Abstract
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 .
Highlights
Basic region-leucine zipper proteins are a class of transcription factors (TFs) that play diverse roles in eukaryotes
With the assistance of high-throughput technology, such as microarray technology, several researchers have attempted to decipher the regulatory networks of Basic region-leucine zipper (bZIP) TFs [4,5,6,7]
While a number of the binding proteins or target genes of bZIP TFs can be retrieved from HPRD or TRANSFAC [8,9], the currently available data are relatively limited, and do not necessarily cover the entire cellular network
Summary
Transcription factors (TFs) are responsible for gene expression in every living organism. To facilitate our understanding of these proteins, we have generated a bZIPDB database containing regulatory network information on the human bZIP TF family. The aim of bZIPDB is to accumulate known regulatory information on human bZIP TFs, protein-protein and protein-DNA interactions. Functional association, which means that both proteins are present in the same pathway, is another important interaction type in transcriptome analysis, which basically assumes that coregulated genes share similar roles [13,14]. Experimental cell lines are classified as an important attribute, since they originate from different organisms and tissues and have a distinct genomic context, which affects protein-protein interactions (described in the CELL_LINE table). In addition to protein-protein and protein-DNA interaction data, genomic information, such as chromosomal locus and exon/introns, synonyms and functional annotation, was obtained from Entrez [15] and the Gene ontology consortium [16]
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