Integrated DB Application System
Genome Network Platform Viewer

User Operation Manual

Sorry. The English version manual of the latest system is made.

April 21, 2006

Research Organization of Information and Systems

National Institute of Genetics

Table of Contents
1.

Acknowledgments(About the system) .....................................................................................32.

Operational Flow ........................................................................................................................4

3.

4.

2.1.

Start-up of Integrated DB Application System..................................................................4

2.2.

Genome Explorer ................................................................................................................6

2.3.

PPI Network Viewer.............................................................................................................7

2.4.

Expression Profile...............................................................................................................9

2.5.

Integrated Database Search .............................................................................................11

Details of Screen ......................................................................................................................12
3.1.

Genome Explorer Page.....................................................................................................12

3.2.

PPI Network: Select Gene Page .......................................................................................15

3.3.

PPI Network Viewer page..................................................................................................17

3.4.

Expression Profile: Select Gene Page.............................................................................20

3.5.

Heatmap Page ...................................................................................................................22

3.6.

Search Bar .........................................................................................................................26

3.7.

Gene Search Page.............................................................................................................27

3.8.

Gene Description Page .....................................................................................................29

3.9.

Interactors Property page.................................................................................................30

3.10.

mRNA List page .............................................................................................................31

3.11.

CAGE Tag List page.......................................................................................................32

3.12.

TSS Details page............................................................................................................33

General Dos and Don'ts ...........................................................................................................34

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1.

Acknowledgments(About the system)

The National Institute of Genetics has developed "Genome Network Platform Viewer" to make use of the integrated
database of the Genome Network Project. This system integrates experimental data generated from the project inassociation with the public databases. The following functions are available:

Genome Explorer(->2.2 Genome Explorer)This function provides annotation of landmarks (genes, transcription start sites, etc.) aligned in accordancewith their genome locations.

PPI Network (->2.3 PPI Network)
This function provides a graphical view of protein-protein interaction (PPI) network from the experimental data
generated under the project and the public datasets.

Expression Profile (->2.4 Expression Profile)
This is a function to cluster genes by expression pattern and display the result with heatmap. The function
provides genes which have relation of coregulation and anti-coregulation.

Integrated Database Search (->2.5 Integrated Database Search)
This is the function to search the integrated database by using keywords and public IDs. The search results
can be visualized by the function listed above.

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2.

Operational Flow

2.1.

Start-up of Integrated DB Application System(1) Genome Network Platform (for Consortium Member)
URL of Genome Network Platform English pageis
http://genomenetwork.nig.ac.jp/index_e.html

Click the ‘Genome Network Platform Viewer’ tab.

(2) Introduction of the Genome Network Platform Viewer
The introduction of the Genome Network
Platform Viewer is displayed. This page is a brief
guidance of the Genome Network Platform
Viewer. Click ‘Genome Network Platform Viewer’
icon.

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(3) Genome Network Platform Viewer Top Page
Select items from the left menu.
Top: Overview of this system
Search:(->2.5 Search)
Genome Explorer:(->2.2 Genome Explorer)
PPI Network:(->2.3 PPI Network)
Expression Profile:(->2.4 Expression Profile)If you would like to check out each viewer, click‘View Sample Data' (marked in red).

【Note】Please install the latest version of'FLASH Player'. Otherwise, all the pages
cannot be displayed accurately.

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2.2.

Genome Explorer(1) Genome Explorer (->3.1Genome Explorer Page)
Click a position on a chromosome (shown in leftor top -> P.12) to display information on Gene,
TU and CAGE tag in its region. Click 'Gene' or'TU'(marked in red) to display the summaries
below the viewer.
Click TSS to pop-up 3.12 TSS Details Page.

(2) Statistic Information (->3.1Genome Explorer Page)
To change this data type, select 'Gene', 'TU' or'CAGE tag' in 'Statistic';(marked in red) under thechromosomes map. Short lines attached to thechromosomes are a graphical representation of
the distribution of ‘Gene’, ‘TU’ or ‘CAGE tag’.

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2.3.

PPI Network Viewer(1) Gene Search (->3.2 PPI Network: Select Gene Page)
At the first step to search PPI data, click ‘PPI
Network’ in the menu on the left. Available
retrieval

keys

are

as

follows:‘Symbol’,‘Definition’, ‘EntrezGene ID’, ‘MIM ID’, ‘GO ID’
and ‘GO Term’. Input the retrieval keys and Click‘Search’ button to display (2) Gene Search
Result.

(2) Gene Search Result (->3.2 PPI Network: Select Gene Page)
The search result is shown as a list of genes.
Select genes and click ‘PPI Network Viewer’button to display (3) PPI Network.
Up to 10 genes can be selected.

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(3) PPI Network (->3.3 PPI Network Viewer Page)
The genes selected from the search result arelisted at the left of the graphic pane. The listed
genes and the Genes that interact with them aredisplayed as nodes. The colors of the nodes standfor the following states:
Orange: all interactions are displayed.
Light blue: More than one interaction is not
displayed and 'Expansion' menu is available.
Green: More than one interaction is not displayed
but 'Expansion' menu is not available because of
the restrictions on the number of nodes.
The colors of the edges (lines connected to nodes)
represent the data source of the interaction.
Interactions including multiple data sources areshown in red.

(4) Expansion of network (->3.3 PPI Network Viewer Page)
To expand node, click a light blue node andselect ‘Expansion’ from the menu displayed.
Interactors of the selected node are displayed as
nodes. At that time, Symbol of selected node isadded to gene list at left.

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2.4.

Expression Profile(1)Gene Search (->3.4 Expression Profile: Select Gene Page)
At the first step to search Expression data, click‘Expression Profile’ in the menu on the left.
Available retrieval keys are as follows: ‘Symbol’,‘Definition’, ‘EntrezGene ID’, ‘MIM ID’, ‘GO ID’
and ‘GO Term’. Input the retrieval keys and Click‘Search’ button to display (2) Gene Search
Result.

(2) Gene Search Result (->3.4Expression Profile: Select Gene Page)
The search result is shown as a list of genes.
Select genes and click ‘Expression Profile’
button to display (3) Expression Profile.
Up to 100 genes can be selected.

-9-(3)Expression Profile (->3.5 Heatmap)
Expression pattern (relative amount of mRNA ineach tissue) of each gene is displayed as aheatmap. The colors of the heatmap stand forthe following states:
Red: Tissue with a relatively high expression
level.
Black: Tissue with an average expression level.
Green: Tissue with a relatively low expression
level.
Genes are clustered in accordance with thesimilarities of expression pattern, and the result
is displayed as a dendorogram.

(4) Correlated Gene Search (-> 3.5Heatmap)
To search genes whose expression pattern issimilar to the selected gene, select one geneand click 'Add Coregulated Gene' button. The
search result is added to the heatmap, and theSymbols of newly added genes are displayed inblue. Genes whose expression pattern is
opposite to the selected gene can be obtainedin the same way.

(5) ‘Expression Level’ View (-> 3.5Heatmap)
The target of heatmap color and clustering canbeswitched

fromexpression

patterntoexpression level.
“Z-Score” is the index of expression pattern and“Number (mRNA Copy Number)” is the index of
expression level.

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2.5.

Integrated Database Search(1) Search Execution (->3.8 Search Bar)
Simple search bar (marked in red) is always
displayed at the top of the page.

(2) Search Result (->3.9 Gene Search Page)
The search result is shown as a list of genes.
To access Genome Explorer, PPI Network andExpression Profile, click the icons in ‘Tool’
column. (- 11 -)

3.

Details of Screen

3.1.

Genome Explorer Page
(1)

(3)
(4)

(5)

(6)

(2)

(1) Chromosome Map: The bar chart beside chromosomes is the statistical information of ‘Gene’, ‘TU’,and ‘CAGE(Cap Analysis Gene Expression) Tag’ in 1Mbp distributed on eachchromosome. The statistical information on ‘Gene’ is selected by default. Click on
a chromosome to display the (5) Detailed Chromosome View.

(2) Statistic: To change data type in the charts in (1) and (3), select one data type here. The
available options are ‘No display (blank)’, ‘Gene’, ‘TU’, and ‘CAGE Tag’.

(3) Figure of Chromosome: The chromosome selected in (1) Chromosome Map is displayed here. The
statistical information are attached to figure of chromosome as well as in(1)Chromosome Map. The region clicked on this figure is displayed in(5) Detailed
Chromosome View.

(4) Shift Button: Click these buttons to shift the displayed region of (5) Detailed Chromosome View.
ButtonExplanation<<

Shift to left by 1Mbp.

<<

Shift to left by 500Kbp.

>

Shift to right by 500Kbp.

>>

Shift to right by 1Mbp.

- 12 -

(5) Detailed Chromosome View : The window size is 1Mbp. Click the (4) ‘Shift’ buttons to move to upstream or
downstream region from the current view.
The following information is displayed:(6) Summary of Gene

Items

Explanation

Gene(+)

Genes on the + strand are displayed
together with the gene symbols and theEntrezGene ID. Click to show thesummary.

TU(+)

TU(Transcriptional Unit)s on the + strand
are displayed together with TU IDs. Clickto show the summary.

TSS(+)TSS(Transcriptional Starting Site)s on the+ strand are displayed. Light orange
stands for a single TSS. Tangerine
signifies grouped TSSs. Click either ofthem to pop-up 3.12 TSS Details Page.

Gene(-)

Genes on the - strand are displayed.

TU(-)

TUs on the - strand are displayed.

TSS(-)TSSs on the - strand are displayed.

: Click a gene on the ‘Detailed chromosome view’ to display the summary of the geneas follows:

Items

Explanation

SymbolIndicates the EntrezGene symbol. Click it to pop-up 3.8
Gene Description Page.

Definition

Indicates the definition on this gene.

LocateIndicates the genomic position.

Toolmeans that this gene has the information ofprotein-protein interaction. Click the icon to jump to 3.3 PPINetwork Viewer Page.
means that this gene has the expression information.
Click the icon to jump to 3.5 Heatmap Page.

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Summary of TU: Click a TU on the (5) ‘Detailed chromosome view’ to display the summary of the TU
as follows:

Items

Explanation

TU ID

Indicates the TU ID.

LocateIndicates the genomic position.

Component mRNA

Indicates the number of mRNA constituting thisTU. Click the number to pop-up 3.10 mRNA List
page.

Linked CAGE tag

Indicates the number of CAGE tag linked to thisTU. Click the number to pop-up 3.11 CAGE Tag
List page.

Linked TSS

Indicates the number of TSS linked to this TU.
Click the number to pop-up 3.12 TSS Details
Page.

Linked Gene

Indicates the corresponding gene with this TU.
Click the gene symbol to pop-up 3.8 Gene
Description Page.

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3.2.

PPI Network: Select Gene Page
(2)
(1)
(3)
(4)
(5)

(6)

(7)

(1) Search Gene for(8): Input retrieval keys for searching genes. Multiple keys separated with spaceor commas are available. Retrieval keys are divided into two categories:
ID/Symbol or free words. OR search is carried out for ID/Symbol, while AND
search is carried out for free words.

(2) ‘Search’ button: Search for genes from interaction data based on the retrieval keys. The
search results are displayed in (5) Search Result List.

(3) Limited to(Field Name)(4) Limited to(Data Source): Select the data type of retrieval key items. The following items are selectable.
Items

Explanation

All Field

All the following are searched.

SymbolLimited to EntrezGene symbol.

Definition

Limited to definition of gene.

EntrezGene ID

Limited to EntrezGene ID.

MIM ID

Limited to MIM ID.

GO ID

Limited to GO ID.

GO Term

Limited to GO Term.

: Select data source of PPI information.
Items

Explanation

Y2H

Includes interaction described in Y2H.

BIND

Includes interaction described in BIND.

MINT

Includes interaction described in MINT.

HPRD

Includes interaction described in HPRD.

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(5) Gene: The genes that match the search conditions are listed.
Items

Explanation

Mark

Tick items for PPI Network Viewer.

SymbolIndicates the EntrezGene symbol.
Click it to pop-up 3.8 Gene Description Page.

Definition

Indicates the definition on this gene.

Y2H

Indicates the number of PPI in Y2H data that bindto this gene.

BIND

Indicates the number of PPI in BIND data that bindto this gene.

MINT

Indicates the number of PPI in MINT data that bindto this gene.

HPRD

Indicates the information of HPRD in the pertinent
gene.

EntrezGene*

Indicates the EntrezGene ID.

OMIM*

Indicates the OMIM ID.

Gene Ontology*

Indicates the GO ID and GO term.

Toolmeans that this gene has the information of
Genome Position. Click the icon to jump to 3.1
Genome Explorer Page.
means that this gene has the information ofprotein-protein interaction. Click the icon to jump to
3.3 PPI Network Viewer Page.
means that this gene has the expression
information. Click the icon to jump to 3.5 Heatmap
Page.

The columns with *(asterisks) are displayed only when these keys are usedin the search condition.
(6) ‘Check All’ button: Ticks all the check boxes.

(7) ‘Uncheck All’ button: Takes off all the check marks.

(8) ‘PPI Network Viewer’ button: Displays ‘PPI Network Viewer’ on the selected genes.
Up to 10 genes can be selected.
(->3.3 PPI Network Viewer Page)- 16 -

3.3.

PPI Network Viewer page
(2)
(1)

(3)
(4)

(5)
(6)

(1) Gene List

(7)

(9)

(8)

: Indicates the gene list corresponding to nodes with number in the network
displaying area. Those genes were specified in 'Select Gene Page' or added
by 'Add to List' menu or 'Expansion' menu.
Click on a gene name in the 'Gene list' to display 3.8 Gene Description
Page.

(2) Interaction: The color sample of edge (lines connected between the nodes) is shown.
Edges are classified by using different colors based on the data source:
Purpledenotes Y2H, green

denotes MINT, and blue

denotes BIND, browndenotes HPRD. Red

represents thoseinteractions that are described in the multiple databases.

These check boxes are used to change the adopted data source. After the‘Renewal on Selected Gene’ button is clicked, the check is reflected in thescreen.

- 17 -

(3) Network Displaying Area

: The network diagram is displayed based on the interaction information of theselected genes. The nodes can be dragged to any positions. The colors of
the nodes stand for the following states:
Orange: all interactions are displayed.
Light blue: More than one interaction is not displayed and 'Expansion' menu
is available.
Green: More than one interaction is not displayed but 'Expansion' menu is notavailable because of the restrictions on the number of nodes.

(4) Menu(5) Information Indication Area

: Click a node to display the following operational menu.
Items

Explanation

Expansion

Target node is expanded and Interactors
are displayed as nodes.
The Symbol of target node is added toGene List.

Folding

Small nodes connected only with target
node are deleted.

DeleteTarget node is deleted. Small nodes
connected only with target node are alsodeleted.

Add to List

The Symbol of target node is added toGene List.

Gene Description…

3.8 Gene Description Page is displayed.

Interactors Property…

3.9 Interactors Property page isdisplayed. In that page, statisticalinformation of Gene Ontology andInterPro on interactors are shown.

: The following information on the gene is displayed by the mouse over orclicking on a node.

Definition
SymbolItems

Explanation

SymbolIndicates the EntrezGene symbol.

Definition

Indicates the definition on the pertinent gene.

- 18 -

: The following information on the interaction is displayed by the mouse over orclicking on an edge (a line between connected nodes).

Interaction Data
Items

Explanation

Interaction Data

Indicates the data sources of the interactions. If
there are two or more data sources, they areseparated by commas.

(6) ‘Check All’ button: Ticks all the check boxes of the genes in (1) ‘Gene list’.

(7) ‘Uncheck All’ button: Takes off all the check marks of the genes in (1) ‘Gene list’.

(8) ‘Renewal on Select Gene’ button : Renews the ‘PPI Network Viewer’ for the ticked genes in (1) ‘Gene list’.
(->3.3 PPI Network Viewer Page)(9) ‘Expression Profile’ button: Displays the ‘Expression Profile’ for the ticked genes in the expression genelist.(->3.5 Heatmap Page)- 19 -

3.4.

Expression Profile: Select Gene Page
(2)
(1)
(3)
(5)

(6)

(7)

(1)Search Gene for

(4)

(8)

: Input retrieval keys for searching genes. Multiple keys separated with spaceor commas are available. Retrieval keys are divided into two categories:
ID/Symbol or free words. OR search is carried out for ID/Symbol, while AND
search is carried out for free words.

(2)‘Search’ button: Search for genes from interaction data based on the retrieval keys. The
search results are displayed in (5) Search Result List.

(3)Limited to(1): Select the data type of retrieval key items. The following items are
selectable.

(4) Limited to(2)Items

Explanation

All Field

All the following are searched.

SymbolLimited to EntrezGene symbol.

Definition

Limited to definition of gene.

EntrezGene ID

Limited to EntrezGene ID.

MIM ID

Limited to MIM ID.

GO ID

Limited to GO ID.

GO Term

Limited to GO Term.

: Limited to genes with tissue-specific expression. ‘Tissue-specific’ meansthat the expression level in a particular tissue is especially high or low for
the gene.

- 20 -

(5) Gene: The genes corresponding to the search conditions are listed.
Items

Explanation
Select genes for heatmap page.

Mark

Indicates the EntrezGene symbol.
Click it to pop-up 3.8 Gene Description Page.

SymbolIndicates the definition on the pertinent gene.

Definition

Indicates specific expression tissues on the
Expression［+］ pertinent gene.
Expression［-］EntrezGene*

Indicates non-specific expression tissues on thepertinent gene.
Indicates the EntrezGene ID.
Indicates the OMIM ID.

OMIM*
Gene Ontology*
Tool

Indicates the GO ID and GO term.
means that this gene has the information of
Genome Position. Click the icon to jump to 3.1
Genome Explorer Page.
means that this gene has the information ofprotein-protein interaction. Click the icon to jump to
3.3 PPI Network Viewer Page.
means that this gene has the expression
information. Click the icon to jump to 3.5 Heatmap
Page.

The columns with *(asterisks) are displayed only when there arecorresponded items at the results of the search.

(6) ‘Check All’ button: Ticks all the check boxes.

(7) ‘Uncheck All’ button: Takes off all the check marks.

(8) ‘Expression Profile’ button: Displays ‘Expression Profile’ on the selected genes.(->3.5 Heatmap page)- 21 -

3.5.

Heatmap Page

■Expression Pattern View

(4)

(11)
(12)

(2)

(6)

(1)

(7)
(8)
(9)
(5)
(3)

(13)

(14)

■Expression Level View

- 22 -(10)

(1) Gene Symbol: Indicates the gene symbols of the genes displayed in a heatmap.
Click the gene symbol to pop-up 3.8 Gene Description Page.

(2) Tissue: Indicates the tissue names. *(Asterisk) denotes the cell lines. In the case of
the cell lines, the library names are displayed.

(3) Heatmap: Expression pattern (pattern of expression level over different tissues) ofeach gene is displayed with the heatmap. The colors of the cells in theheatmap stand for the following states:
Red: Tissue with relatively high expression level
Black: Tissue with average expression level
Green: Tissue with relatively low expression level
The target of heatmap color can be switched from expression pattern toexpression level.

(4) ‘Clustering’ button: Re-clusters and redraws the heatmap. At that time, tissues which are notchecked become invalid. The following example shows that the cell lines(unchecked tissue) are removed and the heatmap is redrawn.

(5) Dendrogram: Correlations between clusters are indicated by a dendrogram. The target ofclustering can be switched from expression pattern to expression level.

- 23 -

(6) Information Indication Area

: The information on the expression shown below is displayed by mouse over on
the cells in the heatmap.
SymbolTissue (or Library)
Z-ScoremRNA Copy Number
Correction Rate
Items

Explanation

SymbolIndicates the EntrezGene symbol.

TissueIndicates the tissue name (library name incase of cell line)

Z-ScoreThe value is used as the indicator of theexpression pattern.

mRNA Copy Number

The value is converted from the Ct value(product of qRT-PCR experiment) using theamplification curve of gene. It stands for thenumber of transcription products and it isused as the indicator of the expression
level.

Correction Rate

It is used to normalize the validation of thedata by the library. The correction rate ineach library is multiplied for ‘mRNA Copy
Number’. The correction rate is converted
from the average amount of ‘mRNA Copy
Number’ in each library.

: The information shown below about the pertinent gene is displayed by mouseover on the gene symbol beside the heatmap.
Definition
SymbolItems

Explanation

SymbolIndicates the gene symbol.

Definition

Indicates the definition of the pertinent gene.

- 24 -

(7) 'Renewal on Select Gene' button: Genes, except for the ticked ones, are deleted and the heatmap isredisplayed.

(8) 'Add Coregulated Gene' button: Genes that have the expression pattern coregulated to the selected gene
(only one gene can be selected) are searched and added to the heatmap.
Newly added gene symbols are displayed in blue.

(9) 'Add Anti-coregulated Gene' button : Genes that have the expression patterns anti-coregulated to the selectedgene (only one gene can be selected) are searched and added to theheatmap. Newly added gene symbols are displayed in blue.
(10)'PPI Network Viewer' button: 'PPI Network Viewer' based on the ticked genes is displayed. Up to 10 genes
can be selected. Genes without interaction information are ignored.
(->3.3 PPI Network Viewer Page)(11) 'clustering' switch button: Switch the target for clustering.
Items(12)'color' switch button

Explanation

Z-ScoreCluster genes by expression pattern.

NumberCluster genes by expression level.

: Switch the target for hearmap color.
Items

Explanation

Z-ScorePaint heatmap by expression pattern.

Number

Paint heatmap by expression level.

(13)'Check All' button: Ticks all the check boxes.

(14)'Uncheck All' button: Takes off all the check marks.

- 25 -

3.6.

Search Bar(1)(1) Search(2) for(3)(2): The following search functions are selectable.
Items

Explanation

Gene

Gene Search: Input retrieval keys. Multiple keys can be input by separating with spaces or commas.
When IDs are entered, OR search is carried out. Otherwise, when items except for IDs
are keyed in, AND search (search refinement) is performed.

(3) 'Search' button: Perform a search for the integrated database based on the retrieval keys and search
condition. The retrieval result is displayed on these pages.
Function

Search Result Page

Gene

3.7 Gene Search Page

- 26 -

3.7.

Gene Search Page
(1)
(3)

(2)
(4)

(5)

(6)

(7)

(1) Search Gene for

(8)

(9)

: Input retrieval keys for searching genes. Multiple keys separated with space orcommas are available. Retrieval keys are divided into two categories:
ID/Symbol and free words. OR search is carried out for ID/Symbol, while AND
search is carried out for free words.

(2) ‘Search’ button: Search for genes from interaction data based on the retrieval keys. The search
results are displayed in (5) Search Result List.

(3) Limited to(1)(4) Limited to(2): Select data type of retrieval key items. The following items are selectable.
Items

Explanation

All Field

All the following are searched.

SymbolLimited to EntrezGene symbol.

Definition

Limited to definition of gene.

EntrezGene ID

Limited to EntrezGene ID.

MIM ID

Limited to MIM ID.

GO ID

Limited to GO ID.

GO Term

Limited to GO Term.

: Limited to genes by the accompanied information.
Items

Explanation

Interaction

Limited to genes with protein-protein interactions
information.
Limited to genes with expression information.

Expression- 27 -

(5) Search Result List

: The search result list is displayed.
Items

Explanation

Mark

Only genes with interaction or expression
information can be checked. All the check boxes
are checked in default.

SymbolIndicates the EntrezGene symbol.
Click it to pop-up 3.8 Gene Description Page.

Definition

Indicates the definition on the pertinent gene.

EntrezGene*

Indicates the EntrezGene ID.
Indicates the OMIM ID.

OMIM*
Gene Ontology*
Tool

Indicates the GO ID.
means that this gene has the information of
Genome Position. Click the icon to jump to 3.1
Genome Explorer Page.
means that this gene has the information ofprotein-protein interaction. Click the icon to jump
to 3.3 PPI Network Viewer Page.
means that this gene has the expression
information. Click the icon to jump to 3.5
Heatmap Page.

The columns with *(asterisks) are displayed only when there are corresponded
items at the results of the search.

(6) ‘Check All’ button: Ticks all the check boxes.

(7) ‘Uncheck All’ button: Takes off all the check marks.

(8) ‘Expression Profile’ button: Displays 'Expression Profile' for the ticked genes in 'Mark' at the results of thesearch.
(->3.5 Heatmap page)(9) ‘PPI Network Viewer’ button: Displays 'PPI Network Viewer' for the ticked genes in 'Mark' at the results ofthe search.
(->3.3 PPI Network Viewer Page)- 28 -

3.8.

Gene Description Page
(1)

(2)

(3)

(1) Gene Description: Indicates the gene annotations.
Items

Explanation

Definition

Indicates the definition on the pertinent gene.

LocateIndicates the region information.

Interactions

Indicates the number of the interactions.

EntrezGene

Indicates the EntrezGene ID.

OMIM

Indicates the associated information on OMIM.

Gene Ontology

Indicates the associated information on GO.

UniProt

Indicates the associated information on UniProt.

InterPro

Indicates the associated information on InterPro.

(2) Expression Profile: Indicates the expression level (mRNA Copy Number) in each tissue.

(3) Interactor(s): Indicates the interactors list of the pertinent gene. As for the databases with
the interaction information, the check marks are displayed.

- 29 -

3.9.

Interactors Property page
(1)
(2)

(3)

(1) Interactions: The number of interactions in each data source.

(2) Gene Ontology Statistical Information : Statistics on GO denoted in gene annotation.
(3) InterPro Statistical Information: Statistics on InterPro denoted in gene annotation.

- 30 -

3.10. mRNA List page
(1)

(2)

(3)

(1)TU ID

: Indicates the TU ID.

(2)Locate: Indicates the region of TU.

(3)mRNA list

: Indicates the list of mRNAs constituting the TU.
Items

Explanation

Public DB

Indicates the public databases which are the original
source of mRNAs are GB (GenBank), RefSeq, andEnsembl.

mRNA ID

Indicates the ID on the source of the pertinent mRNA.

Position in TU

Indicates the relative position of mRNA in TU.

LengthIndicates the length of the pertinent mRNA.

- 31 -

3.11. CAGE Tag List page(1)
(2)(1) TU ID: Indicates the TU ID.

(2) CAGE Statistical Information: Indicates CAGE statistical information about the TU.
Items

Explanation

RNA Library

Indicates the RNA library name used in the CAGE
experiment.
Indicates the number of tags in each RNA libraryassociated with the pertinent TU.
These are the tag rates calculated by the following
formula:(The number of CAGE tags per library associated withthe pertinent TU) / (The number of CAGE tags perlibrary) × 1000000

Tags
Tpm

- 32 -

3.12. TSS Details page
<Aligned Format (Initial Pane)>

(2)

(3)
(4)

(5)
(1)

<FASTA Format>

(4)

(6)

(1)TSS ID list

: When multiple TSSs are selected, a TSS ID list is displayed at the right side of
the page. Click the TSS ID to show ‘Tag sequence view’ at the right side of thepage.
When a single TSS is specified, the TSS ID list is not displayed.

(2)TSS ID: Indicates the TSS ID.

(3)Locate: Indicates the region of TSS.

(4)->FASTA Format: Selects either FASTA or Aligned format as display style.

->Aligned(5)Tag sequence view (aligned)(6)Tag sequence view

: CAGE tag sequences included in TSS are displayed in alignment.
Items

Explanation

Rep Tag ID

This is the ID of CAGE tag with the pertinent
sequence. When there are multiple tags withidentical sequences, the ID of the representative
tag is shown.

Tags

When there are multiple tags with identicalsequences, the quantity is displayed.

Sequence

Indicates the sequences of the pertinent tag.

: CAGE tag sequences included in TSS are displayed in FASTA format.

(FASTA Format)- 33 -

4.

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