Transcription Regulatory Regions Database (TRRD): its status in 1999

Abstract

The Transcription Regulatory Regions Database (TRRD) is a curated database designed for accumulation of experimental data on extended regulatory regions of eukaryotic genes, the regulatory elements they contain, i.e., transcription factor binding sites, promoters, enhancers, silencers, etc., and expression patterns of the genes. Release 4.1 of TRRD offers a number of significant improvements, in particular, a more detailed description of transcription factor binding sites, transcription factors per se, and gene expression patterns in a computer-readable format. In addition, the new TRRD release provides considerably more references to other molecular biological databases. TRRD 4.1 is installed under SRS and is available through the WWW at http://www.bionet.nsc.ru/trrd/

HbVar: A relational database of human hemoglobin variants and thalassemia mutations at the globin gene server

“…Ideally, this information should be readily accessible at the same time one is searching the database. It currently is available from many sources, such as a figure in Huisman et al [1997], or other databases such as TRRD [Kolchanov et al, 1999], or the literature [Feng et al, 1994]. However, more complete recording of information in databases and tight integration among them will facilitate access to these data by a wide community of users.…”

Structural variants of glucocorticoid receptor binding sites and different versions of positive glucocorticoid responsive elements: Analysis of GR-TRRD database

“…Being a part of the TRRD database, GR-TRRD utilizes its system for recording the published experimental data [19][20][21]. The database entry is a gene.…”

Network integration and graph analysis in mammalian molecular systems biology

“…ChIP-chip [58] and chIP-seq [59], comparative genomics (identifying conserved non-coding sequences as potential binding sites), or purely computational approaches that use known consensus DNA binding motifs [60, 61] can also be used to reconstruct in silico gene-regulatory networks. Several tools are developed to integrate such data to allow novice users easy access to identify gene-regulatory interactions For example, MYBS [62], YEASTRACT [63], SGD [64, 65], SCPD [66], TRANSFAC [67], MAPPER [68], TRANSCompel [69], TRRD [70, 71] and SWISS-REGULON [72] are web-based tools providing a user interface for an underlying gene-regulatory network database.…”