Bioinformatics 101: Pathway Analysis

Gene List Enrichment Tools (Requires Differenital Expression Analysis):

• Gene Ontology (GO) Enrichment Tools
• FuncAssociate
• PANTHER
• ErmineJ
• Pathway-Express
• GoMiner
• General Gene List Enrichment Tools
• Enrichr - can provide gene symbols, with or without weights
• WebGestalt
• Generalized tool covering many different functional databases
• DAVID
• functional enrichment tool provided by the NIH
• provides GO, KEGG, etc. enrichment analysis
• T-profiler
• only valid for analyzing yeast gene lists
• ConceptGen
• Other GO Enrichment Tools
• FIDEA - provides functional enrichment for GO, KEGG, and Interpro for human, mouse, fly, zebrafish, and yeast
• IPA (Ingenuity Pathway Analysis)
• commercial program curating information about genes, metabolites, etc.

Other Systems-Level Analysis Tools (No Upstream Filtering Necessary):

• Gene Set Enrichment Analysis (GSEA)
• very popular tool from the Broad Institute that analyzes data from MSigDB
• Reactome enrichment analysis - Reactome is an open-source pathway database
• ErmineJ
• PAGE
• LRpath
• GSVA

Bioinformatics 101: Protein Analysis

Protein Domain / Structure / Homology Tools:

• Pfam
• HMMER - specific tool that can be used to search for homology (using a database like Pfam)
• In practice, I would typically just use the web interface for Pfam
• SAM (Sequence Alignment and Modeling System) - tool for UCSC for remote homology detection and protein structure prediction
• Protein Data Bank (PDB) - database of 3D structures for proteins
• ExPASy - suite of many useful tools for protein analysis
• ScanProsite - search for similar proteins within Prosite
• Tools to predict protein secondary structure

3D-Structure Viewers:

• RasMol (free)
• Swiss-Pdb Viewer (free)
• Cn3D
• free tool from NCBI
• Other tools for NCBI for 3D Macromolecular Structures
• PyMOL
• initially an open-source program, it is now a commercially available program licensed by Schrodinger
• there is an educational-use-only demo version that can be downloaded for free (but only
• Maestro
• Part of the commercially available Schrodinger Suite
• can be linked to PyMOL, th
• ereby providing more advanced analysis options

Mass Spectrometry:

• PRIDE - mass-spectrometry sample database managed by EMBL-EBI
• PRIDE User Manual
• PeptideAtlas - database for mass spectrometry data - includes links to relevant publications
• MaxQuant - popular tool for mapping proteomics spectra from mass spectrometry data
• ProteinProphet - another popular tool for mapping proteomics spectra to proteins
• DanteR - R implementation of the popular DAnTE algorithm for differential expression of mass spectrometry proteomics data
• LabKey / CPAS - open-source LIMS + basic analysis pipeline
• PIR - UniProt Protein Information Resource: includes links to databases and peptide mapping tools

Protein-Protein Interaction Databases:

• IntAct - database for protein-protein interactions
• BioGRID - database of genetic and protein interactions
• MINT - protein-protein interaction database
• STRING - database for known and predicted protein-protein interactions
• HIPPIE: database of human protein-protein interactions, integrating data from several other databases

Other

• STITCH: database of drug-protein interactions
• PaxDb - database of protein expression across different tissues and organisms
• MOPED - database of protein expression across different tissues and model organisms

Bioinformatics 101

I thought it would be nice to provide a set of links for bioinformatics resources that I find to be useful.  A lot of this information comes from the experience that I gained working in the Bioinformatics Core at City of Hope.  Unlike my other blog posts, I will come back and modify these lists over time (since new bioinformatics resources are constantly being developed.

In order to help organize this huge amount of information, I have divided my annotations into the following sub-posts (all with the "Bioinformatics 101" label):

• Gene Expression Analysis
• Pathway Analysis
• DNA Sequence Analysis
• RNA Sequence Analysis
• Protein Analysis
• DNA Methylation Analysis
• Genomic Databases
• Short Read Aligners
• Image Analysis
• Literature / Text Mining
• General Coding Information
• Bioinformatics Journals

Also, feel free to leave your own suggestions as comments on the relevant pages!