• NeuroGenes_01

Neurological Gene-sets

Neurological Phenotypes and Brain-specific Expression Gene-sets

Last update: May 2011
Text files

• ExpHsBr: Human Brain-specific Expression

• PhMmAll: Mouse Neurological Phenotypes converted to Human

• PhHsPsy: Human Neuropsychiatric Disorders

• PhHsDev: Human Neurodevelopmental Disorders and Intellectual Disability

• PhHsMsc: Human Other Neurological Disorders

R Workspace

• Neurological Phenotypes and Brain-specific Expression Gene-sets Rws

Details

• ID System: human Entrez-Gene

• Documentation

  • PDF

  • pptx

• Notes on use

  • All gene-sets have good quality with respect to enrichment in neuropsychological functions and phenotypes

  • ExpHsBr and PhMmAll are the ones I found of higher quality when overlapping with my autism gene-set analysis results

    • A sizable number of genes inPhMmAll may have neurological system development phenotypes at relatively early stages (e.g. neural tube formation)

  • PhHsPsy probably includes several genes from candidate gene studies, but is otherwise of good quality

  • The distinction between PhHsPsy and PhHsDev is a bit loose, these two gene-sets could be collapsed

  • PhHsMsc is quite heterogeneous, and its neurovascular and neurodegenerative auto-immune components are probably source of bad candidates for researchers working on autism, schizophrenia or ADHD

  • PhMmAll is not completely unbiased, as investigators will make KO mouse models for genes of interest

  • ExpHsBr may be partially biased towards well characterized genes

Gene Ontology Neurological Gene-sets

Last update: April 2011
Text files

• Human Nervous System Development (GO:0007399)

• Human Nervous System Process (without sensory receptors)

  • Cognition (GO:0050890), Neuronal action potential propagation (GO:0019227), Transmission of nerve impulse (GO:0019226)

• Human Synapse (GO:0045202)

R Workspace

• Gene Ontology Neurological Gene-sets Rws

Details

• ID System: human Entrez-Gene

• Documentation

  • Manually selected Gene Ontology terms

• Notes on use

  • I removed sensory receptors (e.g. olfactory receptors) from Human Nervous System Process, otherwise they would be the majority of genes in this gene-set

  • Nervous System Process includes interesting stuff like Neuron differentiation and Axon guidance

  • These gene-sets depend on Gene Ontology annotations; genes that are poorly annotated are likely to be covered by neurological phenotypes or brain-specific expression gene-sets

Neurological Pathways as Gene-sets

Last update: March/April 2011
Text files

• Neurological Pathways (collapsed)

R Workspace

• Neurological Pathways Rws (by pathway)

Details

• ID System: human Entrez-Gene

• Documentation

  • Manually selected pathways (Reactome, KEGG, Biocarta, NCI)
• Breakdown by pathway only in the R ws

R ws Object Structure (common)

• each ws has only one object: a list with two slots:
  • $gs2gene: list
    • names: gene-set IDs
    • slot content: genes (character vector)
  • $gs2name: character vector
    • names: gene-set IDs
    • values: genes

All Pathways and Gene Ontology Gene-sets

Provided as a reference in case somebody wants to tease out additional gene-sets

• Gene Ontology
• Pathways: Reactome, KEGG, Biocarta, NCI
• PFAM (protein domains)

R Workspace

• All gene-sets

Useful Links

Genes and Phenotypes

• Mouse genes phenotypes from MGI

  • Look up Mammalian Phenotype Ontology (MPO) Terms

  • Mouse Gene to Human Homologue Gene to Top MPO Terms

• DiseaseHub

  • Resource compiling human gene-phenotype associations from different sources
  • Last update: 2009

Gene Ontology Browser

• QuickGO

Gene-set Enrichment Analysis

• ConceptGen

  • I usually use this tool to check if gene-sets make sense
  • I usually select these sources for the analysis
    • core: GO (BP, CC), Pathways (all)
    • extended: MeSH (particularly useful for disease associations)

    • usually crappy: gene expression, TransFac