Dataset Information

Decoding the genome with an integrative analysis tool: combinatorial CRM Decoder.

ABSTRACT: The identification of genome-wide cis-regulatory modules (CRMs) and characterization of their associated epigenetic features are fundamental steps toward the understanding of gene regulatory networks. Although integrative analysis of available genome-wide information can provide new biological insights, the lack of novel methodologies has become a major bottleneck. Here, we present a comprehensive analysis tool called combinatorial CRM decoder (CCD), which utilizes the publicly available information to identify and characterize genome-wide CRMs in a species of interest. CCD first defines a set of the epigenetic features which is significantly associated with a set of known CRMs as a code called 'trace code', and subsequently uses the trace code to pinpoint putative CRMs throughout the genome. Using 61 genome-wide data sets obtained from 17 independent mouse studies, CCD successfully catalogued ?12?600 CRMs (five distinct classes) including polycomb repressive complex 2 target sites as well as imprinting control regions. Interestingly, we discovered that ?4% of the identified CRMs belong to at least two different classes named 'multi-functional CRM', suggesting their functional importance for regulating spatiotemporal gene expression. From these examples, we show that CCD can be applied to any potential genome-wide datasets and therefore will shed light on unveiling genome-wide CRMs in various species.

SUBMITTER: Kang K

PROVIDER: S-EPMC3177223 | biostudies-literature | 2011 Sep

REPOSITORIES: biostudies-literature

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Decoding the genome with an integrative analysis tool: combinatorial CRM Decoder.

Kang Keunsoo K Kim Joomyeong J Chung Jae Hoon JH Lee Daeyoup D

Nucleic acids research 20110630 17

The identification of genome-wide cis-regulatory modules (CRMs) and characterization of their associated epigenetic features are fundamental steps toward the understanding of gene regulatory networks. Although integrative analysis of available genome-wide information can provide new biological insights, the lack of novel methodologies has become a major bottleneck. Here, we present a comprehensive analysis tool called combinatorial CRM decoder (CCD), which utilizes the publicly available informa ...[more]

PMID: 21724599

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Dataset Information

Decoding the genome with an integrative analysis tool: combinatorial CRM Decoder.

Publications

Decoding the genome with an integrative analysis tool: combinatorial CRM Decoder.

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