This is a selected set of tools (there are many others that perform similar kinds of analysis or have similar types of data).

Repositories and tools for large-scale analysis of gene-expression data

• Gene Expression Omnibus (a huge repository of large-scale gene-expression experiments)
• Mouse Gene Expression Database
• Gemma (co-expression analysis to identify genes with similar expression profiles)

Protein interaction databases

• BioGRID database of physical and genetic interactions
• IntAct

Gene and protein network tools

• STRING database
• Gene Mania tool

Cancer gene-expression and disease-associated mutations

• Cosmic database of somatic mutations in cancer
• HGMD database
• OMIM database
• The Cancer Genome Atlas (TCGA)
• The Cancer Dependency Map (large-scale knock-out screens)

Tools for performing gene-set enrichment analysis

• GOrilla tool for Gene Ontology enrichment and visualization
• Gene set enrichment using Enrichr

Gene Ontology and other useful sources of information

• Gene Ontology
• GeneCards
• Other biological databases

Additional software for this tutorial

• Download and install the Scaffold Software (for spectral count analysis)
• Download and install X!Tandem (to run the GPM search engine from the command line)
• Download and unzip this human SwissProt fasta sequence file
• Parameters, input and output are all specified in xml files when running X!Tandem from the command line