UCSC Genes tables: Difference between revisions

From Genecats
Jump to navigationJump to search
(→‎proteome database: adding note about RGD Genes)
 
(10 intermediate revisions by 4 users not shown)
Line 2: Line 2:


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.
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.
==wiki pages about known genes==
[[QAing UCSC Genes]]<br>
[[UCSC Genes tables]]<br>
[[UCSC Genes Staging Process]]<br>
[[Post-Release-Checklist]]


== Assembly databases ==
== Assembly databases ==
;hg38 (released May 2014)
:bioCycMapDesc
:bioCycPathway
:ceBlastTab
:cgapAlias
:cgapBiocDesc
:cgapBiocPathway
:dmBlastTab
:drBlastTab
:foldUtr3
:foldUtr5
:humanHprdP2P
:humanVidalP2P
:humanWankerP2P
:keggMapDesc
:keggPathway
:kg7ToKg8
:kgAlias
:kgColor
:kgProtAlias
:kgProtMap2
:kgSpAlias
:kgTargetAli
:kgTxInfo
:kgXref
:knownAlt
:knownBlastTab
:knownCanonical
:knownGene
:knownGeneMrna
:knownGenePep
:knownGeneTxMrna
:knownGeneTxPep
:knownIsoforms
:knownToHprd
:knownToKeggEntrez
:knownToLocusLink
:knownToLynx
:knownToNextProt
:knownToPfam
:knownToRefSeq
:knownToSuper
:knownToVisiGene
:knownToWikipedia
:mmBlastTab
:pfamDesc
:rnBlastTab
:scBlastTab
:scopDesc
:spMrna
:ucscGenePfam
:ucscScop
;mm10 (released March 2014)
:bioCycMapDesc
:bioCycPathway
:ccdsKgMap
:ceBlastTab
:cgapAlias
:cgapBiocDesc
:cgapBiocPathway
:dmBlastTab
:drBlastTab
:foldUtr3
:foldUtr5
:hgBlastTab
:keggMapDesc
:keggPathway
:kg6ToKg7
:kgAlias
:kgColor
:kgProtAlias
:kgProtMap2
:kgSpAlias
:kgTargetAli
:kgTxInfo
:kgXref
:knownAlt
:knownBlastTab
:knownCanonical
:knownGene
:knownGeneMrna
:knownGeneOld6
:knownGenePep
:knownGeneTxMrna
:knownGeneTxPep
:knownIsoforms
:knownToEnsembl
:knownToKeggEntrez
:knownToLocusLink
:knownToPfam
:knownToRefSeq
:knownToSuper
:knownToVisiGene
:pfamDesc
:rnBlastTab
:scBlastTab
:scopDesc
:spMrna
:ucscScop
;hg19 (released June 2013)
:bioCycMapDesc
:bioCycPathway
:ccdsKgMap
:ceBlastTab
:cgapAlias
:cgapBiocDesc
:cgapBiocPathway
:dmBlastTab
:drBlastTab
:foldUtr3
:foldUtr5
:gnfAtlas2Distance
:gnfU95Distance
:humanHprdP2P
:humanVidalP2P
:humanWankerP2P
:keggMapDesc
:keggPathway
:kg6ToKg7
:kgAlias
:kgColor
:kgProtAlias
:kgProtMap2
:kgSpAlias
:kgTargetAli
:kgTxInfo
:kgXref
:knownAlt
:knownBlastTab
:knownCanonical
:knownGene
:knownGeneMrna
:knownGenePep
:knownGeneTxMrna
:knownGeneTxPep
:knownIsoforms
:knownToAllenBrain
:knownToEnsembl
:knownToGnfAtlas2
:knownToHInv
:knownToHprd
:knownToKeggEntrez
:knownToLocusLink
:knownToPfam
:knownToRefSeq
:knownToSuper
:knownToU133
:knownToU133Plus2
:knownToU95
:knownToVisiGene
:mmBlastTab
:pfamDesc
:rnBlastTab
:scBlastTab
:scopDesc
:spMrna
:ucscScop
;mm10 (released November 2012)
:bioCycPathway
:ceBlastTab
:cgapAlias
:cgapBiocDesc
:cgapBiocPathway
:dmBlastTab
:drBlastTab
:foldUtr3
:foldUtr5
:hgBlastTab
:keggMapDesc
:keggPathway
:kgAlias
:kgColor
:kgProtAlias
:kgProtMap2
:kgSpAlias
:kgTargetAli
:kgTxInfo
:kgXref
:knownAlt
:knownBlastTab
:knownCanonical
:knownGene
:knownGeneMrna
:knownGenePep
:knownGeneTxMrna
:knownGeneTxPep
:knownIsoforms
:knownToEnsembl
:knownToKeggEntrez
:knownToLocusLink
:knownToPfam
:knownToRefSeq
:knownToSuper
:knownToVisiGene
:pfamDesc
:rnBlastTab
:scBlastTab
:scopDesc
:spMrna
:ucscScop


;hg19 (released January 2012)
;hg19 (released January 2012)
Line 109: Line 325:


== proteome database ==
== proteome database ==
;proteins120806 (released November 2012)
:hgnc                     
:hgncXref                 
:history                 
:interProXref             
:pdbSP                   
:pfamDesc                 
:pfamXref                 
:spDisease               
:spOldNew                 
:spReactomeEvent         
:spReactomeId             
:spSecondaryID           
:spVariant               
:spXref3                 
:swInterPro               
:tableDescriptions       
:uniProtAlias


;proteins111004 (released January 2012)
;proteins111004 (released January 2012)
Line 145: Line 381:
:uniProtAlias
:uniProtAlias


;note: RGD Genes used a proteome database already on the public site so no proteome database was pushed.
;note RGD Genes used a proteome database already on the public site so no proteome database was pushed.


== uniProt database ==
== uniProt database ==
Line 188: Line 424:
:varAcc
:varAcc
:varProtein
: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==
== blastTab tables going to the new gene set==
Line 201: Line 439:
:ce6
:ce6
:sacCer3
:sacCer3
For the February 2012 rat RGD Genes release, the table:
:rnBlastTab
was pushed in each of these databases:
:hg19
:mm9
:dm3
:ce6
:sacCer3


There is much more information on [[BlastTabs]] available.
There is much more information on [[BlastTabs]] available.

Latest revision as of 18:40, 14 May 2014


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.

wiki pages about known genes

QAing UCSC Genes
UCSC Genes tables
UCSC Genes Staging Process
Post-Release-Checklist


Assembly databases

hg38 (released May 2014)
bioCycMapDesc
bioCycPathway
ceBlastTab
cgapAlias
cgapBiocDesc
cgapBiocPathway
dmBlastTab
drBlastTab
foldUtr3
foldUtr5
humanHprdP2P
humanVidalP2P
humanWankerP2P
keggMapDesc
keggPathway
kg7ToKg8
kgAlias
kgColor
kgProtAlias
kgProtMap2
kgSpAlias
kgTargetAli
kgTxInfo
kgXref
knownAlt
knownBlastTab
knownCanonical
knownGene
knownGeneMrna
knownGenePep
knownGeneTxMrna
knownGeneTxPep
knownIsoforms
knownToHprd
knownToKeggEntrez
knownToLocusLink
knownToLynx
knownToNextProt
knownToPfam
knownToRefSeq
knownToSuper
knownToVisiGene
knownToWikipedia
mmBlastTab
pfamDesc
rnBlastTab
scBlastTab
scopDesc
spMrna
ucscGenePfam
ucscScop
mm10 (released March 2014)
bioCycMapDesc
bioCycPathway
ccdsKgMap
ceBlastTab
cgapAlias
cgapBiocDesc
cgapBiocPathway
dmBlastTab
drBlastTab
foldUtr3
foldUtr5
hgBlastTab
keggMapDesc
keggPathway
kg6ToKg7
kgAlias
kgColor
kgProtAlias
kgProtMap2
kgSpAlias
kgTargetAli
kgTxInfo
kgXref
knownAlt
knownBlastTab
knownCanonical
knownGene
knownGeneMrna
knownGeneOld6
knownGenePep
knownGeneTxMrna
knownGeneTxPep
knownIsoforms
knownToEnsembl
knownToKeggEntrez
knownToLocusLink
knownToPfam
knownToRefSeq
knownToSuper
knownToVisiGene
pfamDesc
rnBlastTab
scBlastTab
scopDesc
spMrna
ucscScop
hg19 (released June 2013)
bioCycMapDesc
bioCycPathway
ccdsKgMap
ceBlastTab
cgapAlias
cgapBiocDesc
cgapBiocPathway
dmBlastTab
drBlastTab
foldUtr3
foldUtr5
gnfAtlas2Distance
gnfU95Distance
humanHprdP2P
humanVidalP2P
humanWankerP2P
keggMapDesc
keggPathway
kg6ToKg7
kgAlias
kgColor
kgProtAlias
kgProtMap2
kgSpAlias
kgTargetAli
kgTxInfo
kgXref
knownAlt
knownBlastTab
knownCanonical
knownGene
knownGeneMrna
knownGenePep
knownGeneTxMrna
knownGeneTxPep
knownIsoforms
knownToAllenBrain
knownToEnsembl
knownToGnfAtlas2
knownToHInv
knownToHprd
knownToKeggEntrez
knownToLocusLink
knownToPfam
knownToRefSeq
knownToSuper
knownToU133
knownToU133Plus2
knownToU95
knownToVisiGene
mmBlastTab
pfamDesc
rnBlastTab
scBlastTab
scopDesc
spMrna
ucscScop
mm10 (released November 2012)
bioCycPathway
ceBlastTab
cgapAlias
cgapBiocDesc
cgapBiocPathway
dmBlastTab
drBlastTab
foldUtr3
foldUtr5
hgBlastTab
keggMapDesc
keggPathway
kgAlias
kgColor
kgProtAlias
kgProtMap2
kgSpAlias
kgTargetAli
kgTxInfo
kgXref
knownAlt
knownBlastTab
knownCanonical
knownGene
knownGeneMrna
knownGenePep
knownGeneTxMrna
knownGeneTxPep
knownIsoforms
knownToEnsembl
knownToKeggEntrez
knownToLocusLink
knownToPfam
knownToRefSeq
knownToSuper
knownToVisiGene
pfamDesc
rnBlastTab
scBlastTab
scopDesc
spMrna
ucscScop
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

proteins120806 (released November 2012)
hgnc
hgncXref
history
interProXref
pdbSP
pfamDesc
pfamXref
spDisease
spOldNew
spReactomeEvent
spReactomeId
spSecondaryID
spVariant
spXref3
swInterPro
tableDescriptions
uniProtAlias
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

For the February 2012 rat RGD Genes release, the table:

rnBlastTab

was pushed in each of these databases:

hg19
mm9
dm3
ce6
sacCer3


There is much more information on BlastTabs available.