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| = Neurobiological Gene-sets = == Phenotypes and Expression Specificity == * [[attachment:Neuro_ExpHsBr.txt|ExpHsBr: Human Specific Brain Expression]] * [[attachment:Neuro_PhMmAll.txt|PhMmAll: Mouse Neurological Phenotype converted to Human]] * [[attachment:Neuro_PhHsPsy.txt|PhHsPsy: Human Neuropsychiatric]] * [[attachment:Neuro_PhHsDev.txt|PhHsDev: Human Neurodevelopmental and Intellectual Disability]] * [[attachment:Neuro_PhHsMsc.txt|PhHsMsc: Human Other Neurological]] |
= Neurological Gene-sets = == Neurological Phenotypes and Brain-specific Expression Gene-sets == '''Last update: May 2011'''<<BR>> Text files * [[attachment:Neuro_ExpHsBr.txt|ExpHsBr: Human Brain-specific Expression]] * [[attachment:Neuro_PhMmAll.txt|PhMmAll: Mouse Neurological Phenotypes converted to Human]] * [[attachment:Neuro_PhHsPsy.txt|PhHsPsy: Human Neuropsychiatric Disorders]] * [[attachment:Neuro_PhHsDev.txt|PhHsDev: Human Neurodevelopmental Disorders and Intellectual Disability]] * [[attachment:Neuro_PhHsMsc.txt|PhHsMsc: Human Other Neurological Disorders]] R Workspace * [[attachment:coreNeuroLists.RData|Neurological Phenotypes and Brain-specific Expression Gene-sets Rws]] |
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| * Documentation | * __Documentation__ |
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| * Notes on use | * __Notes on use__ |
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| * A sizable number of genes in''!PhMmAll'' may have neurological system development phenotypes at relatively early stages (e.g. neural tube formation) | |
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| * ''!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 | |
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== Gene Ontology Neurological Gene-sets == '''Last update: April 2011'''<<BR>> Text files * [[attachment:GO_neuro_dev.txt|Human Nervous System Development (GO:0007399)]] * [[attachment:GO_neuro_process.txt|Human Nervous System Process (without sensory receptors)]] * Cognition (GO:0050890), Neuronal action potential propagation (GO:0019227), Transmission of nerve impulse (GO:0019226) * [[attachment:GO_synapse.txt|Human Synapse (GO:0045202)]] R Workspace * [[attachment:coreNeuroGO.RData|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'''<<BR>> Text files * [[attachment:Pathways_neuro.txt|Neurological Pathways (collapsed)]] R Workspace * [[attachment:coreNeuroPathways.RData|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 * [[attachment:coreAllGs.RData|All gene-sets]] == Useful Links == === Genes and Phenotypes === * Mouse genes phenotypes from MGI * [[http://www.informatics.jax.org/searches/MP_form.shtml|Look up Mammalian Phenotype Ontology (MPO) Terms]] * [[ftp://ftp.informatics.jax.org/pub/reports/HMD_HumanPhenotype.rpt|Mouse Gene to Human Homologue Gene to Top MPO Terms]] * [[http://zldev.ccbr.utoronto.ca/~ddong/diseaseHub/|DiseaseHub]] * Resource compiling human gene-phenotype associations from different sources * Last update: 2009 === Gene Ontology Browser === * [[http://www.ebi.ac.uk/QuickGO/|QuickGO]] === Gene-set Enrichment Analysis === * [[http://conceptgen.ncibi.org/core/conceptGen/index.jsp|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 |
Neurological Gene-sets
Neurological Phenotypes and Brain-specific Expression Gene-sets
Last update: May 2011
Text files
R Workspace
Details
ID System: human Entrez-Gene
Documentation
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 Process (without sensory receptors)
Cognition (GO:0050890), Neuronal action potential propagation (GO:0019227), Transmission of nerve impulse (GO:0019226)
R Workspace
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
R Workspace
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
- $gs2gene: list
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
Useful Links
Genes and Phenotypes
- Mouse genes phenotypes from MGI
- Resource compiling human gene-phenotype associations from different sources
- Last update: 2009
Gene Ontology Browser
Gene-set Enrichment Analysis
- 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