seqMINER: an integrated ChIP-seq data interpretation platform (2011)

by T Ye, A Krebs, A M Choukrallah, C Keime, F Plewniak, I Davidson, L Tora
Venue:Nucleic Acids Res
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Modification of a

by Chen Chen, Shihua Zhang, Xiang-sun Zhang , 2001
"... Discovery of cell-type specific regulatory elements in the human genome using differential chromatin ..."
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Discovery of cell-type specific regulatory elements in the human genome using differential chromatin
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VAP: a versatile aggregate profiler for efficient genome-wide data representation and discovery

by Charles Coulombe, Christian Poitras, Alexei Nordell-markovits , 2014
"... The analysis of genomic data such as ChIP-Seq usu-ally involves representing the signal intensity level over genes or other genetic features. This is often illustrated as a curve (representing the aggregate profile of a group of genes) or as a heatmap (rep-resenting individual genes). However, no sp ..."
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The analysis of genomic data such as ChIP-Seq usu-ally involves representing the signal intensity level over genes or other genetic features. This is often illustrated as a curve (representing the aggregate profile of a group of genes) or as a heatmap (rep-resenting individual genes). However, no specific re-source dedicated to easily generating such profiles is currently available. We therefore built the versa-tile aggregate profiler (VAP), designed to be used by experimental and computational biologists to gen-erate profiles of genomic datasets over groups of regions of interest, using either an absolute or a relative method. Graphical representation of the re-sults is automatically generated, and subgrouping can be performed easily, based on the orientation of the flanking annotations. The outputs include sta-tistical measures to facilitate comparisons between groups or datasets. We show that, through its intu-itive design and flexibility, VAP can help avoid mis-interpretations of genomics data. VAP is highly effi-cient and designed to run on laptop computers by us-ing a memory footprint control, but can also be easily compiled and run on servers. VAP is accessible at
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Genome-Wide Analysis of Alpharetroviral Integration in Human

by Hematopoietic Stem/progenitor Cells, Arianna Moiani, Julia Debora Suerth, Francesco G, Ermanno Rizzi, Marco Severgnini, Gianluca De Bellis, Axel Schambach, Fulvio Mavilio , 2014
"... genes ..."
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unknown title

by Olivier Alibert, Yad Ghavi-helm, Sylvie Jounier, Jean-christophe Aude, Janos Murvai, Mario Foglio, Marta Gut, Ivo Gut, Mark Lathrop, Julie Soutourina, Michel Werner , 2011
"... Genomic binding of Pol III transcription machinery and relationship with TFIIS transcription factor distribution in mouse embryonic stem cells ..."
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Genomic binding of Pol III transcription machinery and relationship with TFIIS transcription factor distribution in mouse embryonic stem cells
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unknown title

by Olivier Alibert, Yad Ghavi-helm, Sylvie Jounier, Jean-christophe Aude, Janos Murvai, Mario Foglio, Marta Gut, Ivo Gut, Mark Lathrop, Julie Soutourina, Michel Werner , 2011
"... Genomic binding of Pol III transcription machinery and relationship with TFIIS transcription factor distribution in mouse embryonic stem cells ..."
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Genomic binding of Pol III transcription machinery and relationship with TFIIS transcription factor distribution in mouse embryonic stem cells
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SEE PROFILE

by Sébastien Graziani, École Polytechnique, See Profile, Yad Ghavi-helm, Matthieu Gérard, Olivier Alibert, Yad Ghavi-helm, Janos Murvai, Mario Foglio, Marta Gut, Ivo Gut, Mark Lathrop, Julie Soutourina, Michel Werner , 2011
"... Genomic binding of Pol III transcription machinery and relationship with TFIIS transcription factor distribution in mouse embryonic stem cells ..."
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Genomic binding of Pol III transcription machinery and relationship with TFIIS transcription factor distribution in mouse embryonic stem cells
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unknown title

by Olivier Alibert, Yad Ghavi-helm, Sylvie Jounier, Jean-christophe Aude, Janos Murvai, Mario Foglio, Marta Gut, Ivo Gut, Mark Lathrop, Julie Soutourina, Michel Werner , 2011
"... Genomic binding of Pol III transcription machinery and relationship with TFIIS transcription factor distribution in mouse embryonic stem cells ..."
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Genomic binding of Pol III transcription machinery and relationship with TFIIS transcription factor distribution in mouse embryonic stem cells
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in

by Mohamed-amin Choukrallah, Dominique Kobi, Igor Martianov, Nikolai Mischerikow, Tao Ye, Albert J. R. Heck , 2011
"... Interconversion between active and inactive TATA-binding protein transcription complexes ..."
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Interconversion between active and inactive TATA-binding protein transcription complexes
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in

by Mohamed-amin Choukrallah, Dominique Kobi, Igor Martianov, Nikolai Mischerikow, Tao Ye, Albert J. R. Heck , 2011
"... Interconversion between active and inactive TATA-binding protein transcription complexes ..."
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Interconversion between active and inactive TATA-binding protein transcription complexes
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unknown title

by Mohamed-amin Choukrallah, Dominique Kobi, Igor Martianov, Nikolai Mischerikow, Tao Ye, Albert J. R. Heck, H. Th, Marc Timmers, Irwin Davidson , 2011
"... doi:10.1093/nar/gkr802 Interconversion between active and inactive TATA-binding protein transcription complexes in the mouse genome ..."
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doi:10.1093/nar/gkr802 Interconversion between active and inactive TATA-binding protein transcription complexes in the mouse genome
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