Wu Jinyu, Zhao Fangqing, Wang Shengqin, Deng Gang, Wang Junrong, Bai Jie, Lu Jianxin, Qu Jia, Bao Qiyu
Institute of Biomedical Informatics/Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou Medical College, Wenzhou 325000, China.
BMC Genomics. 2007 Apr 18;8:104. doi: 10.1186/1471-2164-8-104.
Comprehensive identification and classification of the transcription factors (TFs) in a given genome is an important aspect in understanding transcriptional regulatory networks of a specific organism. Cyanobacteria are an ancient group of gram-negative bacteria with strong variation in genome size ranging from about 1.6 to 9.1 Mb and little is known about their TF repertoires. Therefore, we constructed the cTFbase database to classify and analyze all the putative TFs in cyanobacterial genomes, followed by genome-wide comparative analysis.
In the current release, cTFbase contains 1288 putative TFs identified from 21 fully sequenced cyanobacterial genomes. Through its user-friendly interactive interface, users can employ various criteria to retrieve all TF sequences and their detailed annotation information, including sequence features, domain architecture and sequence similarity against the linked databases. Furthermore, cTFbase provides phylogenetic trees of individual TF family, multiple sequence alignments of the DNA-binding domains and ortholog identification from any selected genomes. Comparative analysis revealed great variability of the TF sequences in cyanobacterial genomes. The high variance on the gene number and domain organization would be related to their diverse biological functions and their adaptation to various environmental conditions.
cTFbase provides a centralized warehouse for comparative analysis of putative TFs in cyanobacterial genomes. The availability of such an extensive database would be of great interest for the community of researchers working on TFs or transcriptional regulatory networks in cyanobacteria. cTFbase can be freely accessible at http://cegwz.com/ and will be continuously updated when the newly sequenced cyanobacterial genomes are available.
全面鉴定和分类给定基因组中的转录因子（TFs）是理解特定生物体转录调控网络的一个重要方面。蓝藻是一类古老的革兰氏阴性细菌，其基因组大小差异很大，范围从约1.6到9.1 Mb，而关于它们的转录因子库却知之甚少。因此，我们构建了cTFbase数据库来分类和分析蓝藻基因组中的所有假定转录因子，随后进行全基因组比较分析。
在当前版本中，cTFbase包含从21个全测序蓝藻基因组中鉴定出的1288个假定转录因子。通过其用户友好的交互界面，用户可以采用各种标准检索所有转录因子序列及其详细注释信息，包括序列特征、结构域结构以及与链接数据库的序列相似性。此外，cTFbase提供单个转录因子家族的系统发育树、DNA结合结构域的多序列比对以及从任何选定基因组中鉴定直系同源物。比较分析揭示了蓝藻基因组中转录因子序列的巨大变异性。基因数量和结构域组织的高变异性与其多样的生物学功能以及对各种环境条件的适应性有关。
cTFbase为蓝藻基因组中假定转录因子的比较分析提供了一个集中的仓库。这样一个广泛的数据库对于研究蓝藻转录因子或转录调控网络的研究人员群体将具有极大的吸引力。cTFbase可通过http://cegwz.com/免费访问，并且当有新测序的蓝藻基因组时将持续更新。
