Comp-Bio for beginners

Tools

• Convert between various gene symbols and IDs - biomart

  • Bioconductor http://www.bioconductor.org/

  • Find homologs: biomart. Simple instructions here

Major databases

• Brain transcriptome, microarrays and RNA-seq in brainspan:

• Transcriptome databases - NCBI GEO

• /cortex/data/microarrays, /cortex/data/RNAseq/

• Pathways: KEGG

  • Transcription Factor databases:

  • AnimalTFDB

  • Jolma et al, Cell 2013

  • Encode

  • Protein domains: PFAM,

  • Protein data bank: PDB

  • Pheotypes:

    • Human genes and associated phenotypes: OMIM

    • Genetic Association Database: GAD

Super-standard methods (that you have to know)

• Functional analysis:

  • GO Enrichment (matlab) (GOrilla)

  • GSEA

  • Network analysis: WGCNA - Weighted Gene Co-Expression Network

See also

• Brain transcriptome