#acl All:read DanieleMerico:write,delete,revert
= 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]]

'''Details'''
 * __ID System__: human Entrez-Gene
 * __Documentation__
   * [[attachment:Documentation_v01.pdf|PDF]]
   * [[attachment:Documentation_v01.pptx|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 in''!PhMmAll'' 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'''<<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