Searching across hundreds of databases
The TRANSFAC database on transcription factors, their binding sites, nucleotide distribution matrices and regulated genes as well as the complementing database TRANSCompel on composite elements have been further enhanced on various levels. A new web interface with different search options and integrated versions of Match and Patch provides increased functionality for TRANSFAC. The list of databases which are linked to the common GENE table of TRANSFAC and TRANSCompel has been extended by: Ensembl, UniGene, EntrezGene, HumanPSD and TRANSPRO. Standard gene names from HGNC, MGI and RGD, are included for human, mouse and rat genes, respectively. With the help of InterProScan, Pfam, SMART and PROSITE domains are assigned automatically to the protein sequences of the transcription factors. TRANSCompel contains now, in addition to the COMPEL table, a separate table for detailed information on the experimental EVIDENCE on which the composite elements are based. Finally, for TRANSFAC, in respect of data growth, in particular the gain of Drosophila transcription factor binding sites (by courtesy of the Drosophila DNase I footprint database) and of Arabidopsis factors (by courtesy of DATF, Database of Arabidopsis Transcription Factors) has to be stressed. The here described public releases, TRANSFAC 7.0 and TRANSCompel 7.0, are accessible under http://www.gene-regulation.com/pub/databases.html.
Pubmed ID: 16381825 RIS Download
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In an effort to strongly support the collaborative nature of scientific research, BIOBASE offers access to their tools. Programs that are available through this portal are: * AliBaba 2.1: AliBaba2 is a program for predicting binding sites of transcription factor binding sites in an unknown DNA sequence. Therefore it uses the binding sites collected in TRANSFAC. AliBaba2 is currently the most specific tool for predicting sites. * Boxshade 3.3.1: Pretty Printing and Shading of Multiple-Alignment files. * ClustalW 1.8: ClustalW Multiple Sequence Alignment Program. * Dialign2.0: Multiple Sequence Alignment Program. * F-Match 1.0: F-MATCH is a program for identifying statistically overrepresented Transcription Factor Binding Sites (TFBS) in a set of sequences compared against a control set, assuming a binomial distribution of TFBS frequency. The program reads MATCH output files for the query and control sets. F-Match uses a library of mononucleotide weight matrices from TRANSFAC 6.0 * Match 1.0 Public: Match is designed for searching potential binding sites for transcription factors (TF binding sites) nucleotide sequences. MatchTM uses a library of mononucleotide weight matrices from TRANSFAC 6.0 * molwSearch 1.0: Search for transcription factors with a certain molecular weight. * P-Match 1.0: P-Match is a new tool for identifying transcription factor binding sites (TF binding sites) in DNA sequences. It combines pattern matching and weight matrix approaches thus providing higher accuracy of recognition than each of the methods alone. P-Match uses a library of mononucleotide weight matrices from TRANSFAC 6.0 along with the site alignments associated with these matrices. * Patch 1.0: Search for potential transcription factor binding sites in your own sequences with the pattern search program using TRANSFAC 6.0 public sites. * m2transfac 1.0: m2transfac is a PWM-PWM alignment interface for the TRANSFAC(R) database. For given user motifs, m2transfac reports all non-overlapping pairwise alignments to a TRANSFAC(R) matrix which satisfy a specified threshold. * MatrixCatch 2.7: The MatrixCatch tool is designed for searching potential composite elements (CEs) for transcription factors (TFs) in any DNA sequence, which may be of interest. MatrixCatch uses a library of CE matrix models, which were compiled on a basis of experimentally identified CEs collected in TRANSCOMPEL database and mononucleotide weight matrices for single TF-binding sites collected in TRANSFAC 6.0 public database. * Composite Module Analyst (CMA) 1.0: CMA reads output of Match program and applies a genetic algorithm in order to define promoter models based on the composition of transcription factor binding sites and their pairs. * PolyA Scan 0.000707: Scanning a Sequence for potential Polyadenylation Sites. * ReadSeq 2.0: ReadSeq reads and writes nucleic/protein sequences in various formats. * SignalScan: Analysis of DNA Sequences for known Eukaryotic Signals * SbBlast 1.0: Search Tool for Sequence Search in the S/MARt Binder Database. SbBlast makes use of the BLAST Sequence Similarity Search Tool - Version 2.0.13 (May-26-2000). * SnpFind 0.3: SNPFIND is a tool for searches in the Database of Single Nucleotide Polymorphisms. The search algorithm used for the database search is the BLAST algorithm. * TfBlast 0.1: Search Tool for Sequence Search in the TRANSFAC Factor Table. SbBlast makes use of the BLAST Sequence Similarity Search Tool - Version 2.0.13 (May-26-2000).
View all literature mentionsIn an effort to strongly support the collaborative nature of scientific research, BIOBASE offers academic and non-profit organizations free access to reduced functionality versions of their products. TRANSFAC Professional provides gene regulation analysis solutions, offering the most comprehensive collection of eukaryotic gene regulation data. The professional paid subscription gives customers access to up-to-date data and tools not available in the free version. The public databases currently available for academic and non-profit organizations are: * TRANSFAC: contains data on transcription factors, their experimentally-proven binding sites, and regulated genes. Its broad compilation of binding sites allows the derivation of positional weight matrices. * TRANSPATH: provides data about molecules participating in signal transduction pathways and the reactions they are involved in, resulting in a complex network of interconnected signaling components.TRANSPATH focuses on signaling cascades that change the activities of transcription factors and thus alter the gene expression profile of a given cell. * PathoDB: is a database on pathologically relevant mutated forms of transcription factors and their binding sites. It comprises numerous cases of defective transcription factors or mutated transcription factor binding sites, which are known to cause pathological defects. * S/MARt DB: presents data on scaffold or matrix attached regions (S/MARs) of eukaryotic genomes, as well as about the proteins that bind to them. S/MARs organize the chromatin in the form of functionally independent loop domains gained increasing support. Scaffold or Matrix Attached Regions (S/MARs) are genomic DNA sequences through which the chromatin is tightly attached to the proteinaceous scaffold of the nucleus. * TRANSCompel: is a database on composite regulatory elements affecting gene transcription in eukaryotes. Composite regulatory elements consist of two closely situated binding sites for distinct transcription factors, and provide cross-coupling of different signaling pathways. * PathoSign Public: is a database which collects information about defective cell signaling molecules causing human diseases. While constituting a useful data repository in itself, PathoSign is also aimed at being a foundational part of a platform for modeling human disease processes.
View all literature mentionsThe SciCrunch Infrastructure was developed as a cooperative data platform to be used by diverse communities in making data more FAIR.
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