................................................................... 71

9-3. Correlation Data ..................................................................................................... 76ii

KaPPA-View4 Advanced Manual

9-3-1. Format .......................................................................................................................... 77
9-3-2. Sample.......................................................................................................................... 77

9-4. User Map ................................................................................................................ 78
9-5. Data for POST Transferring ................................................................................... 79
9-5-1. Structure of POST Data ................................................................................................ 79
9-5-2. Format .......................................................................................................................... 80
9-5-3. Sample.......................................................................................................................... 82

10. Default Data ................................................................................................ 84
10-1. System Data, Species, and Correlation Data ...................................................... 84
10-2. Experiment Data .................................................................................................. 84

11. Hints and Trouble Shootings .................................................................... 86
11-1. Getting a Screen Shot .......................................................................................... 86
11-2. Two-color Microarray Data ................................................................................... 86
11-3. One-color Microarray Data ................................................................................... 87
11-4. Investigating Compound IDs ................................................................................ 87
11-5. Representation of non-omics data on the maps .................................................. 87

12. Acknowledgements ................................................................................... 89
13. References.................................................................................................. 90
Papers about KaPPA-View ........................................................................................... 90
Other Related Papers .................................................................................................... 90

14. About Us ..................................................................................................... 91
Team KaPPA-View ........................................................................................................ 91
Axiohelix Co. Ltd............................................................................................................ 91
Corporate Headquarters.......................................................................................................... 91
Tokyo Office ............................................................................................................................ 91

15. Manual Versions......................................................................................... 92iii

Contentsiv

KaPPA-View4 Advanced Manual

1. Introduction
1-1. Background and History
The application of DNA array technology and chromatographic separation techniques coupled with mass
spectrometry (MS) to transcriptomic and metabolomic analyses in plants has resulted in the generation of
considerable quantitative data related to transcription and metabolism. The integration of "omic" data is oneof the major concerns associated with research into identifying gene function. Thus, we developed a
web-based tool, KaPPA-View, (The Kazusa Plant Metabolic Pathway Viewer), for representing quantitativetranscript and/or metabolite data using comprehensive metabolic pathway maps for Arabidopsis thaliana(Tokimatsu et al. 2005, Tokimatsu et al. 2006, and Sakurai et al. 2006). We prepared about 130 leaves oforiginal metabolic pathway maps in Scalable Vector Graphics (SVG) format to represent the values of geneand compound on the map symbols dynamically according to the experiment data.
In 2006, we released the second version of the tool, KaPPA-View2, which implemented a function to
overlay curves on a pathway map representing gene-to-gene and metabolite-to-metabolite relationships suchas co-expression and co-accumulation correlation coefficients. This novel representation of the data
facilitated better understanding of metabolic regulation within the genes of a pathway map. In
KaPPA-View3 which released in 2008, we expanded this function to draw the curves across maps. In
addition, users able to analyze correlations between genes on the maps and non-metabolic genes such astranscription factors and genes for signal transductions by creating simple maps which are automaticallygenerated according to the users input of arbitral gene IDs. Furthermore, KaPPA-View3 can deal withmetabolic maps of any organisms, means these pathway analyses are applicable not only to Arabidopsis but
also various kind of plants.
As the size of the correlation data become huge, the performance of the data analysis was not so goodwhen correlation curves were drawn on the map(s) with a lot of gene and compound symbols. Therefore, we
reviewed the database system, web application programs, and the representation procedures based on the
SVG. By using Flash technology, a drastic speed up has accomplished for the representation of the maps.
Thus we released the latest version of the system, KaPPA-View4 in 2010 (Sakurai et al. 2011,
http://kpv.kazusa.or.jp/kpv4/). The version is also improved on the function to access from the external
systems, by which developers of other databases or applications can easily incorporate a viewer function toview their omics data on KaPPA-View4. In addition to the KaPPA-View4 system with the original
pathway maps (KaPPA-View4 Classic), we provide another version of KaPPA-View4 where pathway maps
from KEGG PATHWAY (http://www.genome.jp/kegg/) are available (KaPPA-View4 KEGG,
http://kpv.kazusa.or.jp/kpv4-kegg/). We wish the KaPPA-View4 families would be a powerful tool on yourdesk side to discover novel gene functions.

What is "KaPPA"?
"KaPPA" stands for the real name of the tool "Kazusa Plant Metabolic Pathway Viewer". It also stands forthe name of an imaginary creature in Japanese fairy story. "Kappa", which looks like a man but with a dishon his head and a large shell on his back, lives in a stream, such as a turtle does, and catches game from thesurrounding world. KaPPA is always looking at transcriptome and metabolome to catch big game from theplant world.

1-2. Overview of KaPPA-View4

1

1. Introduction

When you upload your own DNA microarray data and/or metabolite data to the system through the webbrowser, KaPPA-View4 displays the fitting of data for each gene or compound on the metabolic pathwaymaps.

UploadDNA microarray
Data

Metabolite
Data

Pathway
Map Data

Display on
the browser

KaPPA-View4
ServerUser's PC

On the pathway maps, genes and compounds are represented by squares and circles respectively. The
symbols are painted in different colors depending on the values such as changes in the ratio between two
experiments and the amounts detected in one experiment.

Ratio(Exp. A/ Exp. B)

Expression(Accumulation)amount

High

Large

No

Low

Small

On the "Bird's-Eye Maps", you can view the summarized values for all maps and find out the pathways
which have changed considerably.

2

KaPPA-View4 Advanced Manual

Non-metabolic genes which do not exist on the maps - such as transcription factors - can be analyzed. By
entering the gene IDs, you can create simplified maps.

In addition, the users can also use the pathway maps prepared by themselves.

Up to four maps can be viewed at once in a single browser window.

31. Introduction

Furthermore, gene-to-gene and/or metabolite-to-metabolite relationships such as co-expression correlationsof genes can be displayed on the maps. This is the distinctive feature of KaPPA-View and will help you, forexample, to analyze the relationships between metabolic genes and transcription factors that control theirexpressions.

KaPPA-View4 can handle multiple species, and genes of several species can be displayed side by side on
the maps. The system also provides functions to upload and view the omics data from external applications.

1-3. User Setup
As KaPPA-View4 is a web-based system, it works well with major web browsers (Microsoft
InternetExplorer, Firefox, Google Chrome, Safari and Opera) on any operating systems (Windows
XP/Vista/7, Mac OS X and Linux).
Although the Adobe Flash Player plug-in (ver.9 or higher) is required to display the pathway maps, it isalready installed in your browser in the most cases. If your browser doesn't have it, please install it
according to the following site.
http://www.adobe.com/products/flashplayer/

Please be sure to install the latest version of java plug-in in your browser. The older version might be causeof unexpected trouble in page constructions.
The operation of KaPPA-View4 was tested in the following settings.

4

KaPPA-View4 Advanced ManualOS

Windows XP / Vista / 7 (Microsoft)

Mac OS X (Apple)

BrowserInternet Explorer 6, 7, 8

Safari 4.0.4

Mozilla Firefox 3.0.10, 3.5.2, 3.6.10

Mozilla Firefox 3.5.6, 3.6.10

Google Chrome 3.0, 6.0

Opera 9.63, 10.10*In the case of Opera on Mac OS X, the full screen view of the maps does not work.
*Disable the pop-up blocking function of your browser. It is enabled in default for Safari, Opera, and recent
Firefox and Google Chrome.

1-4. Other Manuals
This manual describes all the functions of KaPPA-View4. Refer to "Manual for Beginners" to learn the mainfunctions and work flow of the analyses. The procedure to create User Maps using free-software "Inkscape"is described in detail in "Manual on User Map Creation". These manuals are also available from the top pageof the KaPPA-View4 site.

52. Login, Logoff and User Privileges

2. Login, Logoff and User Privileges
For the first step of the analyses, we introduce the way to login, main menu and how to upload theexperimental data to KaPPA-View4. There are two types of users in KaPPA-View4, Guest Users and Power
Users.

2-1. Access to KaPPA-View4
Visit to the URL below to show the top page of KaPPA-View4.
http://kpv.kazusa.or.jp/kpv4/

2-2. Login as a Guest User
Click "Enter" button at the top page.

After logging-in, you can see the main window.

6

KaPPA-View4 Advanced Manual

2-3. Main Menu
The main menu is places at the top of the window.

• MainReturn to the main window.

• Temporary Upload
Uploading your experimental data, User Map data and correlation data for your analyses is operated throughthis menu. All the uploaded data is going to be deleted completely after you are logging-out.

• Analysis
Uploaded data is displayed on the pathway maps through this menu. It serves the central function of
KaPPA-View4.

• Map View
You can browse plain pathway maps with no data from here.

• Search
You can search genes, metabolites and enzyme reactions from here, and access to the pathway maps which
they are on. Homology search function by blast to find genes is also provided.

• Download
The default experimental data publicly available on the KaPPA-View4 and information data for genes,
metabolites, reactions and maps for each species are downloadable as text files.

72. Login, Logoff and User Privileges

2-4. User privileges

2-4-1. Guest and Power Users
There are two types of users, Guest User and Power User. Power Users can save their experiment data on
the KaPPA-View4 server, facilitating to start analyses immediately after logging-in. There are nodifferences on the analysis functions between the user types.
Guest User

The data uploaded to the KaPPA-View4 is removed when the user
logging-off, therefore data have to be uploaded at the beginning of eachanalysis.

Power User

The data can be registered on the KaPPA-View4 server, therefore they are
immediately utilized for the analyses.

The Guest Users can create a Power User account by simple steps.

2-4-2. Create User AccountClick on "Create Account" at the top right of the window after logging-in.

A pop up window appears. Enter your favorite name and e-mail address, then press "Submit".

An e-mail informing the login password will be sent immediately to the address.

2-4-3. Expiration of Power User
The Power User account will be removed automatically if the Power User have not logged-in to the systemfor 30 days. The data uploaded by the Power User will be deleted too. An e-mail alerting this will be sent to
the Power User a week before the expiration date.

8

KaPPA-View4 Advanced Manual

2-5. Login as a Power UserEnter user name and password at the top page of KaPPA-View4 and press "Login" to enter as a Power User.

The main window for Power Users appears.

2-5-1. Power User Menu (Side Menu)
An additional menu for Power Users is visible on the left hand side of the main window.

• "Personal" Column
Uploading of experiment data, User Maps, and correlation data can be operated. The data uploaded throughthe side menu are stored in the KaPPA-View4 server. Editing and removing of the data can be done on the"Personal Data List". The data are securely managed in the system and never accessed by the other users.

9

2. Login, Logoff and User Privileges• "Utilities" Column
The password and user information such as e-mail address can be edited.

2-5-2. Changing the Password
We have done our best to manage securely the Power Users' data, but we recommend changing the
password periodically to ensure it more secure.

Click "Password Change" on the Side Menu.

Enter old and new passwords and click "Submit".

2-5-3. Editing Power User Information
The Power User can edit the user information. The information is never used for any propose without apermission of the Power User other than recognizing the user and sending announcement e-mails by the
KaPPA-View4 administrator.

Click "Profile Edit" on the Side Menu.

10

KaPPA-View4 Advanced Manual

Edit the information and press "Submit".

2-6. Logoff
You can log-off from the system, by clicking "Log off" on top-right of the main window.

All your data uploaded according to the next chapter will be deleted from the system after logging-off.

2-6-1. Automatic Logoff
If you don't do any operations for 60 min after you log-in, the system regards as you are log off. The
message below appears when you do an operation again.

You are automatically log off when you close all the browser's windows too.

11

3. Uploading and Management of Data

3. Uploading and Management of Data
The users can upload their own experiment data, map data, and correlation data to KaPPA-View4 and cananalyze them on it. This chapter covers the procedures for uploading and management of these user's data.
Refer to the 9. File Format for the details of the uploading files.

3-1. Temporary and Permanent Uploading
There are two types of data uploading procedures as follows.
Temporary Uploading

The uploading is performed through the "Temporary Upload" function on
the Main Menu.
The uploaded data are treated as temporary data and deleted after
logging-off.

Permanent Uploading

The uploading is performed through the Side Menu of Power Users'
main window.
The uploaded data are stored in the KaPPA-View4 server and can beutilized by the user immediately after logging-in. The data are removed
from the server when the Power User's account is deleted.

The uploading procedures are essentially the same, except the menu to access them differs.

3-2. Uploading Experiment Data
Experiment data are those such as gene expression data obtained by DNA microarrays and metabolite datadetected with metabolomics technologies. The experiment data uploaded to the KaPPA-View4 can beaccessed through the "Analysis" function and utilized for representation on the pathway maps.
Follow the step below to show the Experiment Data uploading interface.
Temporary Uploading

Click "Temporary Upload" on the Main Menu and then select"Experiment" tab.

Permanent Uploading

Click "Experiment Upload" on the Side Menu.

Click "Browse" to select the uploading file on your PC, and press "Upload".

The selected file is scanned and the the names and repetition numbers of the experiment are listed. Select a
type of data (Transcript or Metabolite) and species name, and change experiment names and repetition

12

KaPPA-View4 Advanced Manual

numbers if it needed, and then click "Submit" to start uploading and registration the data to the
KaPPA-View4 server.

*Click "Preview" to confirm the data by listing first 100 lines of the file before submitting.

After completing the process, you can see the following message. It takes a few tens of seconds.

If the file contained experiment IDs that are already used in the KaPPA-View4, the following message
appears. By clicking "execute" the old data will be overwritten by new one.

3-3. Uploading User Maps
In addition to the metabolic pathway maps that are provided by KaPPA-View4 as defaults, users can upload
their own pathway maps (User Maps) and utilize them for their analyses. The free software "Inkscape" isused to create the User Maps in scalable vector graphics (SVG) format. Refer to "Manual on User Map
Creation" for the details of User Map preparations.
Follow the step below to show the User Map uploading interface.
Temporary Uploading

Click "Temporary Upload" on the Main Menu and then select "Map"tab.

Permanent Uploading

Click "User Map Upload" on the Side Menu.

Click "Browse" to select the User Map file (.svg) on your PC, and then press "Upload".

13

3. Uploading and Management of Data

A preview appears under the interface. Enter the map name and press "Submit" button. The "Comment" canbe left blank.

The map name will be displayed on the Metabolic Pathway Tree on the "Analysis" and the "Map View"functions.

After completing the process, you can see the following message.

3-4. Uploading Correlation Data
Gene-to-gene and metabolite-to-metabolite relationships such as correlation coefficients of gene
co-expressions and metabolite co-accumulations can be overlaid on the pathway maps. This is the uniquefunction of KaPPA-View4, facilitates researchers to find new functions of the genes and their regulatory
mechanisms.
Follow the step below to show the Correlation Data uploading interface.
Temporary Uploading

Click "Temporary Upload" on the Main Menu and then select"Correlation" tab.

Permanent Uploading

Click "Correlation Upload" on the Side Menu.

Click "Browse" button to select the correlation data file on your PC. Select the data type (Gene orCompound), enter the data name and comment, and press "Upload".

After completing the process, you can see the following message. It might take a few dozen of seconds toseveral minutes according to the file size.

14

KaPPA-View4 Advanced Manual

3-5. Management of Uploaded Data (for Power Users)
The data uploaded by a Power User according to the procedure for permanent uploading can be edited anddeleted by the Power User.

Click "Personal Data List" on the Side Menu.

Select "Data Type" and click "Search" button to list up the uploaded files. The resulted items can be filteredby keywords and date of uploading.

3-5-1. Editing of Data Information"Edit" buttons appear at the right of each row of the list when "Experiment Set" was selected. Press the"Edit" button to pop up detailed information (meta data) for the experiment data.

Press "Update" after editing the meta data to reflect the alteration.

15

3. Uploading and Management of Data

3-5-2. Removing Data
Check the items to delete and Click "Delete" button.

3-6. Sending User Maps to the KaPPA-VIew4 Administrator (forPower Users)
Despite our best effort, there may be information error or deficiency in the default map. Once user maps
with corrected errors or species specific pathways that default map didn’t cover are completed, consideration
them to the public is greatly appreciated.
Power Users can send their user map to the KaPPA-View4 administrator with simple steps. The
administrators will discuss on using the user map for improving the default map. We acknowledge the mapdonor with a great appreciation.

The "Send to Admin" button appears when "Map" is selected as a data type. Check an item and click "Sendto Admin" button.

A window pops up to show the preview of the map. Enter comments to the administrators and press"Submit" to send the map data.

16

KaPPA-View4 Advanced Manual

The message can be either in English or Japanese. The administrator will e-mail the user to discuss thetreatment of the user map.

Do not forget to send the following information.

- NameUsed for specifying the contribution.
- Affiliation
Used for specifying the contribution.
- Contact e-mail address
The administrator may contact regarding the user map information.
- Use of the user map
1) Information addition to the default map
2) Curation of the default map
3) Adding a new map
Please let us know the suitable species and position on the Pathway Tree.

Note:
Convert all characters to outlines when the user map to be sent uses any fonts other than Arial.

174. Data Analysis

4. Data Analysis
This chapter covers the functions of data analyses on the metabolic pathway maps which are available
through the "Analysis" on the Main Menu. KaPPA-View4 provides various analysis functions as listed
below.

- The genes, compounds and enzymatic reactions represented as squares, circles and arrows, respectively,
are painted with proper colors according to the experiment data.
- Up to 4 maps can be simultaneously displayed and used for the analysis on a single browser window.
- Genes not drawn on the default maps can be analyzed by creating "Simple Maps" from the user-input gene
IDs.
- Gene-to-gene and/or metabolite-to-metabolite relationships such as correlation coefficients of gene
co-expressions and metabolite co-accumulations can be overlaid on the pathway maps.
- Overview of experiment data and correlation data are available through Bird's Eye Maps.
- Experiment data can be compared between the species and the results are represented on the maps.
- Two experiment data from a species can be compared and represented on the maps.

4-1. Data Selection for Browsing
In KaPPA-View4, a unit of analyzing data is defined as a compared data between two experiments. We refer
this unit as a "Compared Experiment". One Compared Experiment is comprised of a pair of gene expression
data, a pair of metabolite data, or both of them.

Compared Experiment
Gene expression data
Exp. Data 1
Exp. Data 2

Metabolite data
Exp. Data 1
Exp. Data 2

4-1-1. Creation of a "Compared Experiment Pair"

18

KaPPA-View4 Advanced Manual

Click "Analysis" on the Main Menu.

A data search window appears. Select a species, check Experiment Type (TRANSCRIPT or
METABOLITE) and press "Search" button to list up the registered data. The results can be filtered by otherconditions such as uploaded date if it needed.

The data uploaded by the users according to 3. Uploading and Management of Data and the default
data provided by KaPPA-View4 are available from the list.

In KaPPA-View4, several experiment data can be grouped and managed as "Experiment Set". For example,
DNA microarray data obtained at several time points after a drug treatment can be registered as anexperiment set. The items appeared in the list show the names of the Experiment Sets. By clicking an arrowhead ( ) placed on the left of each row, each experiment experiment data belonged to the Experiment Set
appears.

19

4. Data Analysis

Click a data icon () to add the data on the "Selected Experiment" panel at the top-right.

By clicking the icon of another data, the data is registered as the second data.

The added data can be removed by clicking the remove data icon () on the "Selected Experiment" panel.

After selecting a pair of gene expression data, users can further select a pair of metabolite data as following
the similar procedure described above. Select "METABOLITE" for Experiment Type for adding metabolite
data.

20

KaPPA-View4 Advanced Manual

After adding a pair of transcript data, a pair of metabolite data, or both of them, enter a name and click"Add" to register a Compared Experiment Pair.

The registered Compared Experiment Pairs will be listed at "Compared Experiment List" as shown below.

Click remove icon ( ) or edit icon ( ) placed beside the Compared Experiment Pairs to delete or edit
them. When the edit icon ( ) clicked, the registered information appears in the "Selected Experiment"
panel. Edit the selection of the data and/or the name, and click "Add" button again to fix the alteration.

21

4. Data Analysis

The users can register several Compared Experiment Pairs by repeating these steps.

The registered Compared Experiment Pairs are effective until logoff.

• Type of Experiment Data
There are two types of experiment data, "quantitative" data and "ratio" data, which are recognized at theright most column of the experiment list.
A "quantitative" data holds quantitative values from a single experiment data. The users can register a pairof two quantitative data as a Compared Experiment Pair.
A "ratio" data holds ratio data such as gene expression ratio values detected by a 2-color DNA microarrayexperiment. The ratio data can be registered by itself alone without pairing to another data to create a
Compared Experiment Pair.

As the gene expression data and metabolite data must be described in log scale and linear scale, respectively,
the changed values between the two quantitative data of the Compared Experiment Pair are calculated by thesubtraction (for genes) and division (for metabolites) of them during the process of color representations on
the maps. In the actual data processing, the "ratio" data is treated as a special case of a "quantitative" data
which is paired to a control data where all the genes have value of 0 and all the metabolites have value of 1.

• Representation of Quantitative Data
In addition of representations of a pair of two quantitative data (normal usage), a quantitative data from asingle experiment can be represented also on the pathway maps to use this property. There are two
approaches.

1) Upload the quantitative data obtained from a single experiment as a "ratio" data.

22

KaPPA-View4 Advanced Manual2) Upload the quantitative data obtained from a single experiment as a "quantitative" data, and upload
another control data as "quantitative" which contains expression values of all the genes as 0 or values of all
the metabolites as 1. Create a Compared Experiment Pair with the two data.

Note:
The color gradation which indicates the magnitude of the values in KaPPA-View4 is set so that no change
genes and metabolites are painted in the color at the center of the gradation. As gene expression values aretreated as log scale and metabolite values as linear scale, 0 and 1 as calculated ratio are the values
corresponding to no change for the genes and the metabolites respectively. Therefore, to represent
transcriptome and metabolome changes appropriately on the maps with the maximum range of color
gradation, we recommend normalizing the data by a proper value such as global mean and median to adjust
the representative to be colored in the center color of the gradation.

4-1-2. Selection of Compared Experiment Pairs for Browsing
Select Compared Experiment Pairs to be represented on the pathway maps. Up to 8 pairs can be selected
here. The names of the selected pairs are listed at the upper part of the map browsing window, and byclicking them each data can be quickly displayed on the maps.

Check the Compared Experiment Pairs to browse at the "Compared Experiment List".

Click "Next" to transit to the next page.

23

4. Data Analysis

In this page appeared, users can change the directions of ratio calculations and can select the repetition data
to be calculated.

Select directions of the ratio calculations from the pull-down lists. This is disabled for "ratio" data.

An experiment data can include more than one experimental repetition and they can be distinguished by therepetition number (Refer to 9. File Format for more details of data file format). The repetitions included in
the data showed in the "Repetition" column. Uncheck the repetitions if you don't like to include them for the
analysis. Representative values for the genes and metabolites are the mean values calculated only with thechecked repetitions. And then, the ratios are calculated as the decided directions.

Click "Next" to proceed.

The data browsing window appears.
Select a species corresponds to the selected Compared Experiment Pair from the pull-down list.

24

KaPPA-View4 Advanced Manual

Select a pathway map from the "Metabolic Pathway Tree" to show the pathway map on the right side of thewindow.

4-2. Data Browsing on the Maps

4-2-1. The Data Browsing Window
The data browsing window is composed of 4 parts.

25

4. Data Analysis

B
A

C

D

A: Pathway Tree
Metabolic pathway maps are categorized and represented as a tree structure. By selecting a species from thepull-down list, the metabolic pathway tree for the species displayed. Click a leaf of the tree to show thecorresponding metabolic pathway map in the area C. When a branch of the tree is clicked a category
indicator map corresponding to the category appears in the area C (Bird's Eye Maps, see 4-2-6. Bird's Eye
Map). When "Universal" is selected from the pull-down list, maps for representing all species genes will be
displayed (Universal Map Mode, see 4-2-3. Map Mode). The "Create Simple Map" button appears if a
species other than "Universal" is selected, which is utilized for creating a Simple Map according to theuser-input gene IDs (see 4-4-1. Simple Map).

B: Upper Control Panel
The names of the selected Compared Experiment Pairs are displayed. By clicking one of them thecorresponding data are represented on the maps in the area C. Data comparison between the Pairs can be
performed through the interface in Universal Map Mode.

C: Map Area
According to the settings of the Pathway Tree and the Control Panels, metabolic pathway maps and categorymaps are displayed.

26

KaPPA-View4 Advanced Manual

D: Lower Control Panel
There is a setting button for Multiple Map Mode where up to 4 maps are displayed in the area B (see 4-4-2.
Multiple Map Mode). There is also a control panel for correlation data overlaying (see 4-4-3. Overlay of
Correlation Data).

4-2-2. Metabolic Pathway Tree
The Metabolic Pathway Tree provides an interface to select species and pathway maps to view.

When a leaf (lower most layer of the tree) is selected, the individual pathway map is displayed.

When a branch (internal node of the tree) is selected, a map is displayed where all the pathway maps
belonging to the category are schematically indicated as indicator bars (Bird's Eye Map, see 4-2-6. Bird's
Eye Map).

27

4. Data Analysis

Click "View Thumbnails" button when a Bird's Eye Map is displayed to switch the Map Area to a tree-like
representation of pathway map thumbnails.

4-2-3. Map Mode
The pull-down list above the Pathway Tree is an interface to switch the species to view. When a speciesname is selected in the pull-down list, the Pathway Tree corresponding to the species appears, and thepathway maps with the gene symbols for the species are displayed. We call this mode as "Species Map
Mode".

28

KaPPA-View4 Advanced Manual

When an item "Universal" is selected in the pull-down list, a Pathway Tree for all species appears and thepathway maps with the genes from all the species are displayed. We call this as "Universal Map Mode".

29

4. Data Analysis

Users can select the kind of the species that are represented on the pathway maps in Universal Map Mode.
Click "Select Species" button below the Map Area to show a pop up window for species settings. Check the
species, click "Submit" to fix the change, and click "Redraw" to refresh the Map Area.

4-2-4. Metabolic Pathway Map• Map Symbols
The elements on the pathway maps such as genes, compounds, and enzymatic reactions are represented as
the following symbols.
Element
genes

30

SymbolNote(Squares)KaPPA-View4 Advanced Manual

metabolites(Circles)enzymereactions(arrows)

The color of the arrows correspond to the meanvalue of the genes assigned
to the reactions.

links to the othermaps

By clicking, the corresponding pathway maps is
displayed.

pathway name(round rectangles with a
text)

genes

(Squares with)

When there is not an enough space to draw all
the genes near by the enzyme reactions, thissymbol is displayed. By clicking this, thesymbols of the genes are shown in a pop-up
window.

• Color Painting on the Symbols

31

4. Data Analysis

In the "Analysis" function, the symbols are painted as colors according to the experiment data. Click "Color
Legend" to check the color settings.

The pop up shows the colors and the corresponding ranges of the values of genes and metabolites that arecalculated as ratio between the experiment data paired in the Compared Experiment Pair. The value ranges
are shown in the scale of logarithm based on 10 for transcripts and linear scale for metabolites.
A color of an arrow representing enzymatic reaction is based on the average value calculated with the valuesof the genes assigned to the reaction. The arrow never painted in the Universal Map Mode.

Users can change the range of the values for the color paintings. Click "Histogram" to show a setting
window.

32

KaPPA-View4 Advanced Manual

A histogram of changes of gene expression values in the current data is represented. The boundary values of
the ranges are displayed in both log and linear scale. Click "Metabolite" to refer a similar histogram forchanges of metabolite values.
In default, 5 for transcripts and 100 for metabolites (as linear scale) are set as a boundary value to express
the strongest color (red). In other words, genes that expressions were changed more than 5 fold isrepresented in red.

Users can change the boundary value for the strongest color. Input a value into the "Highest Linear Value"
field, and click "Calc" button. The histogram is refreshed.

33

4. Data Analysis

Click "Submit" to fix the alteration. Press "Redraw" button to refresh the Map Area.

• Experiment Values
The value of each symbol can be seen in several ways.

- Place the mouse cursor on the symbols. The change value appears in a tool chip.

- Click a symbol to open the Pop-up Information Window for more details (see 4-2-5. Pop-up
Information Window).

34

KaPPA-View4 Advanced Manual- Click "Element List" to show a list of the genes, compounds and reactions on the current pathway map.

In Universal Map Mode, users can select the species to list up.

35

4. Data Analysis• Printing Maps
Click "Print Map" to print the current map. A pop up window opens to show the printout image. Right clickon the image and select "Print" to print.

• Downloading Maps
The pathway maps on the KaPPA-View4 are prepared in scalable vector graphics (SVG) format. Click"Print Pain Map" to download the SVG file for the current map. The downloaded files can be used as
templates for creating User Maps (Refer to the Manual on User Map Creation).

4-2-5. Pop-up Information Window
By clicking on the symbols for genes, compounds, and enzymatic reactions, the Pop-up Information
Window opens to show detailed information for the element. Users can see the experiment values, the othermaps which also have the element on them, links to the related databases and so on.

36

KaPPA-View4 Advanced Manual

An example of a Pop-up Information Window for a gene is shown below. When several Compared
Experiment Pairs are analyzed, the values are represented in a line graph.

On the information window for an enzymatic reaction, the values of all the genes assigned to the reaction are
represented. By clicking on a line in the graph, users can jump to the information page for the clicked gene.

37

4. Data Analysis

An example of compound information page is shown below.

4-2-6. Bird's Eye Map

38

KaPPA-View4 Advanced Manual

By clicking on an inter nodes of the Pathway Tree, the corresponding categories are represented as a Bird's
Eye Map where all the pathway maps belong to the category are indicated as indicator bars. Users can jump
to the individual pathway maps and other Bird's Eye Maps for child categories by clicking on the indicator
bars and the area surrounding the bars, respectively.

As described below, Bird's Eye Map can be used to summarize the experiment data for each pathway map
and overview all of them.

• Map Names
Just after clicking on the internal nodes on the Pathway Tree, the names of the pathway maps are
represented in the indicator bars.

When experiment data or correlation data are represented on the Bird's Eye Map in Species Map Mode,select "Name" from the "Display Mode" pull-down list at the top-right of the Map Area to switch to the map
name representation.

39

4. Data Analysis• Experiment Data
Select "Experiment" from the "Display Mode" pull-down list in the Species Map Mode to represent
summaries of experiment data.

Each indicator bar shows following information.

ex.)

T: Transcripts

40

KaPPA-View4 Advanced Manual

The denominator shows the number of genes drawn on the pathway map (43), and the numerator shows thenumber of genes having valid values in the current experiment data (42).
M: Metabolites
The denominator shows the number of compounds drawn on the pathway map (14), and the numerator
shows the number of compounds having valid values in the current experiment data (8).
Colors on the bar:
It shows proportions of the genes (left) and metabolites (right) painted in the color on the pathway map.

Therefore, if a large proportion of the color bar for genes on a pathway map was painted heavily in red, we
can recognize that expressions of most of the genes on the pathway were enhanced in the current datacomparison, implies the pathway might be activated.

When multiple Compare Experiment Pairs were analyzed, a data selection pull-down list appears at thebottom-left of the Map Area. Select an item and click "Select" button to switch the data.

• Correlation Data
Number of gene-to-gene and metabolite-to-metabolite relationships on the pathway maps can be represented
on the Bird's Eye Maps. Refer to 4-4-3. Overlay of Correlation Data for more details on representationof correlation data.

Select "Correlation" for "Display Mode" and click "Select" button in Species Map Mode.

The correlation control panel appears in the Lower Control Panel. Select a data and set ranges to compile
and view data.

41

4. Data Analysis

The relationship numbers are represented in the Bird's Eye Map as shown below.

The numbers written beside "T:" or "M:" (numerators) show the numbers of the correlation lines on thepathway maps. The numbers after the slashes ("/") (denominators) indicate the numbers of the genes or
metabolites drawn on the maps. For the indicators of the middle tiers, both of the numerators and thedenominators are the sum of the line and element numbers included under the tier.

The color of the bar is decided as follows.

When defined,
D: log10( line number / element number ) of a map,
Dmax: The maximum value of D among the maps under the current tier, andDmin: The minimum value of D among the maps under the current tier,the bar of the map having Dmax is painted in the strongest color (red), and the map of Dmin is painted in theweakest color (green).
Therefore, the maps having dense relationships are painted stronger colors.
*Correlations calculated in an element (self correlations) are excluded from the line number counting, even
if they are included in the uploaded files.

42

KaPPA-View4 Advanced Manual

4-2-7. Thumbnails of the Maps
Click on a internal node of Pathway Tree and then on "View Thumbnails" button to view the thumbnails of
the pathway maps arranged as a tree-like structure. Click on the thumbnails to jump to the corresponding
pathway maps.

4-3. Data Analysis Functions
This section covers various data analysis functions available on KaPPA-View4. Combinations of thesefunctions will accelerate the studies for gene functions.

4-3-1. Simple Map
As KaPPA-View4 provides data viewing functions based on the pathway maps, the genes not drawn on themaps cannot be analyzed even if the values of such genes are included in the experiment data. To represent
the values of the genes not drawn on the default pathway maps, we provide the Simple Map function.
Any genes registered in the system with proper IDs can be automatically aligned on a Simple Map (asshown below) according to the user input of IDs, and the resulted Simple Map can be used in the data
analysis as same as the default pathway maps. The gene IDs registered in the KaPPA-View4 are available
through "Download" function (see 7. Download).

43

4. Data Analysis

Click "Create Simple Map" at the bottom of the Pathway Tree in the Species Map Mode. This button isdisabled in the Universal Map Mode, Bird's Eye view mode, and thumbnail view mode. A pop up window
appears.

Input the IDs into the "Gene List", give a name of the Simple Map.

Click "Add" button to fix the input.

44

KaPPA-View4 Advanced Manual

Click "Redraw" to refresh the main window. The created Simple Map appears in the Pathway Tree.

There are three ways to input the gene IDs into the "Gene List" area.

- Direct input by manual
Input the gene IDs directly into the area. The IDs must be separated by newlines (returns).

- Load from FileClick "Browse" button to select a text file where gene IDs are written in each row. Click "Load From File"to load and input the IDs into the Gene List area.

- Load from current Map
Gene IDs are retrieved from the pathway map currently displayed. Click "Load From Map" button.

4-3-2. Multiple Map Mode
Up to 4 maps are displayed on a single browser window and they can be used simultaneously for color
representations and correlation overlaying. The mode referred as "Multiple Map Mode" helps users to45

4. Data Analysis

compare omics values between several maps, investigating regulatory relationships between genes on apathway map and maps for gene families such as transcription factors, and so on.

Click "Add Relation Map" button at the bottom-left of the Map Area in Species Map Mode. A setting
window pops up.

Select a pathway map from the pathway tree on the pop up window to set the map on the preview panel on
the right. Up to three maps can be selected here. The upper-left position of the resulted multiple map isinterlocked to the Pathway Tree on the data browsing window, therefore users cannot select the map for thisposition (indicated as "Current Map" as shown below).

Click "Clear" button at the bottom of each map preview if you want to remove the selection.

After selecting the maps, enter the map set name and click "Add" button to register the combination of themaps.

Click "Redraw" to refresh the main window.

46

KaPPA-View4 Advanced Manual

Close the pop up window.
A pull-down list named "Multiple Map" appears at the bottom of the Map Area. Select the registered nameand click "Select" to show the map set (Multiple Map Mode).

The upper-left panel of the Multiple Map is interlocked to the Pathway Tree. By selecting a pathway map
from the Pathway Tree, the upper-left map on the Multiple Map is replaced to the selected map.

Select "- Single Map-" from the pull-down list and click "Select" button to return to the normal display ofthe maps (Single Map Mode).

4-3-3. Overlay of Correlation Data
In the recent years, a huge number of microarray data are available on public, and it contributes to generate
co-expression data as a novel data resource. A group of genes which are involved in a certain biologicalsystem could be expressed in coordinate manner throughout various conditions. Therefore, focusing on theunknown genes which co-expressing with well known genes could give a hint to uncover the functions of47

4. Data Analysis

the unknown genes. ATTED-II (http://atted.jp/), for example, is one of vanguards of such approaches, and it
can list up co-expressing genes of Arabidopsis for a query gene of researcher's interest.
KaPPA-View4 provides a function to overlay gene co-expression data onto the pathway maps. Data
representation in this manner helps to grasp the gene-to-gene relationships on the aspect of metabolisms.
KaPPA-View4 can represent metabolite-to-metabolite correlations too.
As an index of co-expression between the genes, correlation coefficients have been typically used.
Hence, the functions of KaPPA-View4 concerning to the co-expression of the genes or co-accumulation of
the metabolites are referred like "correlation functions". However, the data which KaPPA-View4 accepts is
not restricted in the correlations. Any data which represents gene-to-gene or metabolite-to-metabolite
relationships as numerical values can be utilized. For example, protein to protein interaction data describedby 0 or 1 is acceptable. Please try to project your own ideas onto the pathway maps with KaPPA-View4.

• Data Selection and Display
A control panel entitled "Correlation Line" appears at the Lower Control Panel in Species Map Mode
(Correlation Control Panel). Select correlation data for genes and/or compounds from the pull-down lists
and click "Update Correlation" button to overlay the data on the pathway map.

Gene-to-gene and/or metabolite-to-metabolite relationships are represented as curves. The color of thecurves can be set on the Correlation Control Panel too.

Information about the default correlation data are available on the "Statistics" page of the KaPPA-View4.
Refer to the supplemental file of KaPPA-View4 paper too for more details.

48

KaPPA-View4 Advanced Manual

Users can upload their own correlation data too (see 3-4. Uploading Correlation Data). The uploaded
data can be selected from the pull-down lists.

Users can filter the correlation data to display by the following ways.

• Data Filtering by Value Ranges
Set the ranges of the correlation data at the "Range" column on the Control Panel. In default, the ranges are
set as 0.6 - 1.0.

49

4. Data Analysis

Note:
A correlation coefficient takes a value in a range from -1.0 to 1.0. However, in some default data, similarity
values are not represented in correlation coefficient but in mutual rank (MR) which can take more than zeroand up to several tens of thousands. Please be sure to set ranges properly.

• Data Filtering by Curve Numbers
Users can set the number of curves to be represented on the pathways in the "Number" column. Select"High" or "Low" to determine which of the correlation values to be displayed, the higher most ones or the
lower most ones, and enter the number of the curves. Click "Update Correlation" to refresh therepresentation. The number setting is applied to the curves that passed through the range filter, and thenumber of filtered curves by range settings is shown as a number after the slash "/".
An example is shown below. In total 30 curves for gene correlations are filtered by the range settings (0.6 1.0). By the number settings of "High" and "3", only the curves having the higher most 3 correlation values
within the range are to be represented.

50

KaPPA-View4 Advanced ManualEnter "0" and click "Update Correlation" button to unset the number settings.

• Correlation Curves in Multiple Map Mode
The overlaying function of correlation data is available in the Multiple Map Mode too. The figure below
shows an example of correlation representations between a default pathway maps, a Simple Map, and a User
Map.

51

4. Data Analysis• Correlation Data List
Click "Correlation List" at the bottom of the window to view a list of the correlation curves currently
displayed.

A pop up opens.

4-3-4. Comparison of Two Experiments in One Species
When multiple Compared Experiment Pairs for one species are included in the current analysis, two of themcan be selected and comparatively displayed on the maps (Compare Mode). The Compare Mode is notavailable in Universal Map Mode, on User Maps, and on Simple Maps.

Check two of the Compared Experiment Pairs on the Upper Control Panel, and click "Compare" button.

52

KaPPA-View4 Advanced Manual

The selected data are numbered as [1] and [2] and the details are shown on top of the Map Area. Two set ofgene symbols are created on the pathway maps to show the values derived from each data.

The compound symbols (circles) are divided into upper and lower parts and they represent values from eachdata as abbreviated on the top-left corner of the map.

The arrows for the enzymatic reactions are not colored in the Compare Mode.

4-3-5. Data Comparison between the Species
When Compared Experiment Pairs derived from multiple species are included in the current analysis, one ofthe data for each species can be compared and displayed on the pathway maps. This function is only
available in Universal Map Mode.

53

4. Data Analysis

Click the "Show All" button in the Upper Control Panel in the Universal Map Mode. An extra menu
appears.

Select one of data for each species, and then click "Submit". The figure below is an example of the case two
Arabidopsis data and one Lotus japonicus data exist.

A representation similar to the Compare Mode appears, except the caption of the genes are the abbreviationsof the species.

Note:
The species compared by this function must be the same as the species that allowed to display on the
Universal Maps. If you got unexpected results, try to set the species again according to the section 4-2-3.
Map Mode, and then perform the Show All settings.

54

KaPPA-View4 Advanced Manual

4-3-6. Displaying All Experiment Data
When multiple Compared Experiment Pairs are included in the current analysis, all of them can be displayed
in a single browser window. This function is not available in Universal Map Mode.

Click "Show All Experiments" on the Upper Control Panel.

A window pops up that shows a list of the current maps representing each data.

55

5. Map Browsing Functions

5. Map Browsing Functions
The map representations without color painting by the experiment data are available too. Click "Map View"
on the Main Menu.

The user interfaces for the functions depending on the omics data, such as Compare Mode, are not shown in
the Map View function, but similar representations of the maps are available.

56

KaPPA-View4 Advanced Manual

6. Searching
The "Search" on the Main Menu provides search functions for the genes, compounds, enzymatic reaction. A
gene search functions by the BLAST program based on the sequence similarity is also available. Users caninvestigate the maps where your favorite genes are drawn.

6-1. Gene, Compound and Enzymatic Reactions
Click the "Search" on the Main Menu. The searching user interface appears.
Enter the conditions into the form and click "Search" button. The figure below is an example of a searchingcondition for searching gene annotations matched to a keyword "glutamine" in Arabidopsis thaliana.

The results are listed.

Click the ID to view more details. A window pops up.

57

6. Searching

Click on the links written in the "Map" item to jump to the maps where the gene is drawn. The gene ishighlighted by blinking on the map.

6-2. Blast SearchingThis serves a gene search function based on the similarity of the nucleotide- or amino acid- sequences
between the queried sequence and the genes registered in the KaPPA-View4 system using the Blast
program.

58

KaPPA-View4 Advanced Manual

Click "Blast Search" button.

The Blast searching interface appears. Enter searching conditions and click "Search".

Only a single sequence must be entered in "Query" input area. Multi-FASTA format is not accepted. The
query can be loaded from a file.

The results are listed. Click a gene ID to refer the details.

59

7. Download

7. Download
Click "Download" on the Main Menu to download experiment data and information files used in the
KaPPA-View4 system.

Enter conditions to search files and click "Search".

The results are listed. To start downloading, click a download icon ( ) or right-click on the icon and thenselect "Save as...".

Select "Information" for the "Data Type" to download the basic information file used in the system. The
basic information files are entitled as follows. "[date]" represents the released date. "[Pre]" is theabbreviation of a species or "Uni" used in Universal Map Mode.

• The files commonly used for all species.
Compounds:

Uni_compoundInfo_[date].csv

Enzymatic reactions:60

Uni_enzymeInfo_[date].csv

KaPPA-View4 Advanced Manual• Species specific files
Genes: [Pre]_geneInfo_[date].csv
Gene assignments to reactions:[Pre]_geneBoxInfo_[date].csv or [Pre]_geneGroupInfo_[date].csv
Relationships between the DNA microarray probes and the Genes:[Pre]_featureGene_[date].csv
Map assignment to the Pathway Tree: [Pre]_mapRelation_[date].csv

Tips:
Use the compound information file to investigate the compound IDs in the KaPPA-View4.
We don't provide files for gene-to-map, compound-to-map, or reaction-to-map information. These
relationships are calculated dynamically by the system from the pathway map files provided in SVG format
and the other information files. To investigate the elements drawn on the map, refer to the Element List (seeExperiment Values in the section 4-2-2).

Note:
The Chemical Abstract Service (CAS) numbers are written in the compound information file. A CAS
number consists of three number parts separated by hyphens. Some of them might be miss-recognized byMicrosoft Excel as date data and be replaced to other unexpected values. Be careful to edit and utilize thecompound information file.

618. Utilization from External Systems

8. Utilization from External Systems
This chapter covers the ways for utilization of KaPPA-View4 from external systems. The accessibility fromthe external systems is greatly improved in KaPPA-View4. We newly opened APIs (Application Program
Interface) that allows uploading the experiment data from the external systems without logging-in to the
KaPPA-View4 system through the graphical user interfaces (GUIs) of the website. Therefore, the developersof other databases and application programs incorporate functions to view their omics data directly on
KaPPA-View4.

8-1. Data Uploading APIs
KaPPA-View4 provides new APIs for uploading experiment data and user created map data from external
systems. The outline of the communications between the clients and the KaPPA-View4 server are shown inthe schematic figure below.
External systems(databases, application
programs)

KaPPA-View4 server

Generation of data file
(text)- transcriptome data
- metabolome data
- User Map data

Access to the URL by an
Internet browser

Data processing
Transfer by
POST method

Register the data as atemporary data of a guest
user

Return a text
(URL for browsing
results)

Browse results

The clients must generate a text file to send the data to the KaPPA-View4 server to ensure stable transfer.
Transcriptome data, metabolome data, User created Map data, and some meta data for them can be includedin the file. Refer to 9-5. Data for POST Transferring for details of the file format.
The POST method of HTTP is used to transfer the data to the KaPPA-View4 server. Additional libraries
might be required to execute POST transfer in some programming languages.

8-1-1. Data Transferring Procedure
Send the generated file to the URL below by POST method. Access to the URL received as response by an
Internet browser to view the results.

62

KaPPA-View4 Advanced Manual

URL

http://kpv.kazusa.or.jp/kpv4/upload.action

MethodPOST

Content-Type

multipart/form-data

Parameter

uploaded (Data File)

Response

Success: an URL starts with "http"Error: error messages. It might be written in multiple lines.

8-1-2. Sample Codes• HTML Form
<form action="http://kpv.kazusa.or.jp/kpv4/upload.action" method="post"enctype="multipart/form-data"><input type="file" name="uploaded" /><input type="submit"></form>Open the html file by an Internet Browser. Select a data file from the web form, and click "Submit" button.
If the data file accepted, an URL is displayed on the browser window. Access to the URL by inputting it into
the address field of the browser.

This is not a practical example as a web application, but good for understanding the behavior and usage of
the API.

• PHP
This is a sample code using a PEAR library.
require_once 'HTTP/Client.php';$client = new HTTP_Client();$url = "http://kpv.kazusa.or.jp/kpv4/upload.action";$file = "./uploadfiles/postdata.txt";$postdata = array();$postfile = array('uploaded', $file);$capsule = array($postfile);$client->post($url, $postdata, false, $capsule);$response = $client->currentResponse();63

8. Utilization from External Systems

Redirect to the URL received as the response to browse the results.

8-1-3. Behavior of KaPPA-View4 after the Transferring
The users are recognizes as Guest Users by the KaPPA-View4 system after accessing through the URL
received as the response. The transfered data are registered as temporary files and Compared Experiment
Pairs are automatically created. Therefore, users can start analysis with the KaPPA-View pathway maps justafter accessing to the URL. The individual experiment data appears in the data list of "Analysis" function,
allows users to compare them with other arbitral data.
The data are expired as the same as those of Guest Users', i.e., the data are deleted from the server when theuser logoff, all the browser windows closed or no operation have done in 60 minutes.

The transferred data appears in the "Analysis" window as shown below.

The transferred data is designated as Experiment Set ID of PS[six-digit serial number]. If the transfered data
is a pair of two experiment data, they are registered as quantitative data and the Experiment IDs are assigned
as [Exp. Set ID]_1 and [Exp. Set ID]_2. If the transfered data includes only one experiment data, it isregistered as ratio data and the Experiment ID is assigned as [Exp. Set ID]_1.

8-2. Direct Access by IDs of Gene, Compound, Reaction, andMap
The genes, compounds, enzymatic reactions and the pathway maps used in the KaPPA-View4 system havetheir own ID. The information pages for the elements and pathway maps can be directly accessed from theexternal systems by describing URLs in defined formats with the IDs and by accessing to the URL.
If the user is not logged-in to the system, the user is automatically recognized as a Guest User.

8-2-1. URL Format• Genehttp://kpv.kazusa.or.jp/kpv4/geneInformation/view.action?id=Gene ID

64

KaPPA-View4 Advanced Manualex)
http://kpv.kazusa.or.jp/kpv4/geneInformation/view.action?id=At1g58150

A gene information page appears.

• Compound
http://kpv.kazusa.or.jp/kpv4/compoundInformation/view.action?id=Compound

ID

Ex)
http://kpv.kazusa.or.jp/kpv4/compoundInformation/view.action?id=KPC00697

A compound information page appears.

• Enzymatic Reaction
http://kpv.kazusa.or.jp/kpv4/enzymeInformation/view.action?id=Reaction ID

Ex)

65

8. Utilization from External Systems

http://kpv.kazusa.or.jp/kpv4/enzymeInformation/view.action?id=R0000603

An information page for the enzymatic reaction appears.

• Pathway Map
http://kpv.kazusa.or.jp/kpv4/mapView/view.action?mapNumber=Map Number

Trim initial three alphabets from the Map ID to get "Map Number". The map is shown in Universal Map
Mode with this description of URL. Specify a species by attaching another parameter to the description toshow the species specific maps (see next section).

Ex)
http://kpv.kazusa.or.jp/kpv4/mapView/view.action?mapNumber=00006
http://kpv.kazusa.or.jp/kpv4/mapView/view.action?mapNumber=00028f

The corresponding pathway map appears.

66

KaPPA-View4 Advanced Manual

8-2-2. Specifying Species
By adding a parameter below in the URL, users can specify the species.

&speciesName=Species Name"Species Name" is the name of species registered in KaPPA-View4. You can describe it case-insensitively.
The text must be URL encoded, therefore, try to replace the space between the family name and the genus
name to "%20" if it's not accepted properly. When an unrecognizable Species Name were written, thesystem returns information in Universal Map Mode.

Ex)
http://kpv.kazusa.or.jp/kpv4/geneInformation/view.action?id=At1g58150&sp
eciesName=Arabidopsis%20thaliana

http://kpv.kazusa.or.jp/kpv4/compoundInformation/view.action?id=KPC00697&speciesName=Lotus%20japonicus

http://kpv.kazusa.or.jp/kpv4/enzymeInformation/view.action?id=R0000603&s
peciesName=Oryza%20sativa

http://kpv.kazusa.or.jp/kpv4/mapView/view.action?mapNumber=00006&species
Name=Solanum%20lycopersicum67

8. Utilization from External Systems

http://kpv.kazusa.or.jp/kpv4/mapView/view.action?mapNumber=00415&species
Name=Lotus%20japonicus

68

KaPPA-View4 Advanced Manual

9. File Format
This chapter covers the file formats of the following data.

Experiment Data:
The omics data such as transcriptome data obtained DNA microarray and metabolome data detected bymetabolomics approaches. It is used for the analysis on the pathway maps.

Correlation Data:
Gene-to-gene or metabolite-to-metabolite relationship data such as gene co-expression data and metaboliteco-accumulation data. It is used for the overlaying of relationship data on the pathway maps.

User Map Data:
The map data originally created by the users.

Data for POST transferring:
The data created by the client systems when the data is represented directly on KaPPA-View4 via the POST
transferring API.

9-1. General Notices
Don't include any multibyte letters in the data files. Don't attach the byte order mark (BOM) when the file
has to be encoded in UTF-8.

9-2. Experiment Data for Uploading
The omics data such as transcriptome data obtained DNA microarray and metabolome data detected bymetabolomics approaches. By uploading the data file, users can analyze the data on KaPPA-View4.
In addition to the file format for the previous version, the format for KaPPA-View4 can include someheaders for describing sample information and so on. The previous format is still acceptable, but werecommend attaching header information to avoid confusions if you upload a lot of data.

9-2-1. Data Part
Same as the previous format as described below. The data files for the previous version can be accepted asthey are.

69

9. File Format• Extension from the Previous Version- If the compound data includes 0 as a value, the system alerts it. In the previous version, such compounddata was ignored.
- A tab delimited text (tab separated vector: TSV) format becomes to be acceptable as well as the comma
separated vector (CSV) format.
- Arbitral gene and compound IDs (with prefix of TMG and TMC, respectively) that are not registered in thesystem can be included in the data file. Those IDs enables to paint colors for the gene and compound
symbols that have corresponding IDs on the User Maps.

• Format
The data of transcripts and metabolites have to be prepared in independent files. Prepare data following
below with proper tool such as Microsoft Excel, and save as a CSV or TSV file. When you add headers(described later), save the data in TSV format.
Line

ColumnDescription

1st

Define the type of data. Enter "(arrayexp)" for transcript data or"(compexp)" for metabolite data with the parentheses.

2nd ~Enter the experiment names. Exactly the same experiment names haveto be written in the columns that hold the experimental repetition data
as defined in the 2nd line. The system recognizes the data of different
names as independent experiments. The experiment names written
here also have to match exactly to those in the header information tokeep correct correspondence.

1st

Enter "(rep)" with the parentheses. "rep" stands for "repetition".

2nd ~Enter the repetition numbers like 1, 2, 3... for the data of experimental
repetition. Don't assign the same repetition number for the columns
having the same experiment name (written in line 1).

1st

2nd

Enter IDs for the elements, the feature IDs for transcript data andcompound IDs for metabolite data.
*Download the basic information file to investigate these IDs from the"Download" function.
1stUsers can input other IDs for the representation of values of arbitralgenes and compounds. In such case, enter IDs in the following formats.
"TMG[number]" for genes. ex) TMG1, TMG02"TMC[number]" for compounds. ex) TMC003, TMC045

3rd ~*To represent the data, the corresponding symbols that have the sameIDs have to be drawn on the User Maps.

2nd ~Enter the values. The values for genes have to be log-transferred(based on 10 is recommended). The values for compounds have to belinear scale and 0 (zero) and negative values cannot be included.
The values are treated by the system as log and linear scale for genes
and compounds.

• Sample
The figures below show examples data preparation with Microsoft Excel.

70

KaPPA-View4 Advanced Manual

Transcript data.

Metabolite data.

9-2-2. Header Part
The data files prepared following the directions above can include header information at the head of the files
to describe the metadata of the experiments. The data files without headers can be accepted by the
KaPPA-View4 system, but we recommend attaching header information so that the data are recognizedunambiguously on KaPPA-View4 by the user.

71

9. File Format

Several related experiment data can be grouped in a Experiment Set, the header includes parts forexperiment set and each experiment data. The structure of the whole data file is schematically represented
below.

Experiment Set Info.
Header Part

Exp. A Info.
Exp. B Info.
...
Data PartThe Data File (CSV or TSV)• Format
Each item of header information should be described in a line according to the following formats.

>[Item Name] <tab> [Description]

The lines in the header must start with ">", therefore descriptions must not contain newlines (returns). Blanklines are ignored.

There are two types of the Item Name, the Reserved Headers and User Defined Headers.

• Reserved Headers
The Reserved Headers are recognized and the descriptions are processed properly by the system.

The Reserved Headers for the Experiment Set.

72

Reserved Headers

Explanation

Required>datatypeDefine the type of the data, "array" or "compound". ItisyesKaPPA-View4 Advanced Manual

Define the ID of the Experiment Set. If it's omitted,
the system automatically assigns an ID like
"TempSet_[number]".

no>Set_Set ID

Define the Name of the Experiment Set. If it'somitted, the system automatically attaches a namelike "TempSet_[number]".

no>Set_Experiment Set Nameno

>Set_Species

Define the species name that the data derived. The
name must match exactly to the one used in thesystem. If it's omitted, it has to be defined during the
uploading process.

no>Set_Array TypeDefine the appropriate Array Type namecorresponding to the feature IDs described in thedata file. The array type name must match exactly tothe one registered to the system. If it's omitted, it has
to be defined during the uploading process.
Define the Experiment Set ID that related to thisdata. The ID appears as a link to another Exp. Set on
the data selection list of "Analysis" function.

no> Set_Related Experiment

For example, a transcriptome Exp. Set can be
related a metabolome Exp.Set that are obtained
from the same samples. In this case, link to themetabolome Exp. Set will help a smooth data
selection in the "Analysis".

>Set_***_ID

On the Experiment Information window (see below),users can make arbitral links. Define the caption of
the link as ">Set_***_ID" header, and define the URL
corresponding to the caption as ">Set_***_link".

and>Set_***_linkno(*** is an arbitral text string)

The figure below is an example of the Experiment Information window. The window appears when the Exp.
Set ID is clicked on the experiment data list of the "Analysis" function.

The Array Type names registered to the system can be investigated as followings.

Click "Temporary Upload" on the Main Menu after logging-in to KaPPA-View4. Click "Browse" to select adata file of transcripts and then press "Upload". The system checks the data file and the summary of the fileappears. Click on the "Array Type" pull-down list to check the names of the Array Type (written in the73

9. File Format

parentheses) registered and the corresponding species names. Download the basic information file forfeature-gene relationships to check the Feature IDs (see 7. Download).

The Reserved Headers for experiment data.
Reserved Header

Explanation

Required>Data_Experiment_ID

Define the Experiment D. If it's omitted, the systemassigns automatically an ID like "TempExp_[number]".

noDefines the name of the Experiment. The name has tobe described exactly the same as the corresponding
data name written in the Data part.

yes>Data_Experiment_Name

Define the type of the experiment data, "ratio" or"quantitative" (see Type of Experiment Data). If it'somitted, it's set automatically to "quantitative".

no>Data_Value Type
>Data_Comments

Enter comments.

no>start

The header doesn't have the description. It is a marker
indicating the beginning of one experiment data.

yes

>end

The header doesn't have the description. It is a marker
indicating the end of one experiment data.

yes

On the Experiment Information window (see below),users can make arbitral links. Define the caption of thelink as ">Data_***_ID" header, and define the URL
corresponding to the caption as ">Data_***_link".

no>Data_***_ID
and>Data_***_link(*** is an arbitral text string)

The figure below is an example of the Experiment Information window. The window appears when the Exp.
ID is clicked on the experiment data list of the "Analysis" function.

74

KaPPA-View4 Advanced Manual• User Defined Headers
To describe other metadata, users can define their original headers (User Defined Headers). The headersconcerning to the Experiment Set and Experiment Data must starts with ">Set_" and ">Data_" respectively.
The User Defined Headers must not have the same name as the Reserved Headers.
As the under bar "_" represents a separator and the name of header can be separated into several keywords,
the set of headers are treated by the system as a tree structure where the keywords represent each node.
Users can search the experiment data based on the descriptions of the headers through the "Analysis"
interface which can specify the nodes (see below).

75

9. File Format• Sample

Refer to the sample data too which are available from the KaPPA-View4 main page after logging-in.

9-3. Correlation Data

76

KaPPA-View4 Advanced Manual

The gene-to-gene and metabolite-to-metabolite correlation data are used for representing on the pathway
maps as curves (see 4-4-3. Overlay of Correlation Data).

9-3-1. Format
Make data describing following information in each line, and save it as a CSV file.
ColumnDescription

Data type

Required

1st

ID1

Text string (max. 100 letters)

yes

2nd

ID2

Text string (max. 100 letters)

yes

3rd

A value

Real number

yes

The gene IDs and compound IDs registered to KaPPA-View4 can be entered into the first and second
column. Gene-to-gene relationships and compound-to-compound relationships should be described inseparate files, because they are separately uploaded. Gene-to-metabolite relationships are not accepted by
the system.
If there are multiple lines that having the same combination of ID1 and ID2, an alert message appears in the
uploading process when they have different values, but they are accepted as one record when they have thesame values.

9-3-2. Sample

Note:
File size of correlation data tend to become large. If the file was not accepted by the server due to therestriction of the file size, an alert message appears to inform you it. Consider to reduce the file size by
cutting off the entries based on a certain threshold of correlation values, or by rounding the values at proper
digit to reduce the letter numbers.

77

9. File Format

9-4. User Map
This section introduces briefly about the User Maps and their format restrictions. Refer to the "Manual onUser Map Creation" for more details.
Users can create their own pathway maps (User Maps) and utilize them for their analysis. By creating
pathway maps that are not provided as defaults, are edited and curated more carefully, are better designed
for presentations, and include genes and compounds not registered to the system, the possibility of
KaPPA-View4 analysis can be expanded.
The User Map files can be utilized by being uploaded by the users through KaPPA-View4 GUI, or bytransferring in POST methods through the KaPPA-View4 API. The Power Users can send their own User
Maps to the KaPPA-View administrator with simple steps to discuss about improvement of default maps.

The User Maps should be created in a Scalable Vector Graphics (SVG) format. To paint colors on thesymbols for genes, compounds, and reactions dynamically by the system, a proper ID should be assigned foreach symbol. We recommend using the free drawing software Inkscape (http://www.inkscape.org/).

A summary of ID formats for the SVG objects on the User Maps.
Element

Explanation

ID format

Gene

Represent genes.

text+(integer number)_g
Gene IDs used in KaPPA-View4 system oruser-defined ID starting with "TMG". Use different
integer numbers to draw one gene on more than one
place of the same map.
Ex) At1g12340(1)_g, TMG001(1)_g

Gene box

Used for defining a
region to represent agroup of genes
corresponding to an
enzymatic reaction.

B+number
The number corresponds to the numeric part of
enzymatic reaction ID starting with "R"
Ex) B00001

CompoundRepresent
compounds.

KPC+number,C+number,G+number,D+number, OR
TMC+number
KPC+number is compound ID format used in
KaPPA-View4 Classic system.
C, G or D+number are compound ID format used in
KaPPA-View4 KEGG.
TMC+number is a user-defined ID.
Ex) KPC00005, TMC00001

Enzymatic
reaction

Represent enzymatic
reactions.

R+number
Enzymatic reaction IDs used in the system.
Ex) R0000101

78

KaPPA-View4 Advanced Manual

Link to a related
map

Enables to jump toanother map

3 letters+integer number(+1 letter)
Map IDs used in the system.
Ex) Uni00001, Uni00034f, Lja00017

The SVG objects that are allowed for drawing the element symbols.
Element

SVG object

Note

Gene

rect

Be sure to set color to the fill, not to set "No
paint".

Gene Boxrect

Be sure to set color to the fill, not to set "No
paint".

Compoundrect or circle

Be sure to set color to the fill, not to set "No
paint".
rect を使用する場合、rx, ry 属性で角のカーブを作成することにより、丸い化合物シンボルを作ることができます。

Enzymatic reaction

line or path

Link to a related
map

rect or path

Dotted lines can only be represented properlywith "line" object. Stylized arrow heads of pathobjects are not properly displayed.

About Other SVG objects.
Text objects

Use Arial font. Conversion to outlines is recommended.

ImagesBy embedding image files to the SVG canvas, they can be displayed on
KaPPA-View4.

9-5. Data for POST Transferring
The data transferred by POST transferring APIs (8-1. Data Uploading APIs) is called "POST data" here.

9-5-1. Structure of POST Data
The figure below schematically represents the structure of a POST data file.

799. File Format

POST Header//
Data Header A
Experiment Data A//
Data Header B
Experiment Data B...

//
SVG Header
SVG Map Data

POST Data File (text)

General information such as the species name are described in the POST Header part.
The following Experiment Data part are separated by a delimiter "//", and can include more than one
experiment data.
The SVG Map Data part contains SVG data of User Map. It can be omitted.

9-5-2. Format• Header Part of POST Data
POST Header contains general information on the POST data. Each item of header information should be
described in a line according to the format below.

>[Item Name] <tab> [Description]

The lines in the header must start with ">" and the description must not contain newlines (returns). Blanklines are ignored.

Write following items.

80

Item Name

Explanation

Required>species

Define the species name. It must be exactly the same as
the one registered to the system.

yes

KaPPA-View4 Advanced Manual>array>default_map

Define the Array Type name. It must be exactly match to
the name registered to the system. See p.72 forinvestigating valid Array Type names.

yes(when the fileincluded any
transcriptome
data)

Define the map which appears first after the POST
transferring.

noTrim first three alphabets and write it as [Description].
When an SVG data contained in the file, the map ID
defined in the ">svg_name" header (see below) can be
described.
When it is omitted or invalid ID was described, no default
map appears.

• Experiment Data Part
Be careful that the Experiment Data Part for POST data is different from those of the data files for GUI
uploading (described in 9-2. Experiment Data for Uploading). The Experiment Data in the POST data
corresponds to the Compared Experiment Pairs which are created during the "Analysis" steps.

More than one Experiment Data can be included and they must be separated by a delimiter "//". EachExperiment Data contains Header part and Data part.

The format of the header is the same as POST headers. Describe following information.
Item Name

Explanation>set_nameDefine the name of the data which corresponds to the Compared Experiment
Pair name.

>data_type

Define the type of the experiment, "array" or "compound".

If there is more than one Experiment Data that have the same ">set_name" and ">data_type" among theExperiment Data separated by "//", only the former data is registered.
When there are pair of Experiment Data that have "array" and "compound" for ">data_type" and shares thesame ">set_name", the data is recognized as a Compared Experiment Pair which includes both of transcript
and metabolite data.

The Data part follows to the Header Part. Describe the items below. Be careful that they are different fromthe ones of data for GUI-uploading (described in 9-2. Experiment Data for Uploading).
ColumnExplanation

1stEnter Feature IDs for transcripts data and Compound IDs for metabolites. To
investigate the Feature IDs and Compound IDs used in the system, download thebasic information files (see 7. Download). The user defined IDs, TMG[number] forgenes and TMC[number] for compounds can be entered too to paint colors on the
SVG objects that having these IDs on the User Maps.

2ndEnter experiment values. The values should be transformed to logarithm scale for81

9. File Format

genes (based on 10 is recommended), and linear scale for metabolites. The
compound values must not negative nor 0.
If the 3rd column have a value, values in the 2nd and 3rd column recognized by thesystem as quantitative data of the numerator and the denominator, respectively, for
the Compared Experiment Pair. If there is no data in the 3rd column, the value in the
2nd column recognized as ratio data.

3rdEnter experiment values. It can be omitted. The values should be transformed tologarithm scale for genes (based on 10 is recommended), and linear scale formetabolites. The compound values must not negative nor 0.
The value is used as a denominator for the ratio calculation with the value in 2ndcolumn. If the 3rd column have no data, the value in the 2nd column is recognized as
the ratio data.

• Map Data Part
The header item below is required. The format of the header is the same as the POST header. Following to
the header, the SVG data (text) of the User Map (9-4. User Map) should be written. Open the SVG file of
the User Map with a text editor such as the Notepad for Windows to get the SVG data in text format.
Item

Explanation>svg_nameDefine the name of the map. The name appears on the Pathway Tree. When thename is written in the ">default_map" item in the POST header, the map
appears first on the browser after transferring the POST data.

9-5-3. Sample

82

KaPPA-View4 Advanced Manual8310. Default Data

10. Default Data
10-1. System Data, Species, and Correlation Data
Refer to the KaPPA-View4 paper and the supplement file of it (Sakurai N, et al. (2011) Nucleic Acids
Research 39: D677-684) for details of the default data (at August 15th 2010).
The "Statistics" page of KaPPA-View4 website shows the latest data installed in the system.

10-2. Experiment Data
We provide some sample data for demonstration. Click on the Experiment Set ID or Experiment ID on theexperiment data list of the "Analysis" function. A window pops up to show the metadata.

84

KaPPA-View4 Advanced Manual8511. Hints and Trouble Shootings

11. Hints and Trouble Shootings
11-1. Getting a Screen Shot
Right-click on a pathway map, and select "Go Full Screen". Press "PrtScr" button (Windows) to get a screen
shot in a fixed pixel sizes.

11-2. Two-color Microarray Data
The 2-color DNA microarray data can be properly represented on the pathway maps, by following to theways below.

1)- Prepare the experiment data file for KaPPA-View4 using the log(ratio) data generated by the 2-color
microarray analysis.
- Create a control data file where all the gene expression values are set to 1.
- Upload both of the experiment data and the control data to KaPPA-VIew4.
- Pair the two to create a Compared Experiment Pair.

2)- Prepare the experiment data for KaPPA-View4 using the log(ratio) data generated by the 2-color
microarray analysis.
- Attach header information to the data file (see 9-2. Experiment Data for Uploading). Write "ratio" forthe ">Data_Value" so that the data is recognized as "ratio" data by the system.

86

KaPPA-View4 Advanced Manual- Upload the data file.
- Create a Compared Experiment Pair with the data alone.

11-3. One-color Microarray Data
The log-transformed expression data can be normalized by a global mean (or median) so that the genesymbols are to be painted with a wide color ranges.
Alternatively, create the log-transformed expression data (not normalized) and a control data where allvalues are set to a global mean (or median). Upload the two and create a Compared Experiment Pair withthem. An advantage of the later is that the experiment data can be directly used for other analyses bycomparing to other 1-color data which are uploaded in the same way.

11-4. Investigating Compound IDs
In order to create a metabolite expression data for the analyses, users have to know the Compound IDs usesin the KaPPA-View4. There are several ways to investigate the Compound IDs.
* In KaPPA-View4 KEGG,(http://www.genome.jp/kegg/).

theCompound

IDs

are

the

same

as

those

of

KEGG

1)
Click on the compound symbols on the pathway maps.

2)
Find the compound by "Search" function of KaPPA-View4.

3)
Download the compound information file from the "Download" menu after logging-in.

11-5. Representation of non-omics data on the maps
In usual, the function for the experimental data uploading is used to upload omics data such as gene
expressions (transcriptome data) and metabolite accumulations (metabolome data). Utilizing the function,
we can visualize the other data on the pathway maps as follows:

1) Significances of the data detections on the microarraysex) - P-value (log ratio) from the Agilent's microarray
2) Probabilities of the data changesex) - The results of t-test3) Existence of the genes or compounds

8711. Hints and Trouble Shootingsex) - Gene lists extracted from the microarray analysis- A compound list of a standard chemical library- Gene list for each GO evidence codes
to check the reliability of gene annotations

To prepare a data file as the same format to the experimental data files, we can upload the data and represent
on the pathway maps on KaPPA-View4. In the case of 1) and 2), the significance and probability values aredescribed in the data file instead of the detection values. Of course the values should be scaled to fit to thecolor gradation of KaPPA-View4. In the case of 3), existence of the genes or compounds should be
described as a proper value, ex., 1 (exists) and 0 or null (not exists) for genes. By setting proper values for
multiple categories of the genes or compounds, users can represent up to 9 categories in different colors
simultaneously on the maps.

The functions for switching several experimental data to browse, and for representing two experiments data
simultaneously on a single map, enable users to browse the real experimental data and correlation data while
checking the values of user's interest.

88

KaPPA-View4 Advanced Manual

12. Acknowledgements
KaPPA-View was developed in Kazusa DNA Research Institute with a support from the New Energy andIndustrial Technology Development Organization (NEDO), Japan under the research project named"Development of Fundamental Technologies for Controlling the Material Production Process of Plants"(P02001).

89

13. References

13. References
Papers about KaPPA-View
Sakurai N, Ara T, Ogata Y, Sano R, Ohno T, Sugiyama K, Hiruta A, Yamazaki K, Yano K, Aoki K,
Aharoni A, Hamada K, Yokoyama K, Kawamura S, Otsuka H, Tokimatsu T, Kanehisa M, Suzuki H, Saito
K and Shibata D (2011) KaPPA-View4: a metabolic pathway database for representation and analysis ofcorrelation networks of gene co-expression and metabolite co-accumulation and omics data. Nucleic Acids
Research 39: D677-684
Sakurai N and Shibata D (2006) KaPPA-View for integrating quantitative transcriptomic and metabolomic
data on plant metabolic pathway maps. J Pesticide Science 31: 293-295
Tokimatsu T, Sakurai N, Suzuki H and Shibata D (2006) KaPPA-View: A tool for Integrating
Transcriptomic and Metabolomic Data on Plant Metabolic Pathway Maps. In Saito K, Dixon RA andWillmitzer L eds, Biotechnology in Agriculture and Forestry, Vol. 57, pp. 155-163, Springer-Verlag, Berlin
Heidelberg
Tokimatsu T, Sakurai N, Suzuki H, Ohta H, Nishitani K, Koyama T, Umezawa T, Misawa N, Saito K and
Shibata D (2005) KaPPA-view: a web-based analysis tool for integration of transcript and metabolite dataon plant metabolic pathway maps. Plant Physiol 138: 1289-1300

Other Related Papers
Obayashi T, Hayashi S, Saeki M, Ohta H and Kinoshita K (2009) ATTED-II provides coexpressed gene
networks for Arabidopsis. Nucleic Acids Research 37: D987-991

90

KaPPA-View4 Advanced Manual

14. About Us
Team KaPPA-View
E-mail: kappa-view at kazusa.or.jp (replace at to @)The Administrators and developing team of KaPPA-View in Kazusa DNA Research Institute(http://www.kazusa.or.jp/e/). Please send your all inquiries to this e-mail address.

Axiohelix Co. Ltd.
E-mail: info at axiohelix.com (replace at to @)The system programming was carried out by AXIOHELIX.

http://www.axiohelix.com/en/

Corporate Headquarters
Okinawa Sangyo Shien Center 502,1831-1, Oroku, Naha-shi, Okinawa 901-0152, Japan
TEL:+81-98-858-2887, FAX:+81-98-987-0288

Tokyo Office
Ando Bldg. 8F, 3-6-9, Kitashinagawa, Shinagawa-ku, Tokyo 140-0001, Japan
TEL:+81-3-6698-6731, FAX:+81-3-6698-6734

9115. Manual Versions

15. Manual Versions- 1.0, January 8th 2011
The first release.

92