c9cebe93b5e6f403757fa5d67566f828b2728bfc brianlee Fri Apr 18 15:58:41 2014 -0700 Adding news about Genome Segmentations and Switch to TF ChIP-seq track with new Motifs refs # 12259 diff --git src/hg/htdocs/indexNews.html src/hg/htdocs/indexNews.html index f32bddd..b59f10e 100755 --- src/hg/htdocs/indexNews.html +++ src/hg/htdocs/indexNews.html @@ -16,107 +16,116 @@


	To receive announcements of new genome assembly releases, new software features, updates and training seminars by email, subscribe to the genome-announce mailing list. + 18 April 2014 - + New Motif Displays for Transcription Factor ChIP-seq Track and New Genome Segmentations from ENCODE + + The browser's default displayed Transcription Factor ChIP-seq track is updating to the + latest data release, + which has been enhanced with the display of Factorbook motifs. Within a cluster, a green + highlight indicates the highest scoring site of a Factorbook-identified canonical motif for the + corresponding factor. Upon clicking a transcription factor's cluster with a motif, the details page + now displays the motif's sequence logo, alignment and underlying Positional Weight Matrix. Also, + the track configuration page now enables the filtering of factors. + + + The newly added + Genome Segmentations from ENCODE tracks display multivariate genome-segmentation performed on + six human cell types + (GM12878, K562, H1-hESC, HeLa-S3, HepG2, and HUVEC), integrating ChIP-seq data for + + eight chromatin marks, RNA Polymerase II, the CTCF transcription factor and input data. In total, + twenty-five states were used to segment the genome, and these states were then grouped and colored to + highlight predicted functional elements. These Genome Segmentations are the same data as + found in the + Analysis Working Group Hub, but are now hosted natively in the browser with enhanced + filtering capability where desired segmented states can be selected using the + 'Filter by Segment Type' control on the track configuration page. + + + + 15 April 2014 - New Minke Whale (balAcu1) Assembly Now Available in the Genome Browser A Genome Browser is now available for the minke whale (Balaenoptera acutorostrata scammoni) assembly released October 2013 by the Korea Ocean Research & Development Institute (KORDI version BalAcu1.0, UCSC version balAcu1). For more information and statistics about this assembly, see the NCBI assembly record for BalAcu1.0. There are 10,776 scaffolds with a total size of 2,431,687,698 bases. Bulk downloads of the sequence and annotation data may be obtained from the Genome Browser FTP server or the Downloads page. Please observe the conditions for use when accessing and using these data sets. The annotation tracks for this browser were generated by UCSC and collaborators worldwide. See the Credits page for a detailed list of the organizations and individuals who contributed to this release. - - - - 11 April 2014 - - New UCSC Genes Track Released for GRCm38/mm10 - - We're happy to announce the release of an updated UCSC Genes track for the GRCm38/mm10 - mouse Genome Browser. The new release has 61,642 total transcripts, compared with 59,121 - in the previous version. The total number of canonical genes has increased from 31,469 - to 32,408. Comparing the new gene set with the previous version: - - 54,714 transcripts did not change between versions. - 19 transcripts were not carried forward to the new version. - 3,866 transcripts are "compatible" with those in the previous set, meaning - that the two transcripts show consistent splicing. In most cases, the old and new - transcripts differ in the lengths of their UTRs. - 522 transcripts overlap with those in the previous set, but do not show consistent - splicing (i.e., they contain overlapping introns with differing splice sites). - - - - More details about the new UCSC Genes track can be found on the - UCSC Genes track - description page. - + + 11 April 2014 - New UCSC Genes Track Released for GRCm38/mm10 We're happy to announce the release of an updated UCSC Genes track for the GRCm38/mm10 mouse Genome Browser. Read more. - --> - + 06 March 2014 - The new GRCh38 Human Genome Browser is here! In the final days of 2013, the Genome Reference Consortium (GRC) released the eagerly awaited GRCh38 human genome assembly, the first major revision of the human genome in more than four years. Read more. - - 04 March 2014 - - Introducing Genome Browser highlight feature: - We are excited to announce a new highlight feature in the UCSC - Genome Browser. Using drag-and-select, you can now highlight a - region or gene of interest. - Read more. - -

To receive announcements of new genome assembly releases, new software features, updates and training seminars by email, subscribe to the genome-announce mailing list.

+ 18 April 2014 - + New Motif Displays for Transcription Factor ChIP-seq Track and New Genome Segmentations from ENCODE +

+ The browser's default displayed Transcription Factor ChIP-seq track is updating to the + latest data release, + which has been enhanced with the display of Factorbook motifs. Within a cluster, a green + highlight indicates the highest scoring site of a Factorbook-identified canonical motif for the + corresponding factor. Upon clicking a transcription factor's cluster with a motif, the details page + now displays the motif's sequence logo, alignment and underlying Positional Weight Matrix. Also, + the track configuration page now enables the filtering of factors. +

+ The newly added + Genome Segmentations from ENCODE tracks display multivariate genome-segmentation performed on + six human cell types + (GM12878, K562, H1-hESC, HeLa-S3, HepG2, and HUVEC), integrating ChIP-seq data for + + eight chromatin marks, RNA Polymerase II, the CTCF transcription factor and input data. In total, + twenty-five states were used to segment the genome, and these states were then grouped and colored to + highlight predicted functional elements. These Genome Segmentations are the same data as + found in the + Analysis Working Group Hub, but are now hosted natively in the browser with enhanced + filtering capability where desired segmented states can be selected using the + 'Filter by Segment Type' control on the track configuration page. +

+ +

15 April 2014 - New Minke Whale (balAcu1) Assembly Now Available in the Genome Browser

A Genome Browser is now available for the minke whale (Balaenoptera acutorostrata scammoni) assembly released October 2013 by the Korea Ocean Research & Development Institute (KORDI version BalAcu1.0, UCSC version balAcu1). For more information and statistics about this assembly, see the NCBI assembly record for BalAcu1.0. There are 10,776 scaffolds with a total size of 2,431,687,698 bases.

Bulk downloads of the sequence and annotation data may be obtained from the Genome Browser FTP server or the Downloads page. Please observe the conditions for use when accessing and using these data sets. The annotation tracks for this browser were generated by UCSC and collaborators worldwide. See the Credits page for a detailed list of the organizations and individuals who contributed to this release.

- -

- 11 April 2014 - - New UCSC Genes Track Released for GRCm38/mm10 -

- We're happy to announce the release of an updated UCSC Genes track for the GRCm38/mm10 - mouse Genome Browser. The new release has 61,642 total transcripts, compared with 59,121 - in the previous version. The total number of canonical genes has increased from 31,469 - to 32,408. Comparing the new gene set with the previous version: -

54,714 transcripts did not change between versions.
19 transcripts were not carried forward to the new version.
3,866 transcripts are "compatible" with those in the previous set, meaning - that the two transcripts show consistent splicing. In most cases, the old and new - transcripts differ in the lengths of their UTRs.
522 transcripts overlap with those in the previous set, but do not show consistent - splicing (i.e., they contain overlapping introns with differing splice sites).

- More details about the new UCSC Genes track can be found on the - UCSC Genes track - description page. -

+ +

11 April 2014 - New UCSC Genes Track Released for GRCm38/mm10

We're happy to announce the release of an updated UCSC Genes track for the GRCm38/mm10 mouse Genome Browser. Read more.

- --> - +

06 March 2014 - The new GRCh38 Human Genome Browser is here! In the final days of 2013, the Genome Reference Consortium (GRC) released the eagerly awaited GRCh38 human genome assembly, the first major revision of the human genome in more than four years. Read more.

- 04 March 2014 - - Introducing Genome Browser highlight feature: - We are excited to announce a new highlight feature in the UCSC - Genome Browser. Using drag-and-select, you can now highlight a - region or gene of interest. - Read more. -