bZIPDB : A database of regulatory information for human bZIP transcription factors

BackgroundBasic region-leucine zipper (bZIP) proteins are a class of transcription factors (TFs) that play diverse roles in eukaryotes. Malfunctions in these proteins lead to cancer and various other diseases. For detailed characterization of these TFs, further public resources are required.DescriptionWe constructed a database, designated bZIPDB, containing information on 49 human bZIP TFs, by means of automated literature collection and manual curation. bZIPDB aims to provide public data required for deciphering the gene regulatory network of the human bZIP family, e.g., evaluation or reference information for the identification of regulatory modules. The resources provided by bZIPDB include (1) protein interaction data including direct binding, phosphorylation and functional associations between bZIP TFs and other cellular proteins, along with other types of interactions, (2) bZIP TF-target gene relationships, (3) the cellular network of bZIP TFs in particular cell lines, and (4) gene information and ontology. In the current version of the database, 721 protein interactions and 560 TF-target gene relationships are recorded. bZIPDB is annually updated for the newly discovered information.ConclusionbZIPDB is a repository of detailed regulatory information for human bZIP TFs that is collected and processed from the literature, designed to facilitate analysis of this protein family. bZIPDB is available for public use at http://biosoft.kaist.ac.kr/bzipdb.

[1]  C. Lawrence,et al.  Human-mouse genome comparisons to locate regulatory sites , 2000, Nature Genetics.

[2]  Gene Ontology Consortium,et al.  The Gene Ontology (GO) project in 2006 , 2005, Nucleic Acids Res..

[3]  Dipanwita Roy Chowdhury,et al.  Human protein reference database as a discovery resource for proteomics , 2004, Nucleic Acids Res..

[4]  F. Kaye,et al.  Mect1-Maml2 fusion oncogene linked to the aberrant activation of cyclic AMP/CREB regulated genes. , 2005, Cancer research.

[5]  Adam J. Smith,et al.  The Database of Interacting Proteins: 2004 update , 2004, Nucleic Acids Res..

[6]  T. Tatusova,et al.  Entrez Gene: gene-centered information at NCBI , 2006, Nucleic Acids Res..

[7]  Bruce J. Aronow,et al.  CisMols Analyzer: identification of compositionally similar cis-element clusters in ortholog conserved regions of coordinately expressed genes , 2005, Nucleic Acids Res..

[8]  Michael McClelland,et al.  Identification of promoters bound by c-Jun/ATF2 during rapid large-scale gene activation following genotoxic stress. , 2004, Molecular cell.

[9]  A. Viale,et al.  Induction of C/EBPalpha activity alters gene expression and differentiation of human CD34+ cells. , 2003, Blood.

[10]  C. Sander,et al.  The HUPO PSI's Molecular Interaction format—a community standard for the representation of protein interaction data , 2004, Nature Biotechnology.

[11]  J. Habener,et al.  An isoform of transcription factor CREM expressed during spermatogenesis lacks the phosphorylation domain and represses cAMP-induced transcription. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[12]  Michael A. Beer,et al.  Predicting Gene Expression from Sequence , 2004, Cell.

[13]  Alexander E. Kel,et al.  TRANSFAC®: transcriptional regulation, from patterns to profiles , 2003, Nucleic Acids Res..

[14]  A. Keating,et al.  Comprehensive Identification of Human bZIP Interactions with Coiled-Coil Arrays , 2003, Science.

[15]  G. Church,et al.  Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae. , 2000, Journal of molecular biology.

[16]  H. Hurst,et al.  Transcriptional repression by a novel member of the bZIP family of transcription factors , 1992, Molecular and cellular biology.

[17]  D. Tenen,et al.  Multiple Functional Domains of AML1: PU.1 and C/EBPα Synergize with Different Regions of AML1 , 1998, Molecular and Cellular Biology.

[18]  M. Birrer,et al.  Alterations in the gene expression profile of MCF‐7 breast tumor cells in response to c‐Jun , 2000, International journal of cancer.