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The Eukaryotic Promoter Database: expansion of EPDnew and new promoter analysis tools.

Dreos R, Ambrosini G, Périer RC, Bucher P - Nucleic Acids Res. (2014)

Bottom Line: EPDnew is a collection of automatically compiled, organism-specific promoter lists complementing the old corpus of manually compiled promoter entries of EPD.This new part is exclusively derived from next generation sequencing data from high-throughput promoter mapping experiments.We report on the recent growth of EPDnew, its extension to additional model organisms and its improved integration with other bioinformatics resources developed by our group, in particular the Signal Search Analysis and ChIP-Seq web servers.

View Article: PubMed Central - PubMed

Affiliation: Swiss Institute of Bioinformatics (SIB), CH-1015 Lausanne, Switzerland.

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EPD analysis and selection tools. (a) TATA-box occurrence profile in human promoters. This picture has been obtained by following the OProf link from the human EPDnew home page and then selecting the TATA-box weight matrix from the ‘promoter motifs’ menu on the OPROF input form. (b) Distribution of H3K4me3-marked nucleosomes around human promoters. The figure is based on MNase-processed ChIP-Seq data from (19) stored in the MGA repository and accessible via a pull-down menu from the ChIP-Cor input form. (c) BED file containing genomic TSS coordinates of human promoters containing a match to the TATA-box weight matrix between positions −35 and −20 relative to the TSS. This list has been generated with the program FindM. (d) Genomic TSS coordinates of a promoter subset enriched in CAGE tags from lymphoblastoid cell line GM12878. This list was obtained by following the ‘ChIP-Cor’ link from the human EPDnew home page and then selecting the specific CAGE tag library as target feature via the pull-down menu on the input form. On the results page, the ‘Enriched Feature Extraction Option’ was used to select those promoters which contain at least 100 CAGE tags between positions −50 and +50 relative to the TSS given in EPDnew.
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Figure 1: EPD analysis and selection tools. (a) TATA-box occurrence profile in human promoters. This picture has been obtained by following the OProf link from the human EPDnew home page and then selecting the TATA-box weight matrix from the ‘promoter motifs’ menu on the OPROF input form. (b) Distribution of H3K4me3-marked nucleosomes around human promoters. The figure is based on MNase-processed ChIP-Seq data from (19) stored in the MGA repository and accessible via a pull-down menu from the ChIP-Cor input form. (c) BED file containing genomic TSS coordinates of human promoters containing a match to the TATA-box weight matrix between positions −35 and −20 relative to the TSS. This list has been generated with the program FindM. (d) Genomic TSS coordinates of a promoter subset enriched in CAGE tags from lymphoblastoid cell line GM12878. This list was obtained by following the ‘ChIP-Cor’ link from the human EPDnew home page and then selecting the specific CAGE tag library as target feature via the pull-down menu on the input form. On the results page, the ‘Enriched Feature Extraction Option’ was used to select those promoters which contain at least 100 CAGE tags between positions −50 and +50 relative to the TSS given in EPDnew.

Mentions: The web services directly linked to EPD perform two types of tasks: promoter analysis and subset selection. ChIP-Cor from the ChIP-Seq server is an analysis tool which generates aggregation plots (18) for two genomic features, called reference and target feature. (The generic term feature covers everything that can be mapped to a genome position, e.g. TSSs, mapped ChIP-Seq reads, etc.). The server returns a graph showing the positional distribution of the target features relative to the reference feature (see example in Figure 1b based on data from 19). The web-interface allows users to choose any sample from the MGA repository as a target or reference feature. Alternatively, features can be uploaded as a genome annotation format file in BED, GFF or BAM format. If ChIP-Cor is accessed directly from an organism-specific EPDnew home page, the corresponding promoter collection will automatically appear as the default reference feature in the ChIP-Cor input format.


The Eukaryotic Promoter Database: expansion of EPDnew and new promoter analysis tools.

Dreos R, Ambrosini G, Périer RC, Bucher P - Nucleic Acids Res. (2014)

EPD analysis and selection tools. (a) TATA-box occurrence profile in human promoters. This picture has been obtained by following the OProf link from the human EPDnew home page and then selecting the TATA-box weight matrix from the ‘promoter motifs’ menu on the OPROF input form. (b) Distribution of H3K4me3-marked nucleosomes around human promoters. The figure is based on MNase-processed ChIP-Seq data from (19) stored in the MGA repository and accessible via a pull-down menu from the ChIP-Cor input form. (c) BED file containing genomic TSS coordinates of human promoters containing a match to the TATA-box weight matrix between positions −35 and −20 relative to the TSS. This list has been generated with the program FindM. (d) Genomic TSS coordinates of a promoter subset enriched in CAGE tags from lymphoblastoid cell line GM12878. This list was obtained by following the ‘ChIP-Cor’ link from the human EPDnew home page and then selecting the specific CAGE tag library as target feature via the pull-down menu on the input form. On the results page, the ‘Enriched Feature Extraction Option’ was used to select those promoters which contain at least 100 CAGE tags between positions −50 and +50 relative to the TSS given in EPDnew.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4383928&req=5

Figure 1: EPD analysis and selection tools. (a) TATA-box occurrence profile in human promoters. This picture has been obtained by following the OProf link from the human EPDnew home page and then selecting the TATA-box weight matrix from the ‘promoter motifs’ menu on the OPROF input form. (b) Distribution of H3K4me3-marked nucleosomes around human promoters. The figure is based on MNase-processed ChIP-Seq data from (19) stored in the MGA repository and accessible via a pull-down menu from the ChIP-Cor input form. (c) BED file containing genomic TSS coordinates of human promoters containing a match to the TATA-box weight matrix between positions −35 and −20 relative to the TSS. This list has been generated with the program FindM. (d) Genomic TSS coordinates of a promoter subset enriched in CAGE tags from lymphoblastoid cell line GM12878. This list was obtained by following the ‘ChIP-Cor’ link from the human EPDnew home page and then selecting the specific CAGE tag library as target feature via the pull-down menu on the input form. On the results page, the ‘Enriched Feature Extraction Option’ was used to select those promoters which contain at least 100 CAGE tags between positions −50 and +50 relative to the TSS given in EPDnew.
Mentions: The web services directly linked to EPD perform two types of tasks: promoter analysis and subset selection. ChIP-Cor from the ChIP-Seq server is an analysis tool which generates aggregation plots (18) for two genomic features, called reference and target feature. (The generic term feature covers everything that can be mapped to a genome position, e.g. TSSs, mapped ChIP-Seq reads, etc.). The server returns a graph showing the positional distribution of the target features relative to the reference feature (see example in Figure 1b based on data from 19). The web-interface allows users to choose any sample from the MGA repository as a target or reference feature. Alternatively, features can be uploaded as a genome annotation format file in BED, GFF or BAM format. If ChIP-Cor is accessed directly from an organism-specific EPDnew home page, the corresponding promoter collection will automatically appear as the default reference feature in the ChIP-Cor input format.

Bottom Line: EPDnew is a collection of automatically compiled, organism-specific promoter lists complementing the old corpus of manually compiled promoter entries of EPD.This new part is exclusively derived from next generation sequencing data from high-throughput promoter mapping experiments.We report on the recent growth of EPDnew, its extension to additional model organisms and its improved integration with other bioinformatics resources developed by our group, in particular the Signal Search Analysis and ChIP-Seq web servers.

View Article: PubMed Central - PubMed

Affiliation: Swiss Institute of Bioinformatics (SIB), CH-1015 Lausanne, Switzerland.

Show MeSH
Related in: MedlinePlus