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Integrated Biology operations
Pathway Analysis
between the genes or proteins of interest and provide insight into the mechanism of a specific condition under study.
• Which small molecules might interact with a gene or set of genes?
Getting started requirements
Pathway Analysis requires the following:
1. A valid license for the Pathway Architect module. See the Agilent G3835AA
MassHunter Mass Profiler Professional - Quick Start Guide and the Mass Profiler Professional User Manual for information about licenses in Mass Profiler
Professional.
2. A valid license for the GeneSpring GX module. See the Agilent G3835AA
MassHunter Mass Profiler Professional - Quick Start Guide and the Mass Profiler Professional User Manual for information about licenses in Mass Profiler
Professional.
3. Pathways from sources of interest for the organism under study. See section
“11.1.2 Importing Pathways into Mass Profiler Professional” in the Mass Profiler Professional User Manual for more information about pathway sources
and creating pathways.
4. Supporting databases to perform Pathway Analysis for a single organism or
across different organisms. Pathway Analysis is supported by organism specific interaction databases, BridgeDb databases, and HomoloGene annotations. See section “11.1.5 Supporting Databases for Pathway Analysis” in the
Mass Profiler Professional User Manual for more information.
What is BridgeDb?
Pathways acquired from different sources may refer to the same entity using synonymous names and/or identifiers from different biological databases. Incorporating
data from multiple databases leads to variations in annotations. BridgeDb (http://
www.bridgedb.org) is an identifier mapping framework for bioinformatics applications and provides mapping for the same entity across different biological databases.
Single Experiment Analysis and Multi-Omics Analysis use BridgeDb to search for
pathways that match the entities in the your entity list(s). Click Annotations >
Update BridgeDb > From Agilent Server to update BridgeDb. See section “11.5.2
BridgeDb - ID Mapping” and section “11.1.5 Supporting Databases for Pathway
Analysis” in the Mass Profiler Professional User Manual for more information.
Improving your Pathway
Analysis results
The results from performing a Pathway Analysis are dependent upon (1) the number
of annotated entities in your experiment and (2) the quality of the annotations. Entities from proteomics and genomics experiments typically provide greater pathway
analysis accuracy (less ambiguity) because these entities are more highly annotated. When you are using entities from metabolomics experiments you can improve
your analysis accuracy by (1) using GCMS data that has been identified in a spectral
library search, (2) using data from targeted QQQ experiments, and (3) using ID
Browser to annotate data from high resolution LCMS experiments. By comparing
the pathway results from filtered entity lists (i.e., fold change, K-means clustering)
and unfiltered entity lists (not filtered for fold change or significance) lists can also
improve your results.
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