[Genome] knownCanonical table

[Fan Hsu]

Hi Joseph,

First, the Known Genes are clustered based on if they have overlapping
exons.
Then, within a cluster, the gene with the highest number of coding bases is
chosen as the representative canonical gene.

The details can be found in the source code of hgClusterGenes.c under

	kent/src/hg/near/hgClusterGenes

Fan.
-----Original Message-----
From: genome-bounces at soe.ucsc.edu [mailto:genome-bounces at soe.ucsc.edu]On
Behalf Of Joseph Hegler
Sent: Friday, July 22, 2005 6:09 PM
To: genome at soe.ucsc.edu
Subject: [Genome] knownCanonical table


Hi. Could you explain the process by which a transcript is designated a
'canonical splice variant'? I have searched over the help documents and
cannot find the information. Thanks for your help.

Joe Hegler
UCSD
Chemistry and Biochemistry Department


Known Canonical

table knownCanonical
"Describes the canonical splice variant of a gene"
     (
     string chom;        "Chromosome"
     int chromStart;     "Start position (0 based). Corresponds to txStart"
     int chromEnd;       "End position (non-inclusive). Corresponds to
txEnd"
     int clusterId;      "Which cluster of transcripts this belongs to in
knownIsoforms"
     string transcript;  "Corresponds to knownGene name field"
     string protein;     "SwissProt ID of associated protein"
     )

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