Expressing Scientific Insight

There are a great many bioinformatic tools and resources available online. Below are some of the more useful tools that I either currently use or have used in the past.

Ontologies

• Browse ontologies – Ontology Lookup Service (OLS)

Expression analysis resources

• GeneSpring GX (Agilent Technologies)
• Custom CDF (Brainarray)
• Ingenuity Pathways Analysis (Ingenuity Systems)
• DAVID Bioinformatics Resources 2008 (NIAID)
• BioGPS (GNF)
• UCSC Genome Bioinformatics
• WikiGenes
• GenePattern (Broad Institute)
• TM4 (Dana-Farber Cancer Institute)
• Gene Sifter (Geospiza)
• In silico Transcriptomics Online (GeneSapiens)
• Oncogenomics (NCI)

GeneSet Analysis

• ToppGene (Anil Jegga, Cincinnati Children’s Hospital)
• GATACA (Bruce Aronow, Cincinnati Children’s Hospital)
• WebGestalt (Bing Zhang, Vanderbuilt)

Next Generation Sequencing

• SEQanswers

Microarray repositories

• Gene Expression Omnibus (NCBI)
• Oncomine (Compendia Bioscience)
• Stanford Microarray Database
• Array Express (EMBL-EBI)

Biomarker resources

• Secreted Protein Database (Peking University)
• Infectious Disease Biomarker Database (IDBD) (Korea Institute of Health)

Biological Pathways

• Reactome
• KEGG

Protein interaction data bases

• Human Protein Reference Database (HPRD)
• IntAct (EMBL-EBI)
• BioGRID
• Human Interactome Map (HiMAP)
• mint

Network visualization

• Cytoscape
• OSPREY

Text mining

• Scrappy
• PolySearch

Other resources

• VENNY. An interactive tool for comparing lists with Venn Diagrams.
• Affymetrix NetAffx
• Match Miner (NCI)
• Transcriptional Regulatory Element Database (CSH)
• JASPAR (University of Copenhagen)
• Gene-Regulation dot com
• 1000 Genomes
• Cytokines & Cells Online Pathfinder Encyclopedia
• Gene Ontology Tools