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Construction of Gene Interaction Network with Computational Life

具有计算生命的基因相互作用网络的构建

基本信息

批准号：
13680445
负责人：
MATSUDA Hideo
金额：
$ 2.24万
依托单位：
Osaka University
依托单位国家：
日本
项目类别：
Grant-in-Aid for Scientific Research (C)
财政年份：
2001
资助国家：
日本
起止时间：
2001 至 2002
项目状态：
已结题

来源：
https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-13680445/
关键词：
Gene Exnression Analysis Gene Interactions Functional Annotation cDNA Microarray Gene Sequence Analysis Metabolic Pathway cDNA Genome Information Analysis

项目摘要

The following results were obtained by the construction of gene interaction network with computational life. For the model of gene interaction network, a method was developed for the functional annotation of genes. As the target of our research, the mouse full-length cDNA sequences, which were sequenced by RIKEN Genome Science Center, were clustered with their sequence similarity, the candidates for commonly conserved regions were explored, and 16 new motif candidates were obtained by removing the motifs found in known databases such as Inter Pro. Ten of the detected motif candidates were functionally annotated by various analyses, such as homology to the known gene sequences, the location of chromosomes, the predictions of protein secondary structure and transmembrane regions.Databases for expression profiles of the mouse genes at various developmental phases and tissues were developedfor the mouse cDNA microarray, which were developed at RIKEN Genome Science Center. A set of genes related to developmental phases, tissue specificity and metabolic pathway were elucidated by the clustering of gene expression profiles. Although many researchers have already done the functional predictions of a set of genes with microarray data, the elucidation of functional relationships of given genes and the gene finding with unknown functions became able to do using reliable annotations by the FANTOM consortium.

通过构建具有计算寿命的基因相互作用网络，得到了以下结果。针对基因互作网络模型，提出了一种基因功能注释方法。本研究以RIKEN基因组科学中心测序的小鼠全长cDNA序列为研究对象，对其序列相似性进行聚类分析，探索了共同保守区域的候选序列，并通过去除Inter Pro等已知数据库中的模体，获得了16个新的模体候选序列。通过与已知基因序列的同源性分析、染色体定位分析、蛋白质二级结构预测和跨膜区预测等方法，对其中10个候选基序进行了功能注释，并建立了小鼠基因在不同发育阶段和组织中表达谱数据库，用于RIKEN基因组科学中心开发的小鼠cDNA微阵列。通过对基因表达谱的聚类分析，揭示了一组与发育阶段、组织特异性和代谢途径相关的基因。尽管许多研究人员已经用微阵列数据对一组基因进行了功能预测，但FANTOM联盟使用可靠的注释来阐明给定基因的功能关系和发现具有未知功能的基因变得能够做到。