Regulomics Tree with Putative Cis-elements Clusters upon Upstream Control Regions of Human Genome Subset
Date Issued
2005
Date
2005
Author(s)
Lien, Sheng-Kuei
DOI
en-US
Abstract
The regulation of gene expression is a challenging problem. In the post-genomic era, the analysis of cis-regulation is growing importance. We propose a construct methodology as of the regulomics tree (RegTree) by using a putative set of simplistic cis-elements and algorithms with regulation expression. The cis-elements are created by mining the gapped patterns of direct contacting nucleotides within a selected data set from the public database, EPD[15] and TRANSFAC[21].
The putative set of simplistic cis-elements has been used to construct the regulomics tree by indexing cis-elements in the upper stream control region of gene sequences and data clustering method. By using the hierarchical clustering algorithm, the output is a dendrogram that is desired in the regulomics tree. The regulomics tree reflects the similarity of regulation patterns among genes and is the reference model of dynamic simulation for RegNet. It can do help for microarray experiment to find the transcription factors. The application of regulomics tree is able to deduce that the overall program of the evolution from fertilized egg to individual body in the future.
Subjects
同側因子
對側因子
序列上游調控區
基因調控組系統樹
Cis-regulatory element
Transcriptional Factor
Upper Stream Control Region
Regulomics Tree
Type
thesis
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