Pathway Studio 6 Training Manual

The manual is applicable to:

  • Pathway StudioŽ Desktop 6
  • Pathway Studio PC-Client 6 (Enterprise)
  • MedScan ReaderŽ version 2

This Training Manual provides descriptions and hands-on exercises to support learning to use Pathway Studio 6 and MedScan Reader 2.   (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.) 

In addition to the Training Manual, the User Manual (the information available in the Help section in Pathway Studio) can be downloaded here.

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Pathway Studio 6 Desktop & PC-Client Training Manual v2 * Basic Documentation 7 Mb PDF
Example data files for Pathway Studio 6 Training Manual * Basic Documentation 473 Kb ZIP/Text
ChemEffect Training

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Quick Start Guide for ChemEffect * Basic Documentation 486 Kb PDF
Analysis Guides for Pathway Studio 6

These Analysis Guides provide example workflows to answer specific biological questions using Pathway Studio and the ResNet 6 Mammalian or the ChemEffect 1.1 database.

ResNet 6 Mammalian Database Analysis Guides

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PS RN6 Analysis Guide: How can I find diseases that are involved in the amplification of a specific gene? * Analysis Guide 305 Kb PDF
PS RN6 Analysis Guide: How can I find diseases that are involved in an activation mutation of specific gene? * Analysis Guide 191 Kb PDF
PS RN6 Are fusions of my gene (from chromosomal translocations) involved in any diseases? * Analysis Guide 185 Kb PDF
PS RN6 Analysis Guide: Are splicing variants of my gene involved in diseases? * Analysis Guide 256 Kb PDF
PS RN6 Analysis Guide: What genes are transcriptionally regulated by my protein? * Analysis Guide 171 Kb PDF
PS RN6 Analysis Guide: What proteins regulate the activity or abundance of my protein? * Analysis Guide 200 Kb PDF
PS RN6 Analysis Guide: Does my protein uniquely regulate expression of any genes? * Analysis Guide 239 Kb PDF
PS RN6 Analysis Guide: What small molecules are known to regulate my pathway? * Analysis Guide 186 Kb PDF
PS RN6 Analysis Guide: What cell processes is my protein involved in? * Analysis Guide 145 Kb PDF
PS RN6 Analysis Guide: How can I identify main tissue-specific regulators for my expression signature? * Analysis Guide 1003 Kb PDF
Data File: Cytotoxic T cell gene list.txt * Basic Documentation 365 b ZIP/Text

ChemEffect Database Analysis Guides

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PS RN6 CE Analysis Guide: Can I identify potential drug-drug interactions mediated by alterations of drug metabolism? * Analysis Guide 288 Kb PDF
PS RN6 CE Analysis Guide: Can I identify potential drug-drug interactions through opposing actions on the drug target? * Analysis Guide 357 Kb PDF
PS RN6 CE What are the known and potential side effects of my drug? * Analysis Guide 345 Kb PDF