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| The Co-occurrence of Transcription Factor Binding Sites |
| LI Jia-ping1, ZHANG Xian-wen1,2, CHEN Xin-bo 1,2 |
1. Crop Gene Engineering Key Laboratory of Hunan Province, Changsha 410128, China;
2. College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China |
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Abstract Transcription factor binding sites (TFBS) which bind the same or different transcription factors (TF) tend to co-occur in the promoter regions. TF and target gene was connected by these TFBS, which also provide the clue of TF synergy. The synergism of TF is an important part of the gene regulatory network (GRN). Identifying TFBS co-occurrence in the promoter region is an essential approach to construct GRN. The co-occurring TFBS in the promoter was called motif pair. The regulatory region that contains multiple TFBS was known as cis-regulatory modules (CRM). Accuracy of motif pair and CRM identification algorithm was improved by considering their conservation, specific location and distance, and the regulation of co-expressed genes. Great limitation still exists for constructing GRN by TFBS co-occurrence. Data integration of diverse sources will alleviate the problem in the future.
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Received: 30 December 2011
Published: 25 September 2012
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