Comparison of Gene Coexpression Profiles and Construction of Conserved Gene Networks to Find Functional Modules.
Comparison of Gene Coexpression Profiles and Construction of Conserved Gene Networks to Find Functional Modules.
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DOI：
10.1371/journal.pone.0132039
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发表时间：
2015
期刊：
影响因子：
3.7
通讯作者：
Kinoshita K
中科院分区：
文献类型：
--
作者：
Okamura Y;Obayashi T;Kinoshita K
基因注释的计算方法是一个巨大的挑战，现在许多基因组序列已经确定。每个基因都有自己的功能，但复杂的细胞功能是由一组基因实现的。因此，必须确定具有强功能关系的基因组。为此目的，基因表达模式和基因序列的相似性已被单独利用，尽管组合信息将提供更好的解决方案。我们提出了一种新的方法来寻找功能模块，通过比较物种之间的基因共表达谱。共表达模式表示为与每个指导基因共表达的基因的列表。我们比较了两个共表达列表，一个来自人类向导基因，另一个来自同源小鼠基因，并定义了一个度量来评估列表之间的相似性。基于这种共表达的相似性，我们发现了高度保守的基因，并构建了人与小鼠之间具有保守共表达的人类基因网络。一些紧密耦合的基因（模块）显示出明显的功能富集，如免疫系统和细胞周期，表明我们的方法可以在没有任何先验知识的情况下识别功能相关的基因。我们还发现了一些没有任何注释的功能模块，这可能是新功能模块的良好候选者。所有的比较都可以在http://v1.coxsimdb.info网络数据库中找到。
Computational approaches toward gene annotation are a formidable challenge, now that many genome sequences have been determined. Each gene has its own function, but complicated cellular functions are achieved by sets of genes. Therefore, sets of genes with strong functional relationships must be identified. For this purpose, the similarities of gene expression patterns and gene sequences have been separately utilized, although the combined information will provide a better solution. We propose a new method to find functional modules, by comparing gene coexpression profiles among species. A coexpression pattern is represented as a list of coexpressed genes with each guide gene. We compared two coexpression lists, one from a human guide gene and the other from a homologous mouse gene, and defined a measure to evaluate the similarity between the lists. Based on this coexpression similarity, we detected the highly conserved genes, and constructed human gene networks with conserved coexpression between human and mouse. Some of the tightly coupled genes (modules) showed clear functional enrichment, such as immune system and cell cycle, indicating that our method could identify functionally related genes without any prior knowledge. We also found a few functional modules without any annotations, which may be good candidates for novel functional modules. All of the comparisons are available at the http://v1.coxsimdb.info web database.
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影响因子：
14.9
作者：
Chatr-Aryamontri A;Breitkreutz BJ;Heinicke S;Boucher L;Winter A;Stark C;Nixon J;Ramage L;Kolas N;O'Donnell L;Reguly T;Breitkreutz A;Sellam A;Chen D;Chang C;Rust J;Livstone M;Oughtred R;Dolinski K;Tyers M
通讯作者：
Tyers M
影响因子：
7
作者：
Harrow J;Frankish A;Gonzalez JM;Tapanari E;Diekhans M;Kokocinski F;Aken BL;Barrell D;Zadissa A;Searle S;Barnes I;Bignell A;Boychenko V;Hunt T;Kay M;Mukherjee G;Rajan J;Despacio-Reyes G;Saunders G;Steward C;Harte R;Lin M;Howald C;Tanzer A;Derrien T;Chrast J;Walters N;Balasubramanian S;Pei B;Tress M;Rodriguez JM;Ezkurdia I;van Baren J;Brent M;Haussler D;Kellis M;Valencia A;Reymond A;Gerstein M;Guigó R;Hubbard TJ
通讯作者：
Hubbard TJ
影响因子：
14.9
作者：
NCBI Resource Coordinators
通讯作者：
NCBI Resource Coordinators
影响因子：
3.7
作者：
Chen, Yi-An;Tripathi, Lokesh P.;Mizuguchi, Kenji
通讯作者：
Mizuguchi, Kenji
影响因子：
64.8
作者：
Hartwell, LH;Hopfield, JJ;Murray, AW
通讯作者：
Murray, AW