UCSC Genes tables: Difference between revisions
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;note RGD Genes used a uniProt database already on the public site so no uniProt database was pushed. | |||
== blastTab tables going to the new gene set== | == blastTab tables going to the new gene set== | ||
Revision as of 17:54, 22 February 2012
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
- note RGD Genes used a uniProt database already on the public site so no uniProt database was pushed.
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.
