QAing UCSC Genes

hgGene Page Source Information:

File:Hg19uc002ypa.2.pdf

Click on the image to see an example of the hgGene page annotated with the sources of the different components. The sources annotated in this image are our best deductions.

Gene Sorter Column Sources:

Name	Description	Source
#	Item Number in Displayed List/Select Gene	n/a
Name	Gene Name/Select Gene	kgXref.geneSymbol
UCSC ID	UCSC Transcript ID	knownGene.name
UniProtKB	UniProtKB Protein Display ID	kgXref.spDisplayID or kgXref.spID_organism
UniProtKB Acc	UniProtKB Protein Accession	kgXref.spID
RefSeq	NCBI RefSeq Gene Accession	kgXref.refseq
Entrez Gene	NCBI Entrez Gene/LocusLink ID	knownToLocusLink
GenBank	GenBank mRNA Accession	kgXref.refseq or kgXref.mRNA
Ensembl	Ensembl Transcript ID	knownToEnsembl
GNF Atlas 2 ID	ID of Associated GNF Atlas 2 Expression Data	knownToGnfAtlas2
Gene Category	High Level Gene Category - Coding, Antisense, etc.	kgTxInfo.category
CDS Score	Coding potential score from txCdsPredict	kgTxInfo.cdsScore
VisiGene	UCSC VisiGene In Situ Image Browser	knownToVisiGene
Allen Brain	Allen Brain Atlas In Situ Images of Adult Mouse Brains	knownToAllenBrain & allenBrainUrl
U133 ID	ID of Associated Affymetrix U133 Expression Data	knownToU133
GNF Atlas 2	GNF Expression Atlas 2 Data from U133A and GNF1H Chips	gnfAtlas2
Max GNF Atlas 2	Maximum Expression Value of GNF Expression Atlas 2	calculated?
GNF Atlas 2 Delta	Normalized Difference in GNF Expression Atlas 2 from Selected Gene	gnfAtlas2Distance
BLASTP Bits	NCBI BLASTP Bit Score	knownBlastTab.bitScore
BLASTP E-Value	NCBI BLASTP E-Value	knownBlastTab.evalue
%ID	NCBI BLASTP Percent Identity	knownBlastTab.identity
5' UTR Fold	5' UTR Fold Energy (Estimated kcal/mol)	foldUtr5.energy
3' UTR Fold	3' UTR Fold Energy (Estimated kcal/mol)	foldUtr3.energy
Exon Count	Number of Exons (Including Non-Coding)	knownGene.exonCount
Intron Size	Size of biggest (or optionally smallest) intron	knownGene  exonStarts - exonEnds
Genome Position	Genome Position/Link to Genome Browser	(knownGene.txStart + txEnd)/2
Mouse	Mouse Ortholog (Best Blastp Hit to UCSC Known Genes)	mmBlastTab
Rat	Rat Ortholog (Best Blastp Hit to UCSC Known Genes)	rnBlastTab
Zebrafish	Danio rerio Ortholog (Best Blastp Hit to Ensembl)	drBlastTab
Drosophila	D. melanogaster Ortholog (Best Blastp Hit to FlyBase Proteins)	dmBlastTab
C. elegans	C. elegans Ortholog (Best Blastp Hit to WormPep)	ceBlastTab
Yeast	Saccharomyces cerevisiae Ortholog (Best Blastp Hit to RefSeq)	scBlastTab
Pfam Domains	Protein Family Domain Structure	knownToPfam à pfamDesc
Superfamily	Protein Superfamily Assignments	ucscScop & scopDesc
PDB	Protein Data Bank	kgProtMap2 & sp###### database
Gene Ontology	Gene Ontology (GO) Terms Associated with Gene	kgProtMap2 & sp###### database
M. Vidal P2P	Human Protein-Protein Interaction Network from Marc Vidal	humanVidalP2P
E. Wanker P2P	Human Protein-Protein Interaction Network from Erich Wanker	humanWankerP2P
HPRD P2P	Human Protein-Protein Interaction Network from the Human Reference Protein Database	humanHprdP2P
Description	Short Description Line/Link to Details Page	kgXref.description

Table Descriptions

Attempt to describe the uses of the tables used in or related to UCSC Genes.

UCSC Gene and GS Table Descriptions

• allenBrainGene - "Human Cortex Gene Expression" link in Seq&Links to Tls&Dbs
• allenBrainUrl - w/ knownToAllenBrain creats GS column, "Allen Brain"
• bioCycMapDesc - BioCyc description name in Biochem & Signaling...
• bioCycPathway - BioCyc pathway name in Biochem & Signaling...
• ccdsKgMap - determines the CCDS in the "Other names for this Gene" section
• ceBlastTab - other species C. elegans
• cgapAlias - links cgapID with kgXref.geneSymbol to pull info for gene.
• cgapBiocDesc - BioCarta description in Biochem & Signaling Pathways
• cgapBiocPathway - BioCarta pathway name in Biochem & Signaling Pathways
• dmBlastTab - other species D. melanogaster - leave as open issue for now
• drBlastTab - other species zebrafish
• foldUtr3 - mRNA Secondary Structure....section
• foldUtr5 - mRNA Secondary Structure....section
• gnfAtlas2 - own track, QA'd with that track, GS, micrary exp data sxn
• gnfAtlas2Distance - GS sort by "Expression (GNF Atlas2)" & GS clmn "GNF Atlas 2 Delta"
• humanHprdP2P - Gene Sorter column "HPRD P2P" & "sort by"
• humanVidalP2P - Gene Sorter column "M. Vidal Protein-to-Protein" & GS sort by
• humanWankerP2P - Gene Sorter column "E. Wanker Protein-to-Protein" & "sort by"
• keggMapDesc - KEGG pathway description in Biochem & Signaling Pathways
• keggPathway - KEGG pathway name in Biochem & Signaling Pathways
• kg4ToKg5 - allows searching of an old ID from previous gene set in new gene set or users can check the kg3ToKg4 table directly to find corresponding gene IDs.
• kgAlias - pops "Alternate Gene Symbols" in Other Names... section
• kgColor - colors the gene in browser
• kgProtAlias - intermediate table?
• kgProtMap2 - Scop Domains in Protein Domain & Structure Info & Protein Data Bank in GS needs this to work, also involved with proteome browser (not releasing with proteome browser with hg19; being phased out)
• kgSpAlias - duplicate of kgAlias w/ extra field, spID, that is blank in all records
• kgTxInfo - provides "Gene Model Information"
• kgXref - provides the "other names for the gene"
• knownAlt - separate track "Alt Events"; see tracks/altEvents/hg19/methods
• knownBlastTab - Gene Sorter (GS "ID%"=identity, GS "BLASTP E-Value"=eValue, GS "BLASTP Bits"=bitScore)
• knownCanonical - best transcript from each clusterId - don't display splice variants
• knownGene - primary table
• knownGeneMrna - "mRNA" link in Seq & lnks to Tools &Db section
• knownGenePep - "protein" link in Seq & lnks to Tools & Db section
• knownIsoforms - groups transcripts into clusterId
• knownToAllenBrain - w/ allenBrainUrl creates GS "Allen Brain" column/link
• knownToCdsSnp - Not pushing; Coding SNP column in gene sorter
• knownToEnsembl - used in link to Ensembl
• knownToGnf1h - dropped & didn't see changes on hgGene or Gene Sorter, gnfAtlas1?
• knownToGnfAtlas2 - "Microarray..." sxn & Microarray link, GS "GNF Atlas 2 ID"
• knownToHprd - creates the "HPRD" link in the Seq&lnks to Tls&Dbs section
• knownToLocusLink - used in link to Entrez Gene, see issues below
• knownToPfam - gives Pfam Domains section of Prot Dom & Stre info & GS
• knownToRefSeq - used in link to RefSeq (Other Names)
• knownToSuper - contains scop domain info with gene name & start/end
• knownToTreefam - used for link to Treefam website in Seq&lnks to Tls&Dbs
• knownToU133 - Gene Sorter column "U133 ID"
• knownToVisiGene - used in link to VisiGene
• mmBlastTab - other species mouse
• pfamDesc - gives Pfam description in pfam domains section (step in GS)
• rnBlastTab - other species rat
• scBlastTab - other species S. cerevisiae
• scopDesc - prints acc and description in "SCOP Domains" of Prot Dmn * Strtr Info
• spMrna - intermediate table? Doesn't seem to directly affect hgGene or GS
• ucscScop - from ucscID gets scop domainName

Tables Related to UCSC Genes are Separate tracks

• affyU133
• allenBrainAli
• exoniphy - created by Adam Siepel of Cornell for each assembly (2nd choice is to lift from previous assembly)
• gnfAtlas2
• nibbImageProbes
• omimGene
• omimGeneMap
• omimMorbidMap
• omimToKnownCanonical
• vgAllProbes

No longer UCSC Genes Tables

• knownToCdsSnp - dropping on all assemblies. Found too many issues; Populated Cds Snp column in Gene Sorter.
• knownToGnf1h - part of GNF Atlas 1, which is not on hg19

Proteome Browser Tables (no longer releasing)

• pbAnomLimit
• pbResAvgStd
• pepCCntDist
• pepExonCntDist
• pepHydroDist
• pepIPCntDist
• pepMolWtDist
• pepPi
• pepPiDist
• pepResDist
• pepMwAa