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The UCSC Genome Browser database: 2015 update.

Rosenbloom KR, Armstrong J, Barber GP, Casper J, Clawson H, Diekhans M, Dreszer TR, Fujita PA, Guruvadoo L, Haeussler M, Harte RA, Heitner S, Hickey G, Hinrichs AS, Hubley R, Karolchik D, Learned K, Lee BT, Li CH, Miga KH, Nguyen N, Paten B, Raney BJ, Smit AF, Speir ML, Zweig AS, Haussler D, Kuhn RM, Kent WJ - Nucleic Acids Res. (2014)

Bottom Line: Highlights of the past year include the release of a browser for the first new human genome reference assembly in 4 years in December 2013 (GRCh38, UCSC hg38), a watershed comparative genomics annotation (100-species multiple alignment and conservation) and a novel distribution mechanism for the browser (GBiB: Genome Browser in a Box).We created browsers for new species (Chinese hamster, elephant shark, minke whale), 'mined the web' for DNA sequences and expanded the browser display with stacked color graphs and region highlighting.As our user community increasingly adopts the UCSC track hub and assembly hub representations for sharing large-scale genomic annotation data sets and genome sequencing projects, our menu of public data hubs has tripled.

View Article: PubMed Central - PubMed

Affiliation: Center for Biomolecular Science and Engineering, CBSE, UC Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA kate@soe.ucsc.edu.

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Genome Browser screenshot of the transcription start site of the ZFX gene illustrating the new stacked color graph display. The enrichment of histone marks H3K4me1, H3K4me3 and H3K27ac is shown in three browser tracks, where contribution to the sum of the signal by each of the six different cell types is indicated by color. Note that the K3K4me1 signal is low in all cell types across the promoter and at the beginning of the transcript, but high on either side of the promoter. The other two marks show the opposite tendency, being highest at the promoter and declining with distance from the promoter. In general the signals are strongest in the turquoise cell line (HUVEC).
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Figure 1: Genome Browser screenshot of the transcription start site of the ZFX gene illustrating the new stacked color graph display. The enrichment of histone marks H3K4me1, H3K4me3 and H3K27ac is shown in three browser tracks, where contribution to the sum of the signal by each of the six different cell types is indicated by color. Note that the K3K4me1 signal is low in all cell types across the promoter and at the beginning of the transcript, but high on either side of the promoter. The other two marks show the opposite tendency, being highest at the promoter and declining with distance from the promoter. In general the signals are strongest in the turquoise cell line (HUVEC).

Mentions: A new track configuration option is now available for multi-wiggle (graph) tracks to complement the colored overlay display. Figure 1 shows examples of multiple annotations that are colored and presented vertically in an additive fashion in a single track.


The UCSC Genome Browser database: 2015 update.

Rosenbloom KR, Armstrong J, Barber GP, Casper J, Clawson H, Diekhans M, Dreszer TR, Fujita PA, Guruvadoo L, Haeussler M, Harte RA, Heitner S, Hickey G, Hinrichs AS, Hubley R, Karolchik D, Learned K, Lee BT, Li CH, Miga KH, Nguyen N, Paten B, Raney BJ, Smit AF, Speir ML, Zweig AS, Haussler D, Kuhn RM, Kent WJ - Nucleic Acids Res. (2014)

Genome Browser screenshot of the transcription start site of the ZFX gene illustrating the new stacked color graph display. The enrichment of histone marks H3K4me1, H3K4me3 and H3K27ac is shown in three browser tracks, where contribution to the sum of the signal by each of the six different cell types is indicated by color. Note that the K3K4me1 signal is low in all cell types across the promoter and at the beginning of the transcript, but high on either side of the promoter. The other two marks show the opposite tendency, being highest at the promoter and declining with distance from the promoter. In general the signals are strongest in the turquoise cell line (HUVEC).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4383971&req=5

Figure 1: Genome Browser screenshot of the transcription start site of the ZFX gene illustrating the new stacked color graph display. The enrichment of histone marks H3K4me1, H3K4me3 and H3K27ac is shown in three browser tracks, where contribution to the sum of the signal by each of the six different cell types is indicated by color. Note that the K3K4me1 signal is low in all cell types across the promoter and at the beginning of the transcript, but high on either side of the promoter. The other two marks show the opposite tendency, being highest at the promoter and declining with distance from the promoter. In general the signals are strongest in the turquoise cell line (HUVEC).
Mentions: A new track configuration option is now available for multi-wiggle (graph) tracks to complement the colored overlay display. Figure 1 shows examples of multiple annotations that are colored and presented vertically in an additive fashion in a single track.

Bottom Line: Highlights of the past year include the release of a browser for the first new human genome reference assembly in 4 years in December 2013 (GRCh38, UCSC hg38), a watershed comparative genomics annotation (100-species multiple alignment and conservation) and a novel distribution mechanism for the browser (GBiB: Genome Browser in a Box).We created browsers for new species (Chinese hamster, elephant shark, minke whale), 'mined the web' for DNA sequences and expanded the browser display with stacked color graphs and region highlighting.As our user community increasingly adopts the UCSC track hub and assembly hub representations for sharing large-scale genomic annotation data sets and genome sequencing projects, our menu of public data hubs has tripled.

View Article: PubMed Central - PubMed

Affiliation: Center for Biomolecular Science and Engineering, CBSE, UC Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA kate@soe.ucsc.edu.

Show MeSH
Related in: MedlinePlus