Comparative genomic analysis of transcription regulation elements involved in human map kinase G-protein coupling pathway
Comparative genomic analysis of transcription regulation elements involved in human map kinase G-protein coupling pathway
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DOI：
10.1142/s0219720006001849
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发表时间：
2006-04-01
影响因子：
1
通讯作者：
Horton, Paul
中科院分区：
文献类型：
--
作者：
Polouliakh, Natalia;Natsume, Tohru;Horton, Paul
高等真核生物调控区顺式元件（模体）的识别是计算生物学中一个重要而又具有挑战性的问题。真核生物的转录调控机制给启动子分析带来了一些困难：包括基序位置的高度差异，经常与基序一致模式的巨大差异，以及大量的重复元件（使许多基序发现程序感到困惑）。解决这一难题的一个有希望的方法是跨物种比较。在这项工作中，我们分析了全长调控区的基因参与的C-蛋白偶联MAP激酶途径，并比较结果与核糖体基因使用人类，小鼠和大鼠的基因组数据。我们发现了19个高可能性的转录因子（TF）候选MAPK和12个TF的核糖体数据集。在MAPK数据集的情况下，发现功能上分组为受体和MAP核心基因的基因的调控区在三个物种中大多高度保守。
The identification of cis-elements (motifs) in the regulatory regions of higher eukaryotes is an important and challenging problem in computational biology. Eukaryotic transcriptional regulatory mechanisms pose several difficulties for promoter analysis: including a high variance in the motif locations, frequently large divergence from motif consensus patterns, and a large amount of repetitive elements (confusing to many motif finding procedures). One promising approach to this difficult problem involves cross-species comparison. In this work we analyzed the full-length regulatory regions of genes involved in the C-protein coupling MAP kinase pathway and compared the results with ribosomal genes using human, mouse and rat genomic data. We found 19 high likely transcription factors (TFs) candidates for MAPK and 12 TFs for the ribosomal dataset. In the case of the MAPK dataset, regulatory regions of genes functionally grouped as receptors and MAP-core genes were found mostly highly conserved across the three species.