metagene Profiles Analyses Reveal Regulatory Element's Factor-Specific Recruitment Patterns.
ChIP-Sequencing (ChIP-Seq) provides a vast amount of information regarding the localization of proteins across the genome. The aggregation of ChIP-Seq enrichment signal in a metagene plot is an approach commonly used to summarize data complexity and to obtain a high level visual representation of th...
| Main Authors: | , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2016-08-01
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| Series: | PLoS Computational Biology |
| Online Access: | http://europepmc.org/articles/PMC4990179?pdf=render |
| _version_ | 1818543564792004608 |
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| author | Charles Joly Beauparlant Fabien C Lamaze Astrid Deschênes Rawane Samb Audrey Lemaçon Pascal Belleau Steve Bilodeau Arnaud Droit |
| author_facet | Charles Joly Beauparlant Fabien C Lamaze Astrid Deschênes Rawane Samb Audrey Lemaçon Pascal Belleau Steve Bilodeau Arnaud Droit |
| author_sort | Charles Joly Beauparlant |
| collection | DOAJ |
| description | ChIP-Sequencing (ChIP-Seq) provides a vast amount of information regarding the localization of proteins across the genome. The aggregation of ChIP-Seq enrichment signal in a metagene plot is an approach commonly used to summarize data complexity and to obtain a high level visual representation of the general occupancy pattern of a protein. Here we present the R package metagene, the graphical interface Imetagene and the companion package similaRpeak. Together, they provide a framework to integrate, summarize and compare the ChIP-Seq enrichment signal from complex experimental designs. Those packages identify and quantify similarities or dissimilarities in patterns between large numbers of ChIP-Seq profiles. We used metagene to investigate the differential occupancy of regulatory factors at noncoding regulatory regions (promoters and enhancers) in relation to transcriptional activity in GM12878 B-lymphocytes. The relationships between occupancy patterns and transcriptional activity suggest two different mechanisms of action for transcriptional control: i) a "gradient effect" where the regulatory factor occupancy levels follow transcription and ii) a "threshold effect" where the regulatory factor occupancy levels max out prior to reaching maximal transcription. metagene, Imetagene and similaRpeak are implemented in R under the Artistic license 2.0 and are available on Bioconductor. |
| first_indexed | 2024-12-11T22:37:03Z |
| format | Article |
| id | doaj.art-858dc1055f5c4b449ee71839ffe336d3 |
| institution | Directory Open Access Journal |
| issn | 1553-734X 1553-7358 |
| language | English |
| last_indexed | 2024-12-11T22:37:03Z |
| publishDate | 2016-08-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Computational Biology |
| spelling | doaj.art-858dc1055f5c4b449ee71839ffe336d32022-12-22T00:47:55ZengPublic Library of Science (PLoS)PLoS Computational Biology1553-734X1553-73582016-08-01128e100475110.1371/journal.pcbi.1004751metagene Profiles Analyses Reveal Regulatory Element's Factor-Specific Recruitment Patterns.Charles Joly BeauparlantFabien C LamazeAstrid DeschênesRawane SambAudrey LemaçonPascal BelleauSteve BilodeauArnaud DroitChIP-Sequencing (ChIP-Seq) provides a vast amount of information regarding the localization of proteins across the genome. The aggregation of ChIP-Seq enrichment signal in a metagene plot is an approach commonly used to summarize data complexity and to obtain a high level visual representation of the general occupancy pattern of a protein. Here we present the R package metagene, the graphical interface Imetagene and the companion package similaRpeak. Together, they provide a framework to integrate, summarize and compare the ChIP-Seq enrichment signal from complex experimental designs. Those packages identify and quantify similarities or dissimilarities in patterns between large numbers of ChIP-Seq profiles. We used metagene to investigate the differential occupancy of regulatory factors at noncoding regulatory regions (promoters and enhancers) in relation to transcriptional activity in GM12878 B-lymphocytes. The relationships between occupancy patterns and transcriptional activity suggest two different mechanisms of action for transcriptional control: i) a "gradient effect" where the regulatory factor occupancy levels follow transcription and ii) a "threshold effect" where the regulatory factor occupancy levels max out prior to reaching maximal transcription. metagene, Imetagene and similaRpeak are implemented in R under the Artistic license 2.0 and are available on Bioconductor.http://europepmc.org/articles/PMC4990179?pdf=render |
| spellingShingle | Charles Joly Beauparlant Fabien C Lamaze Astrid Deschênes Rawane Samb Audrey Lemaçon Pascal Belleau Steve Bilodeau Arnaud Droit metagene Profiles Analyses Reveal Regulatory Element's Factor-Specific Recruitment Patterns. PLoS Computational Biology |
| title | metagene Profiles Analyses Reveal Regulatory Element's Factor-Specific Recruitment Patterns. |
| title_full | metagene Profiles Analyses Reveal Regulatory Element's Factor-Specific Recruitment Patterns. |
| title_fullStr | metagene Profiles Analyses Reveal Regulatory Element's Factor-Specific Recruitment Patterns. |
| title_full_unstemmed | metagene Profiles Analyses Reveal Regulatory Element's Factor-Specific Recruitment Patterns. |
| title_short | metagene Profiles Analyses Reveal Regulatory Element's Factor-Specific Recruitment Patterns. |
| title_sort | metagene profiles analyses reveal regulatory element s factor specific recruitment patterns |
| url | http://europepmc.org/articles/PMC4990179?pdf=render |
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