Pathway Studio 7.1 Training Manual

The manual is applicable to:

  • Pathway StudioŽ Desktop 7.1
  • Pathway Studio PC-Client 7.1 (Enterprise)
  • MedScan ReaderŽ version 3.1

This Training Manual provides descriptions and hands-on exercises to support learning to use Pathway Studio 7.1 and MedScan Reader 3.1.   (Included are two example data files for use in the exercises.  While the exercises are designed using the ResNet Mammalian database, the basic workflows are the same for the ResNet Plant or ChemEffect database as well.) 

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Training Manual Pathway Studio 7.1 Desktop and Pathway Studio 7.1 Enterprise PC-Client * Basic Documentation 8 Mb PDF
Pathway Studio 7.1 Training Manual supplemental files * Basic Documentation 497 Kb ZIP/Text

Additional Pathway Studio Training Material

Below are additional training tools for using Pathway Studio.

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Guide to Building Networks in Pathway Studio - An Introduction * Basic Documentation 2 Mb PDF
Quick Start Guide for ChemEffect 2 * Basic Documentation 1008 Kb PDF
Introduction to miRNA Analysis in Pathway Studio * Basic Documentation 580 Kb PDF

Analysis Guides for Pathway Studio 7

These Analysis Guides provide example of more advanced workflows to answer specific biological questions using Pathway Studio 7 and the ResNet 7 Mammalian database, ChemEffect 2 database or the ResNet 3 Plant database.

ResNet 7 Mammalian Database Analysis Guides

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PS RN7 Analysis Guide: How can I find diseases that are involved in the amplification of a specific gene? * Analysis Guide 263 Kb PDF
PS RN7 Analysis Guide: How can I find diseases that are involved in an activation mutation of specific gene? * Analysis Guide 190 Kb PDF
PS RN7 Analysis Guide: Are fusions of my gene (from chromosomal translocations) involved in any diseases? * Analysis Guide 146 Kb PDF
PS RN7 Analysis Guide: Are splicing variants of my gene involved in diseases? * Analysis Guide 211 Kb PDF
PS RN7 Analysis Guide: What genes are transcriptionally regulated by my protein? * Analysis Guide 245 Kb PDF
PS RN7 Analysis Guide: What proteins regulate the activity or abundance of my protein? * Analysis Guide 198 Kb PDF
PS RN7 Analysis Guide: What small molecules are known to regulate my pathway? * Analysis Guide 175 Kb PDF
PS RN7 Analysis Guide: What cell processes are my protein(s) involved in? * Analysis Guide 169 Kb PDF
PS RN7 Analysis Guide: How can I identify main tissue-specific regulators for my expression signature? * Analysis Guide 230 Kb PDF
PS RN7 Analysis Guide example data set: cytotoxic T cell gene list * Analysis Guide 321 b ZIP/Text

ChemEffect 2 Analysis Guides

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PS7 RN7 CE2 Analysis Guide: Can I identify potential drug-drug interactions mediated by alterations of drug metabolism? * Analysis Guide 221 Kb PDF
PS7 RN7 CE2 Analysis Guide: Can I identify potential drug-drug interactions through opposing actions on the drug target? * Analysis Guide 253 Kb PDF
PS7 RN7 CE2 Analysis Guide: What are the known and potential side effects of my drug? * Analysis Guide 218 Kb PDF

ResNet 3 Plant Database Analysis Guides

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PS7 RN3 Analysis Guide: How can I find candidate genes related to a specific plant trait? * Basic Documentation 234 Kb PDF
PS7 RN3 Analysis Guide: How can I find literature supporting a list of candidate genes related to a specific plant trait? * Basic Documentation 251 Kb PDF