UCSC Genes tables
From Genecats
Revision as of 17:53, 22 February 2012 by Mary (talk | contribs) (→proteome database: adding note about RGD Genes)
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.
