Pathway Studio Tutorials

 

Video Presentations
How To
Tutorials

Video Presentations

 

Affymetrix GeneChip-compatible - Pathway Analysis of Expression Data using Ariadne Pathway Studio

We demonstrate advanced methods of analysis and interpretation of Affymetrix microarray data. You will learn how to use Pathway Studio to identify gene clusters and differentially expressed genes, find major regulators responsible for observed expression patterns, identify differentially expressed pathways and affected biological process - all in a few mouse clicks. The demonstration covers import and analysis of CEL files, results from ChIP-on-chip experiments, transcript levels calculated from the Exon arrays, and will show you how to obtain publication-quality pathway diagrams uncovering biological processes which underlay your experimental results. The main part of the demo is the analysis of microarray data to understand mechanism of aggressiveness of uveal melanoma. It includes finding differentially expressed genes in Pathway Studio, their analysis using GO annotation, and identification of pathways contributing to the tumor aggressiveness. (Requires WebEx player)

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Tutorials

Importing Gene or Protein Lists *
Finding Cell Processes Regulated by Your Gene/Protein list *
Calculating P Value for the Find Relevant Groups and Find Relevant Pathways Algorithms *
How to build pathway manually in Pathway Studio *
Intuitive Method to Draw Pathway Diagrams in PathwayStudio *
Adding Custom Images to the PathwayStudio Image Library *
How to Create Your Own Display Style *
Adding Your Own Protein-Protein Interactions *
Working with Pathway Diagrams *
Creating New Object Type *
How to Use Build Pathway Filter Options to Solve Bioinformatics Problems *
Gene expression analysis in Pathway Studio Desktop *
Gene expression analysis in Pathway Studio Enterprise *
Coloring Enzymes in KEGG Pathway by Expression Values *
Transferring Expression Data between GeneSpring and PathwayStudio *
How to Create Your Own Database for Non-Model Organism and Borrow Interactions from the Closest Model Organism *
How to Work with Different Organisms in PathwayStudio *
How to Find Compounds Regulating Transcription Factors in the PathwayStudio Database *
Using PathwayStudio to Store Experimental Data *
Protein Tissue Annotation in the ResNet Database *
Updating Your Database with New Protein-Protein Interactions *
Estimating Statistical Significance of a Pathway Subnetwork *
 

Importing Gene or Protein Lists

Importing gene lists and building pathways from them requires just three steps: * Importing the list of genes into PathwayStudio using the Import Protein List tool * Building a pathway using the Build Pathway tool * Saving the pathway

*  Open [433 Kb ]

Finding Cell Processes Regulated by Your Gene/Protein list

The software is supplied with the ResNet database, which contains objects used in molecular networks studies and pathway analysis, and functional links among them: proteins, small molecules, cell processes, events of regulation, chemical reactions, etc. This tutorial explains how to search the database for cell processes, which are regulated by your protein(s) of interest.

*  Open [850 Kb ]

Calculating P Value for the Find Relevant Groups and Find Relevant Pathways Algorithms

Calculate p-value for "Find Relevant Groups" and "Find Relevant Pathways" algorithms.

*  Open [116 Kb ]

How to build pathway manually in Pathway Studio

Tutorial describes how to find and connect existing entities in the database, how to create new entities and relations and layout the manually built pathway by cell localization.

*  Open [841 Kb ]

Intuitive Method to Draw Pathway Diagrams in PathwayStudio

This tutorial describes the fastest way to: * Draw a pathway diagram * Add entities to a pathway * Create a link between two entities in PathwayStudio

*  Open [246 Kb ]

Adding Custom Images to the PathwayStudio Image Library

Add new cell part images to the image library and the Images Pane

*  Open [289 Kb ]

How to Create Your Own Display Style

A style in PathwayStudio is a named set of formatting attributes for entities and relations. Styles in PathwayStudio work the same way as they do in most word and graphical processing programs such as MS Word or Adobe Photoshop. Styles provide a convenient and powerful way to organize formatting and visualization of pathway maps.

*  Open [2 Mb ]

Adding Your Own Protein-Protein Interactions

Customize a Pathway Studio database by adding new protein-protein interactions

*  Open [273 Kb ]

Working with Pathway Diagrams

Open, inspect, and change pathway diagrams with only a few mouse clicks. You will learn how to add new links to the pathways, create groups of nodes, change visual styles, and other things related to pathway diagrams.

*  Open [670 Kb ]

Creating New Object Type

Create a new object type in the ResNet database. Three import formats are discussed here: Plain Text, RNEF XML, and Tab Delimited

*  Open [279 Kb ]

How to Use Build Pathway Filter Options to Solve Bioinformatics Problems

This tutorial describes on several examples how to use the Build Pathway Filter options to answer your questions.

*  Open [2 Mb ]

Gene expression analysis in Pathway Studio Desktop

Comprehensive manual for analysis of microarray gene expression data in Pathway Studio Desktop.

*  Open [2 Mb ]

Gene expression analysis in Pathway Studio Enterprise

Comprehensive manual for analysis of microarray gene expression data in Pathway Studio Enterprise.

*  Open [2 Mb ]

Coloring Enzymes in KEGG Pathway by Expression Values

Overlay the expression experiment results onto a particular KEGG pathway diagram.

*  Open [154 Kb ]

Transferring Expression Data between GeneSpring and PathwayStudio

The list of genes exported from several microarray data analysis programs can be imported into PathwayStudio. In this tutorial, we explain how to import expression experiment data from the GeneSpring software.

*  Open [594 Kb ]

How to Create Your Own Database for Non-Model Organism and Borrow Interactions from the Closest Model Organism

For researchers working on model organisms, annotation is readily available for most of the sequences on their arrays. However, many researchers are working on the nonmodel organisms, which genomes have not been sequenced or annotated. This tutorial shows how to work with non-model organisms in PathwayStudio. The main principle in this tutorial is using the ortologous relations from the Ariadne's databases for model organisms. Prior to every workflow described below, a user is expected to obtain the orthologous mapping between proteins in nonmodel organism and one of the available model organisms.

*  Open [308 Kb ]

How to Work with Different Organisms in PathwayStudio

For researchers working on model organisms, annotation is readily available for most of the sequences on their arrays. However, many researchers are working on the nonmodel organisms, which genomes have not been sequenced or annotated. This tutorial shows how to work with nonmodel organisms in PathwayStudio. The main principle in this tutorial is using the ortologous relations from the Ariadne's databases for model organisms. Prior to every workflow described below, a user is expected to obtain the orthologous mapping between proteins in nonmodel organism and one of the available model organisms.

*  Open [345 Kb ]

How to Find Compounds Regulating Transcription Factors in the PathwayStudio Database

Find drugs and other chemicals affecting your favorite Transcription Factors (TF) in a PathwayStudio database. TFs are very difficult drug targets. Very often one needs to inhibit proteins regulating the TF in order to modulate TF activity, since the compounds directly binding to TFs are not available.

*  Open [2 Mb ]

Using PathwayStudio to Store Experimental Data



*  Open [217 Kb ]

Protein Tissue Annotation in the ResNet Database

The goal of this tutorial is to show you how to: * Import the tissue annotation available from Ariadne into the database; * Add your own tissue classification to the ResNet Tissue classification; * Annotate proteins with the Tissue Property;

*  Open [455 Kb ]

Updating Your Database with New Protein-Protein Interactions

This tutorial shows how to add new protein-protein interactions (relations) to the PathwayStudio database without requiring programming skills from a user. The first part of the tutorial shows how to manually add new relation using the options provided by the Create/Edit Relation dialog box. The second and third parts show how to import interaction data from an MS Excel spreadsheet.

*  Open [493 Kb ]

Estimating Statistical Significance of a Pathway Subnetwork

Once you build your pathway, how do you know that it is statistically significant, i.e., what is the probability of your pathway to appear as a random subgraph from the ResNet network? The answer of this question is provided in this tutorial. To implement the proposed method, you need to know: a) the number of proteins in your cluster of interest and in the entire network; b) The number of links within the cluster; c) The connectivity of each protein in your cluster

*  Open [113 Kb ]