Identifying Significantly Impacted Pathways and Putative Mechanisms with iPathwayGuide

Sidra Ahsan1, Sorin Drăghici2

1 Advaita Bioinformatics, Plymouth, Michigan, 2 Wayne State University, Department of Obstetrics and Gynecology, Detroit, Michigan
Publication Name:  Current Protocols in Bioinformatics
Unit Number:  Unit 7.15
DOI:  10.1002/cpbi.24
Online Posting Date:  June, 2017
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iPathwayGuide is a gene expression analysis tool that provides biological context and inferences from data generated by high‐throughput sequencing. iPathwayGuide utilizes a systems biology approach to identify significantly impacted signaling pathways, Gene Ontology terms, disease processes, predicted microRNAs, and putative mechanisms based on the given differential expression signature. By using a novel analytical approach called Impact Analysis, iPathwayGuide considers the role, position, and relationships of each gene within a pathway, which results in a significant reduction in false positives, as well as a better ability to identify the truly impacted pathways and putative mechanisms that can explain all measured gene expression changes. It is a Web‐based, user‐friendly, interactive tool that does not require prior training in bioinformatics. The protocols in this unit describe how to use iPathwayGuide to analyze a single contrast between two phenotypes (any number of samples), and provide guidance on how to interpret the results obtained from iPathwayGuide. Even though iPathwayGuide has powerful meta‐analysis capabilities, these are not covered in this unit. © 2017 by John Wiley & Sons, Inc.

Keywords: gene expression analysis; microarrays; RNA‐seq; pathway analysis; differential expression analysis

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Table of Contents

  • Introduction
  • Strategic Planning
  • Basic Protocol 1: Using iPathwayGuide to Analyze a Differential Expression Dataset that Compares Two Experimental Conditions
  • Alternate Protocol 1: Using iPathwayGuide to Analyze Microarray Data Generated from Affymetrix Platforms
  • Commentary
  • Literature Cited
  • Figures
  • Tables
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Literature Cited

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