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Transcription factor footprinting and binding site prediction. Pique-Regi RP, Degner JF, Pai AA, Gaffney DG, Gilad Y, Pritchard JK. "Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data", Genome Research. 2011 Mar;21(3):447-55. [ Full. The CENTIPEDE R-package can be downloaded from R-forge (binary package only available for the latest R version):. Some very basic instructions to get started are [ here. Transcription factor map for lymphoblastoid cell-lines.

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CENTIPEDE @ Pritchard Lab | centipede.uchicago.edu Reviews

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Transcription factor footprinting and binding site prediction. Pique-Regi RP, Degner JF, Pai AA, Gaffney DG, Gilad Y, Pritchard JK. Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data, Genome Research. 2011 Mar;21(3):447-55. [ Full. The CENTIPEDE R-package can be downloaded from R-forge (binary package only available for the latest R version):. Some very basic instructions to get started are [ here. Transcription factor map for lymphoblastoid cell-lines.

<META> KEYWORDS

1 centipede

2 overview

3 pubmed

4 r package

5 library centipede

6 example fitcentipede

7 browse results here

8 acknowledgements

9 greg crawford

10 from the pritchard

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CENTIPEDE @ Pritchard Lab | centipede.uchicago.edu Reviews

https://centipede.uchicago.edu

Transcription factor footprinting and binding site prediction. Pique-Regi RP, Degner JF, Pai AA, Gaffney DG, Gilad Y, Pritchard JK. "Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data", Genome Research. 2011 Mar;21(3):447-55. [ Full. The CENTIPEDE R-package can be downloaded from R-forge (binary package only available for the latest R version):. Some very basic instructions to get started are [ here. Transcription factor map for lymphoblastoid cell-lines.

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R output

http://centipede.uchicago.edu/ALL_NON_OVERLAPPING_FOOTPRINTS/Clustered_all_reformat.html

M00658 = PU.1. MA0057 = MZF1 5-13. M00981 = CREB,. MA0022 = dl 1. MA0023 = Dl 2. M00762 = PPAR,. M00966 = VDR,. Generated on: Sun Jun 20 22:33:32 2010.

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Summary 15 ENCODE cell-lines

http://centipede.uchicago.edu/SimpleMulti

Summary across 15 ENCODE cell-lines. The transcription factor binding site predictions presented here are obtained from data generated by the ENCODE project. In particular we use DNase-seq data obtained in 15 cell-lines by Greg Crawford at Duke University (see details and data release policy at the bottom). We generated maps for each of the following cell-lines:. See it on UCSC browser. See it on UCSC browser. See it on UCSC browser. See it on UCSC browser. See it on UCSC browser. See it on UCSC browser.

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R output

http://centipede.uchicago.edu/ALL_NON_OVERLAPPING_FOOTPRINTS/Clustered_reformat.html

CLUSTER 23 - CTCF. CLUSTER 25 - (ETS-box). CLUSTER 28 - (CRE-box). M00981 = CREB,. CLUSTER 30 - (AP1). M00658 = PU.1. CLUSTER 32 - NFKB1. MA0022 = dl 1. MA0023 = Dl 2. CLUSTER 34 - Interferon stimulus response element (ISRE). CLUSTER 35 - YY1. MA0057 = MZF1 5-13. CLUSTER 39 - (E-box). CLUSTER 43 - NFYA:NFYB (CCAAT-box). CLUSTER 44 - SRF. CLUSTER 45 - SP1 (GC-box). CLUSTER 46 - OCT1. CLUSTER 48 - NRSF. CLUSTER 49 - EBF1. CLUSTER 50 - ZNF143. CLUSTER 57 - E4F1. M00762 = PPAR,. M00966 = VDR,.

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Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data

http://genome.cshlp.org/content/21/3/447

Skip to main page content. Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data. Jacob F. Degner. Athma A. Pai. Daniel J. Gaffney. Jonathan K. Pritchard. Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA;. Committee on Genetics, Genomics and Systems Biology, University of Chicago, Chicago, Illinois 60637, USA;. Howard Hughes Medical Institute, University of Chicago, Chicago, Illinois 60637, USA. July 7, 2010. November 1, 2010.

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http://r-forge.r-project.org/projects/centipede

Search the entire project. CENTIPEDE: Project Home R-Forge. CENTIPEDE is a probabilistic framework that integrates tissue-specific experimental data such as histone modifications and DNaseI cleavage patterns with genomic information such as gene annotation and evolutionary. No tag defined for this project. GNU General Public License (GPL). View list of RSS feeds. Available for this project. View the 2 Member(s).

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Transcription factor footprinting and binding site prediction. Pique-Regi RP, Degner JF, Pai AA, Gaffney DG, Gilad Y, Pritchard JK. "Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data", Genome Research. 2011 Mar;21(3):447-55. [ Full. The CENTIPEDE R-package can be downloaded from R-forge (binary package only available for the latest R version):. Some very basic instructions to get started are [ here. Transcription factor map for lymphoblastoid cell-lines.

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