UCSC Genes tables

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Revision as of 17:53, 22 February 2012 by Mary (talk | contribs) (→‎proteome database: adding note about RGD Genes)
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These are the lists of tables that were pushed with the latest UCSC Genes tracks. Please keep this page up to date when a new UCSC Genes track is released! QAing_UCSC_Genes has descriptions of tables, lists of related tables and lists of tables that we no longer release.

Assembly databases

hg19 (released January 2012)
bioCycMapDesc
bioCycPathway
ccdsKgMap
ceBlastTab
cgapAlias
cgapBiocDesc
cgapBiocPathway
dmBlastTab
drBlastTab
foldUtr3
foldUtr5
gnfAtlas2Distance
gnfU95Distance
humanHprdP2P
humanVidalP2P
humanWankerP2P
keggMapDesc
keggPathway
kg5ToKg6
kgAlias
kgColor
kgProtAlias
kgProtMap2
kgSpAlias
kgTargetAli
kgTxInfo
kgXref
kgXrefOld5
knownAlt
knownBlastTab
knownCanonical
knownGene
knownGeneMrna
knownGeneOld5
knownGenePep
knownGeneTxMrna
knownGeneTxPep
knownIsoforms
knownToAllenBrain
knownToEnsembl
knownToGnfAtlas2
knownToHInv
knownToHprd
knownToKeggEntrez
knownToLocusLink
knownToPfam
knownToRefSeq
knownToSuper
knownToTreefam
knownToU133
knownToU133Plus2
knownToU95
knownToVisiGene
mmBlastTab
pfamDesc
rnBlastTab
scBlastTab
scopDesc
spMrna
ucscScop
rn4 (released February 2012) RGD Genes
affyExonTissuesGsMedianDistRgdGene2
affyExonTissuesGsMedianRgdGene2
affyExonTissuesGsRgdGene2
ceBlastTab
dmBlastTab
drBlastTab
rgdGene2Raw
gnfAtlas2RgdGene2Distance
hgBlastTab
keggMapDesc
keggPathway
mmBlastTab
rgdGene2
rgdGene2BlastTab
rgdGene2Canonical
rgdGene2Isoforms
rgdGene2KeggPathway
rgdGene2Pep
rgdGene2ToDescription
rgdGene2ToDisplayId
rgdGene2ToEnsembl
rgdGene2ToGenbank
rgdGene2ToGenbankAll
rgdGene2ToGnfAtlas2
rgdGene2ToKeggEntrez
rgdGene2ToLocusLink
rgdGene2ToPDB
rgdGene2ToPfam
rgdGene2ToRAE230
rgdGene2ToRefSeq
rgdGene2ToSymbol
rgdGene2ToU34A
rgdGene2ToUniProt
rgdGene2Xref
rgdGenePathway
rgdPathway
scBlastTab

proteome database

proteins111004 (released January 2012)
hgnc
hgncXref
history
interProXref
pbAnomLimit
pbResAvgStd
pbStamp
pdbSP
pepCCntDist
pepHydroDist
pepIPCntDist
pepMolWtDist
pepMwAa
pepPi
pepPiDist
pepResDist
pfamDesc
pfamXref
spDeleted
spDisease
spOldNew
spOrganism
spReactomeEvent
spReactomeId
spSecondaryID
spVariant
spXref2
spXref3
swInterPro
tableDescriptions
taxonNames
uniProtAlias
note
RGD Genes used a proteome database already on the public site so no proteome database was pushed.

uniProt database

sp111004 (released January 2012)
accToKeyword
accToTaxon
author
citation
citationRc
citationRp
comment
commentType
commentVal
commonName
description
displayId
extDb
extDbRef
feature
featureClass
featureId
featureType
gene
geneLogic
history
info
keyword
organelle
otherAcc
pathogenHost
protein
proteinEvidence
proteinEvidenceType
rcType
rcVal
reference
referenceAuthors
tableDescriptions
taxon
varAcc
varProtein

blastTab tables going to the new gene set

For the January 2012 human UCSC Genes release, the table:

hgBlastTab

was pushed in each of these databases:

mm9
rn4
dm3
ce6
sacCer3

There is much more information on BlastTabs available.