#acl All:read DanieleMerico:write,delete,revert
= Neurological Gene-sets =
== Neurological Phenotypes and Brain-specific Expression Gene-sets ==
'''Last update: May 2011'''<
>
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'''<
>
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
* __Notes on use__
* 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
== R ws Object Structure ==
* 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
== Additional Resources ==
* [[|MGI link]] to download mouse genes by phenotype
* [[|DiseaseHub]] is a resource compiling gene-phenotype associations from different sources: last update: 2009