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Pathway and Network Analysis of Omics Data 2015

Workshop pages for students

Laptop Setup Instructions

Instructions for setting up your laptop can be found here: Laptop Setup Instructions

Pre-Workshop Tutorials

1) Cytoscape Preparation tutorials: Complete the introductory tutorial to Cytoscape: http://opentutorials.cgl.ucsf.edu/index.php/Portal:Cytoscape3

  • Introduction to Cytoscape3 - User Interface
  • Introduction to Cytoscape3 - Welcome Screen
  • Filtering and Editing in Cytoscape 3

Pre-Workshop Readings

Day 1

Welcome

*Faculty: Michelle Brazas*

Day 1

Module 1: Introduction to Pathway and Network Analysis

*Faculty: Gary Bader*

Lecture:

Pathways2015_Module1.pdf
Pathways2015_Module1.ppt
Pathways2015_Module1.mp4

Data Set:

module1YeastGenes.txt

Links:

* The Synergizer - identifier mapping
* Ensembl BioMart - (in menu bar, select the BioMart tab) eukaryotic gene query system
* ID Conversion Tool: gConvert  - identifier mapping
* Gene Ontology - gene annotation
* Cytoscape - network visualization and analysis

Module 2: Finding over-represented pathways in gene lists

*Faculty: Quaid Morris*

Lecture:

Pathways2015_Module2.pdf
Pathways2015_Module2.ppt
Pathways2015_Module2.mp4

Lab Practical: Gene-set enrichment analyses using GSEA and g:Profiler

*Faculty: Veronique Voisin*

Pathways2015_Module2_LabSlides.pdf
Pathways2015_Module2_LabExercise.pdf

Data Set:

Launching GSEA:

command line: java -Xmx2G -jar gsea2-2.2.0.jar

Additional Links:

* GSEA - help on format, installation, method,…
* g:Profiler
* DAVID - Enrichment Analysis for simple gene lists (jacknifed Fisher’s Exact Test)
* ConceptGen - Enrichment Analysis for simple gene lists (Fisher’s Exact Test)
* GSEA - Enrichment Analysis for ranked gene lists
* Other Enrichment Analysis tools for simple gene lists: Funspec, GoMiner
* List of 68 Enrichment Tools available as of 2008

Module 3: Cytoscape Intro, Demo and Enrichment Maps

*Faculty: Gary Bader*

Lecture:

Pathways_2015_Module3.pdf
Pathways_2015_Module3.ppt
Pathways_2015_Module3.mp4

Lab Practical: Creating an enrichment map from GSEA and g:Profiler results

* http://baderlab.org/Software/EnrichmentMap

* link to install the latest available version of enrichment map: http://baderlab.org/Software/EnrichmentMap#Development_Versions

* Exercise 1: generate an enrichment map using GSEA results. Follow this protocol:  http://baderlab.org/Software/EnrichmentMap/Tutorial#Step_2:_Generate_Enrichment_Map_with_GSEA_Output

* Exercise 2: generate an enrichment map using g:Profiler results. Follow this protocol:  http://baderlab.org/Software/EnrichmentMap/GProfilerTutorial#Step_2:_Generate_Enrichment_Map_with_g:Profiler_Output

Data Sets:

Result (back up files / cytoscape files):

* ES12_vs_NT12_GSEA_cyto3.cys

* gprofiler_results_12hours.cys

Lab Practical optional: Use your own data set.

Programs Used:

* Open Tutorials for Cytoscape

Useful plugins:
* VistaClara - makes it easy to visualize gene expression data on networks
* Agilent Literature Search - extracts interactions from PubMed abstracts
* clusterMaker - provides multiple ways to cluster gene expression and networks
* BiNGO - provides over-representation analysis using Gene Ontology in Cytoscape - you can select genes in your network or provide a list of genes and see the enrichment results visually mapped to the Gene Ontology
* commandTool, coreCommands - used to control Cytoscape by a series of commands. E.g. automate the process: open network, layout network, save network as PDF. These plugins require Cytoscape 2.7
* jActiveModules - requires gene expression data over multiple samples (>3). Finds regions of a network where genes are active (e.g. differentially expressed) across multiple samples.
* Many more at http://chianti.ucsd.edu/cyto_web/plugins/index.php

Integrated Assignment - Day 1

*Faculty: Veronique Voisin*

Pathways2015_part1_IntegratedAssignment.pdf
Pathways2015_part1_IntegratedAssignmentAnswers.pdf

Input Data sets:

Day 2

Module 4: Depth on Pathway and Network Analysis

*Faculty: Lincoln Stein*

Lecture:

Pathways2015_Module4.pdf
Pathways2015_Module4.ppt
Pathways2015_Module4.mp4

Lab Practical:

*Faculty: Robin Haw*

Pathways2015_Module4_LabSlides.pdf
Pathways2015_Module4_Lab.pdf
Pathways2015_Module4_LabAnswers.pdf

Data Sets:

Module 4 Data Set

Programs Used:

Reactome Website
Reactome User Guide
ReactomeFI User Guide

Papers:

Integrated genomic analyses of ovarian carcinoma

Clustering Algorithms: Newman Clustering and Hotnet

Reactome Website: NAR paper; Website guide

Nature Methods and Perspectives Paper

Supplementary Materials

Links:

Pathway and Interaction databases

Module 5: Gene Function Prediction

*Faculty: Quaid Morris*

Lecture:

Pathways2015_NYC_Module5.pdf
Pathways2015_NYC_Module5.ppt
Pathways2015_NYC_Module5.mp4

Lab Practical:

Pathways2015_Module5_LabSlides.pdf
Pathways2015_Module5_LabExercise.pdf

Data Sets for GeneMANIA exercises:

30_prostate_cancer_genes.txt
mixed_gene_list.txt
CYB11B_pearson_correlation_prostate.txt

Links:

Tools for gene function prediction systems (using functional associations)

* GeneMANIA (or beta version)
* STRING
* FunCoup – similar to STRING and GeneMANIA
* bioPIXIE – an early gene recommender system for yeast
* mouseNET – gene recommender for mouse
* FunctionalNet – composite functional networks for work, yeast, mouse and A thaliana
* FuncBase – a compiled database of gene functional predictions using supervised learning on Gene Ontology categories

Integrated Assignment - Day 2

*Faculty: Veronique Voisin*

Pathways2015_part2_IntegratedAssignment.pdf
Pathways2015_part2_IntegratedAssignmentAnswers.pdf

Input Data sets:

Day 3

Module 6: Gene Regulation Network Analysis

*Faculty: Michael Hoffman*

Lecture:

Pathways2015_Module6.pdf
Pathways2015_Module6.ppt
Pathways2015_Module6.mp4

Lab Practical:

Pathways2015_Module6_Lab.pdf
Pathways2015_Module6_Lab_Addenda.pdf

Precomputed results:

  • A549 c-Myc

The results provided during the workshop do not work outside the workshop. Archived results are in AppMEMECHIP_4.10.114306204728401779362043.tar.gz.

Links:

* ENCODE Project
* UCSC ENCODE file search
* Galaxy
* MEME Suite

View on GitHub