QAing UCSC Genes

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hgGene page source information (see the link below):

File:Hg19uc002ypa.2.pdf

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

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