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3楼2013-04-10 13:04:55
danshw
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已收录 1. Accession number: 20130415927769 Title: Analysis of transcriptional synergy between upstream regions and introns in genes of yeast Authors: Chen, Dan1, 2 ; Hu, Jun2, 3 Author affiliation: 1 School of Mathematics and Statistics, Yunnan University, Kunming 650091, China 2 Laboratory for Conservation and Utilization of Bio-resources, Yunnan University, Kunming, 650091, China 3 Science and Information Engineering, Yunnan Agricultural University, Kunming 650201, China Corresponding author: Chen, D. (zjcdhj@yahoo.cn) Source title: Journal of Convergence Information Technology Abbreviated source title: J. Convergence Inf. Technol. Volume: 8 Issue: 1 Issue date: January 15, 2013 Publication year: 2013 Language: English ISSN: 19759320 E-ISSN: 22339299 Document type: Journal article (JA) Publisher: Advanced Institute of Convergence Information Technology, Myoungbo Bldg 3F,, Bumin-dong 1-ga, Seo-gu, Busan, 602-816, Korea, Republic of Abstract: Computational analyses on transcription factor binding sites (TFBSs) and the combinatorial regulations of these sites mainly focus on the 5' upstream region of genes. However, experimental analyses have indicated that introns also contain some transcriptional regulatory information. Therefore, it is necessary to study combinatorial transcription regulation mechanisms between upstream regions and introns. In this article, we propose a new measure, similarity coefficient, for similarity between data objects. Similarity coefficient cluster based on the new measures on the yeast intron-containing genes suggests that genes in the same group are likely to be co-regulated. Hence we use the Z-score and W-score to predict overrepresented motifs in each group of gene promoters. By pairing these motifs each other, we obtain some potential transcriptional regulatory motif pairs between upstream regions and introns (termed 'UI' motif pairs) in the promoters of highly-transcribed genes (the majority of them are ribosomal protein genes). However, we fail to find 'UI' motif pairs in the promoters of lowly-transcribed genes. These results suggest the synergy between upstream regions and introns is an important form of combinatorial regulation. Number of references: 39 Main heading: Transcription Controlled terms: Genes - Transcription factors - Yeast Uncontrolled terms: Cluster-based - Computational analysis - Data objects - Experimental analysis - Gene promoter - Intron - Regulatory motifs - Ribosomal protein genes - Similarity coefficients - Transcription factor binding sites - Transcription regulations - Transcriptional frequency - Transcriptional synergy - Upstream region - Z-scores Classification code: 461 Bioengineering and Biology - 801.2 Biochemistry DOI: 10.4156/jcit.vol8.issue1.67 Database: Compendex Compilation and indexing terms, © 2013 Elsevier Inc. |
2楼2013-04-10 07:33:22
