CORECLUST: identification of the conserved CRM grammar together with prediction of gene regulation.
CORECLUST: identification of the conserved CRM grammar together with prediction of gene regulation.
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DOI：
10.1093/nar/gks235
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发表时间：
2012-07
影响因子：
14.9
通讯作者：
Mironov AA
中科院分区：
文献类型：
--
作者：
Nikulova AA;Favorov AV;Sutormin RA;Makeev VJ;Mironov AA
转录调控区的识别和追踪其内部组织对于理解真核细胞机制是重要的。高等真核生物的顺式调节模块（CRMs）被认为具有调节“语法”或结合位点的优选排列，这对于适当的调节是至关重要的，因此倾向于进化保守。在这里，我们提出了一种方法CORECLUST（COnservative Regulatory CLUSTER STRUCTURE），预测标准物质的基础上的一组位置权重矩阵。CORECLUST通过揭示描述结合位点相对位置的保守规则，构建了一个CRM模型。因此，所构建的模型可以用于类似的标准物质的全基因组预测，从而检测共调节基因，并用于调查的系统的监管语法。与相关方法相比，CORECLUST在鉴定脊椎动物肌肉特异性基因表达的标准物质和果蝇早期发育的标准物质方面表现出更好的性能。
Identification of transcriptional regulatory regions and tracing their internal organization are important for understanding the eukaryotic cell machinery. Cis-regulatory modules (CRMs) of higher eukaryotes are believed to possess a regulatory ‘grammar’, or preferred arrangement of binding sites, that is crucial for proper regulation and thus tends to be evolutionarily conserved. Here, we present a method CORECLUST (COnservative REgulatory CLUster STructure) that predicts CRMs based on a set of positional weight matrices. Given regulatory regions of orthologous and/or co-regulated genes, CORECLUST constructs a CRM model by revealing the conserved rules that describe the relative location of binding sites. The constructed model may be consequently used for the genome-wide prediction of similar CRMs, and thus detection of co-regulated genes, and for the investigation of the regulatory grammar of the system. Compared with related methods, CORECLUST shows better performance at identification of CRMs conferring muscle-specific gene expression in vertebrates and early-developmental CRMs in Drosophila.
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影响因子：
3
作者：
Fariselli P;Martelli PL;Casadio R
通讯作者：
Casadio R
影响因子：
9.8
作者：
Li XY;MacArthur S;Bourgon R;Nix D;Pollard DA;Iyer VN;Hechmer A;Simirenko L;Stapleton M;Luengo Hendriks CL;Chu HC;Ogawa N;Inwood W;Sementchenko V;Beaton A;Weiszmann R;Celniker SE;Knowles DW;Gingeras T;Speed TP;Eisen MB;Biggin MD
通讯作者：
Biggin MD
影响因子：
64.5
作者：
Hallikas, O;Palin, K;Taipale, J
通讯作者：
Taipale, J
影响因子：
2.5
作者：
Levy, S;Hannenhalli, S
通讯作者：
Hannenhalli, S
影响因子：
5.8
作者：
Johansson, Oe.;Alkema, W.;Lagergren, J.
通讯作者：
Lagergren, J.