QAing UCSC Genes
hgGene page source information (see the link below):
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 |
NCBI BLASTP Bit Score |
knownBlastTab.bitScore |
|
BLASTP |
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 |
