Agilent Pathway Architect

FROM DISCOVERY TO INSIGHTMETABOLOMICSPROTEOMICSPATHWAY ARCHITECTGENOMICS

TRANSCRIPTOMICSAGILENT PATHWAY ARCHITECTSPEED DISCOVERY TO UNDERSTANDING

Today’s scientists face a serious challenge as they try to analyze increasingly larger and more
complex sets of data, such as those generated by genomics, transcriptomics, proteomics, andmetabolomics experiments. An integrated pathway approach for analyzing data can significantly
alleviate bottlenecks and fulfill the ultimate purpose of biological research—understanding thebiology behind the measurements. One successful approach for translating diverse analytical data
into biological understanding is through the projection and visualization of processed data onto
biological pathways.

Gain Deeper Insight
Agilent’s Pathway Architect software is an optional module for GeneSpring and Mass Profiler Professional (MPP) that was developed to offer scientists a seamless platform for gaining deeper insights
into their data. It allows users to take the results from single or multi-omics experiments and mapthem onto canonical biological pathways, concurrently analyzing, visualizing, and interpreting pathway
information. This pathway-centric workflow speeds the route from discovery and insight to validation.
It also enables researchers to efficiently plan and execute their next series of experiments.

The ability to analyze data using apathway-centric view allows scientist to:

METABOLOMICSPROTEOMICSPATHWAY ARCHITECTGENOMICS• Link compounds and omics results
to known biology• Focus research goals with direct
linkage to biological relevance• Integrate multi-omics results for amore holistic interpretation• Generate hypotheses and guide
future experiments

TRANSCRIPTOMICS
The purine metabolism pathway from KEGG, visualized in Pathway Architect. Metabolites (circles) in blue andgenes/proteins (rectangles) in yellow indicate matches with the input entity list.

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VISUALIZE YOUR RESULTS

Pathway Architect is a visualization tool that uses publicly available pathway databases to facilitate
the understanding of biological results. The software maps metabolites, proteins, and genes onto
curated pathways, graphically projecting data onto pathway nodes or edges for interactive useranalysis. Researchers can specify search criteria for particular organisms and browse a table ofpathway results before projecting data onto a particular pathway.

Pathway Databases• KEGG

Simplified Pathway Analysis
Once the software is ready to perform pathway analysis, users can execute a single or multi-omic
analysis in three simple steps:
1. Select the data
2. Specify the organism
3. Choose the pathway database and analyze
List of pathways searched• WikiPathways

Number of entity matches

Match significance score• BioCyc• PathVisio custom pathways• GPML format• BioPAX format

Display data from all
experiments next torelevant nodes• Natural Language Processing (NLP)
Choose among the curated pathways available within Pathway Architect.

Resolve Mismatches
Pathway Architect makes it easy to resolve
nomenclature inconsistencies between thesame compound through the use of apowerful built-in tool, Agilent-BridgeDB.
This resource automatically links anannotated metabolite, protein, or gene
identifier in the experiment to thecorresponding identifier used by a particularpathway database. Pathway Architect
uses only identifiers instead of common
names to minimize errors. Agilent-BridgeDB
has been optimized for KEGG, BioCyc andWikiPathways databases.

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Compound List

Pathway Database

L-Galactose
Theobromine
Paraxanthine

Dextrose

Theophylline
Protionamide
Tetrahydrodeoxycorticosterone
Paraxanthine
17-methyl-6Z-octadecenoic acid
Tridecanoic acid8-iso-PGF2alphaoctadecanamide
Caldarchaeol

AgilentBridgeDB

Acetaldehyde
Ethanol
AcetatePyruvate(S)-Lactate
Oxaloacetate
Phosphoenolpyruvate
Glycerone phosphate
D-Glyceraldehyde 3-phosphate

D-Glucose

3-Phospho-D-glycerate
2-Phospho-D-glycerate
D-Glucose 1-phosphatebeta-D-Glucose 6-phosphate

Agilent-BridgeDB automatically links annotated metabolites, proteins, and gene identifiers used in theexperiment to those in the pathway database.

Filter results

Perform joint or separate analysis

Pathway Architect provides an interactive, user-friendly graphical display.

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PATHWAYS TO INFORM YOUR EXPERIMENTS

The addition of the Pathway Architect module to GeneSpring and MPP facilitates the move fromhypothesis-free to pathway-driven studies. This approach has been demonstrated for both single
omic and multi-omic experiments. The results of primary data analysis from one or multiple omic-level
experiments can be analyzed by Pathway Architect to easily and robustly identify pathways that are
involved in different biological phenomena. The results of such pathway analysis can be used to quickly
direct and design the next experiment using an exported list of metabolites, proteins, or genes from aselected significant pathway.
VALIDATIONEXPERIMENTATION
HYPOTHESIS-FREE

Design Experiment
Data Acquisition
Data Analysis
Build Model

HYPOTHESIS-DRIVEN

6GENESPRING-PA

GENESPRING-GX

STRAND-GENESPRING-NGS

GENESPRING-PA

GENESPRING-GX

STRAND-GENESPRING-NGS

GENESPRING-PA

GENESPRING-PA

STRAND-GENESPRING-NGS

GENESPRING-GX

GENESPRING-MPP

GENESPRING-MPP

GENESPRING-MPP

PATHWAY ARCHITECTAgilent supports and integrates single and multi-omic experiments, simplifying the cyclical journey fromhypothesis-free discovery to pathway-driven validation.

SINGLE OMICSANALYSIS

A list exported from Pathway Architect canbe brought into other Agilent software toenable your next experiment. For example,
a list of protein accession numbers canbe imported into Agilent’s Spectrum Millsoftware and a triple quadrupole MRM
experiment can be designed and loaded into
Agilent’s MassHunter Acquisition software
to run the experiment. The same concept
applies to genes, where a list of genes canbe transferred to Agilent’s eArray website
to build a custom microarray. These usefulsoftware linkages accelerate the planningand execution of the next set of experiments.

DISCOVERY

Agilent’s Integrated Biology software suite, which includes GeneSpring, Mass Profiler Professional,
and Pathway Architect, simplifies the joint analysis of multi-omic data. These software modules jointly
process the data from genomics, NGS, transcriptomics, proteomics, and metabolomics studies andefficiently map entities onto their corresponding pathways. Intuitively explore, verify, and quickly findthe biological pathways that are over-represented in the multi-omics data you are generating. Gain
more insight by integrating your pre-existing knowledge of biological pathways with multi-omics data,
speeding the process from discovery to validation.

MULTI-OMICSANALYSIS

Accelerate Future
Experiments

Integrate Multi-Omics Data

GeneSpring-PA is a stand-alone
tool for pathway annotation anddata integration.

GeneSpring-GX analyzes
microarray data fromgenotyping, gene expression,and miRNA arrays.

Strand-GeneSpring-NGS
manages SureSelect Target
Enrichment, and NGS datafrom RNA, DNA,ChIP, smallRNA, and methylation
experiments.

GeneSpring-MPP processes
mass spectrometry data forboth proteomics andmetabolomics studies.

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Learn more
www.agilent.com/chem/metabolomics
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www.agilent.com/chem/contactus
USA and Canada
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For Research Use Only. Not for use in diagnostic procedures.
This information is subject to change without notice.
© Agilent Technologies, Inc., 2012
Printed in the USA, July 3, 2014
5991-1459EN