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15 September 2008 - Request for Input on ENCODE Data Release Plan
The National Human Genome Research Institute (NHGRI)
has updated the data release plan for the
ENCODE and model organism ENCODE
(modENCODE) projects.
Because the plan is intended to take
into account the needs and responsibilities of the resource
users, NHGRI is soliciting feedback on the proposal from the
research community before the plan is finalized. To
facilitate this review, UCSC has made the
plan available to the community
here on our ENCODE website.
Please send comments directly to
Encode@mail.nih.gov
by Wednesday, October 15, 2008.
3 September 2008 - Updated UCSC Genes Set Released for hg18
We have released an updated UCSC Genes data set on the
latest human assembly (hg18, March 2006). The new annotation
can be found on the hg18 Genome Browser in the "Genes and
Gene Predictions" track group. The previous set of UCSC
Genes on the hg18 assembly has been renamed as Old UCSC
Genes in the same track group.
The UCSC Genes track shows gene predictions based on data
from RefSeq, Genbank, CCDS and UniProt. This is a moderately
conservative set of predictions, requiring the support of
one GenBank RNA sequence plus at least one additional line
of evidence. The RefSeq RNAs are an exception to this,
requiring no additional evidence. The track includes both
protein-coding and putative non-coding transcripts. Some of
these non-coding transcripts may actually code for protein,
but the evidence for the associated protein is weak.
Compared to RefSeq, this gene set has generally about 10%
more protein-coding genes, approximately five times as many putative non-coding genes, and about twice as many splice
variants.
The latest version of UCSC Genes explicitly incorporates
CCDS proteins in addition to the evidence included in
previous versions, as well as additional data from GenBank,
RefSeq, and UniProt. Although we have made every effort to
preserve UCSC Gene IDs across versions, some gene IDs have
changed in the new data set. In general, the ID number has
been incremented if the new version of a gene is larger
than the previous version, and a completely new ID has been
assigned in those instances where a splice site changed or
the protein-coding region shrank. However, searching on an
old discontinued ID from the previous gene set will take you
to the corresponding gene in the updated track.
Alternatively, you can check the kg3ToKg4 table directly to
find corresponding gene IDs.
The UCSC Genes set was produced by Jim Kent. Thanks to Ann
Zweig for heading up the testing of the new data set, and
to the entire Genome Browser QA team for coordinating its
release on our public site.
27 August 2008 - Zebra Finch Genome Browser Released:
We've added the Jul. 2008 release of the zebra finch genome
(Taeniopygia guttata) to our collection of
vertebrate genome browsers.
Read more.
22 July 2008 - Updated C. elegans Browser Released:
Culminating our recent updates of the nematode browsers on
our site, we've released a Genome Browser for the latest
C. elegans assembly based on sequence version WS190
deposited into WormBase in May 2008.
Read more.
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