CardioSignal: a database of transcriptional regulation in cardiac development and hypertrophy.
BACKGROUND
Although extensive research has characterized intricate genetic programs in heart system, the information generated is highly fragmented. Here we have developed a new database called CardioSignal, which was designed for integration of regulatory information on the transcriptional regulation involved in heart development and cardiac hypertrophy.


METHODS
Data about sequences, positions and functional annotation of transcription binding sites, cis-regulatory modules as well as promoters were collected from scientific literature. Genes involved in both processes were also manually gathered, particularly those preferentially expressed in the heart. Data was stored in MySQL database and Perl was used as the server-side programming language.


RESULTS
Currently, CardioSignal contains 677 cardiac genes from twenty species. Among them are 128 cardiac transcription factors. Of the approximately 179 individual promoters from six species, the database also documented 247 experimentally verified binding sites and 64 cis-regulatory modules. CardioSignal may be searched for the promoter of a specific gene by specifying a gene name, Entrez geneID, swissProt accession number and so on. Downstream targets of transcriptional factors and cardiac regulatory modules can also be retrieved through a user-friendly web interface. Also available is experimental supporting evidence. Computational analysis tools were implemented for on-the-fly motif finding and comparative genomic analysis respectively.


CONCLUSIONS
CardioSignal offers a unique resource as it contains simultaneously the promoter collected while correlating the information of transcription factor binding sites and cis-regulatory modules from heart system. We are hopeful that its implementation will contribute toward the elucidation of the complex processes in cardiac development and hypertrophy.
Zhen
Yisong
Y
Sino-German Laboratory for Molecular Medicine and Department of Cardiology, Fu Wai Hospital and Cardiovascular Institute, Chinese Academy of Medical Sciences and Peking Union Medical College, 167 Beilishilu, Beijing 100037, PR China.
Wang
Yibo
Y
Zhang
Weili
W
Zhou
Chunxiao
C
Hui
Rutai
R
D000818:Animals; D006332:Cardiomegaly / Q000235:genetics*; D019295:Computational Biology; D030541:Databases, Genetic; D005786:Gene Expression Regulation; D018507:Gene Expression Regulation, Developmental; D048788:Growth and Development / Q000235:genetics*; D006321:Heart / Q000196:embryology*; D006801:Humans; D020407:Internet; D014158:Transcription, Genetic; D014584:User-Computer Interface