4a137c940e730eeddf1fd887dd56c101ba0bb2f8 katrina Tue Aug 24 15:10:21 2010 -0700 added Donna's regulation track announcement, minimized the most recentannouncement and removed the oldest announcement diff --git src/hg/htdocs/indexNews.html src/hg/htdocs/indexNews.html index e75b0a2..b2e86ef 100644 --- src/hg/htdocs/indexNews.html +++ src/hg/htdocs/indexNews.html @@ -1,89 +1,97 @@
  News

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- 18 August 2010 - Cat Genome Browser Available + 20 August 2010 - +New ENCODE Integrated Regulation Super-track Released +

+ We are pleased to announce the release of the ENCODE Integrated + Regulation super-track, a collection of regulatory tracks containing + state-of-the-art information about the mechanisms that turn genes on and + off at the transcription level. Individual tracks within the set show + enrichment of histone modifications suggestive of enhancer and promoter + activity, DNAse clusters indicating open chromatin, regions of + transcription factor binding, and transcription levels. When viewed in + combination, the complementary nature of the data within these tracks + has the potential to greatly facilitate our understanding of regulatory + DNA.

- We have released a Genome Browser for the latest assembly of Cat (Felis catus). - The GTB V17E assembly (December 2008, UCSC version felCat4) was produced by the NHGRI - Genome Technology Branch and NIH Intramural Sequencing Center, Maryland; Agencourt - Bioscience Corporation, Massachusetts; NCI Laboratory of Genomic Diversity, Maryland; - and Hill's Pet Nutrition, Inc, Kansas. The mitochondrial genome was sequenced by NCI - Laboratory of Genomic Diversity. For detailed sequencing and assembly information, see - the NCBI Felis catus - assembly page. -

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- Downloads of the Cat data and annotations may be obtained from the - UCSC FTP site - or - Downloads - page. These data have been freely provided for use in the UCSC Genome Browser - with specific conditions for use. -

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- Many thanks to NHGRI, Agencourt Bioscience Corporation, NCI and Hill's Pet Nutrition - for providing these data. The felCat4 annotation tracks were generated by UCSC and - its collaborators. We'd also like to acknowledge the UCSC Cat browser team: Chin Li, - Antonio Coelho, Mary Goldman and Donna Karolchik. See the - Credits - page for a detailed list of the organizations and individuals who contributed to - this release. -

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+ The data comprising these tracks were generated from hundreds of + experiments on multiple cell lines conducted by labs participating in + the Encyclopedia of DNA Elements (ENCODE) project, and were submitted to + the UCSC ENCODE Data Coordination Center for display on the Genome + Browser. +

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+ Faced with the problem of how to display such a large amount of data + in a manner facilitating analysis, UCSC has developed new visualization + methods that cluster and overlay the data, and then display the + resulting tracks on a single screen. Each of the cell lines in a track + is associated with a particular color. Light, saturated colors are used + to produce the best transparent overlay. +

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+ ENCODE Regulatory track screenshot
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+ The data in the ENCODE Regulation super-track, as with all data from the + production phase of the ENCODE project, have genome-wide coverage. In + general, Genome Browser tracks that show ENCODE-generated data can be + identified by the double-helix icon preceding the name in the track + list. Currently, the ENCODE Regulation data are available only on the + March 2006 (NCBI Build 36, UCSC version hg18) assembly of the human + genome. +

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+ For a detailed description of the datasets contained in this super-track + and a discussion of how the tracks can be used synergistically to + examine regions of regulatory functionality within the genome, see the + track description page.

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- 23 July 2010 - BigBed/BigWig Paper Published: - We are pleased to announce that we have published a paper on the BigBed and BigWig - format. Read more. -

- Kent WJ, Zweig AS, Barber G, Hinrichs AS, Karolchik D. - BigWig and BigBed: enabling browsing of large distributed data sets. - Bioinformatics. 2010 July 17. Published online in advance of print. -
- + 18 August 2010 - +Cat Genome Browser Available: + We have released a Genome Browser for the latest assembly of Cat (Felis catus). + Read more.

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- 15 July 2010 - Conservation - track available for zebrafish (danRer6): - We are pleased to announce the release of a new Conservation track based - on the zebrafish (danRer6) assembly. - Read more. + 23 July 2010 - BigBed/BigWig Paper Published: + We are pleased to announce that we have published a paper on + the BigBed and BigWig format. + Read more. + Kent WJ et al. BigWig and BigBed: enabling browsing of + large distributed data sets. Bioinformatics. + 2010 July 17. Published online in advance of print.