The Experts below are selected from a list of 1734 Experts worldwide ranked by ideXlab platform
Edgar Wingender - One of the best experts on this subject based on the ideXlab platform.
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Multi-omics "upstream analysis" of regulatory genomic regions helps identifying targets against methotrexate resistance of colon cancer.
EuPA open proteomics, 2016Co-Authors: Alexander E. Kel, O V Kel-margoulis, Philip Stegmaier, Tagir Valeev, Jeannette Koschmann, Vladimir Poroikov, Edgar WingenderAbstract:Abstract We present an “upstream analysis” strategy for causal analysis of multiple “-omics” data. It analyzes promoters using the TRANSFAC database, combines it with an analysis of the upstream signal transduction pathways and identifies master regulators as potential drug targets for a pathological process. We applied this approach to a complex multi-omics data set that contains transcriptomics, proteomics and epigenomics data. We identified the following potential drug targets against induced resistance of cancer cells towards chemotherapy by methotrexate (MTX): TGFalpha, IGFBP7, alpha9-integrin, and the following chemical compounds: zardaverine and divalproex as well as human metabolites such as nicotinamide N-oxide.
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Prevalent motifs in ChIP-seq intervals precipitated with c-Fos antibodies.
2016Co-Authors: Martin Haubrock, Fabian Hartmann, Edgar WingenderAbstract:(a): Logo plot representing the AP-1 PWM from the TRANSFAC database. (b) Logo plot for the NF-Y PWM from TRANSFAC. (c) Summary of the top-ranking motifs obtained with MEME for proximal and distal sequence sets from the four cell lines under study. The rank of the two PWMs shown in (a) and (b) sorted by the AUC values for all 2176 TRANSFAC-related PWMs are given as superscript indices in this Table (see Methods for details).
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ROC curves for AP-1 and NF-Y binding motifs for co-localized c-Fos and NF-YB intervals.
2016Co-Authors: Martin Haubrock, Fabian Hartmann, Edgar WingenderAbstract:The ROC curves were monitored using TRANSFAC matrix V$JUNDM2_04 for the AP-1 motif (red) and V$NFY_01 for the NF-Y binding motif (blue).
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The TRANSFAC project as an example of framework technology that supports the analysis of genomic regulation
Briefings in bioinformatics, 2008Co-Authors: Edgar WingenderAbstract:Since its beginning as a data collection more than 20 years ago, the TRANSFAC project underwent an evolution to become the basis for a complex platform for the description and analysis of gene regulatory events and networks. In the following, I describe what the original concepts were, what their present status is and how they may be expected to contribute to future system biology approaches.
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TRANSFAC transpath and cytomer as starting points for an ontology of regulatory networks
in Silico Biology, 2004Co-Authors: Edgar WingenderAbstract:Building an ontology of a defined knowledge domain can help to model an appropriate database structure for the relevant contents. On the other hand, having a comprehensive overview of the knowledge of a certain domain as it may be provided by corresponding databases facilitates building an appropriate ontology, or ontologies with different granularities, which may then provide many additional benefits in handling the stored and in retrieving additional information from heterogenous sources. In this communication, the first steps are reported how we may derive an ontology for the domain of "molecular regulation" from our databases TRANSFAC (transcriptional regulation), TRANSPATH (signal transduction) and CYTOMER (cellular locations).
Alexander E. Kel - One of the best experts on this subject based on the ideXlab platform.
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Multi-omics "upstream analysis" of regulatory genomic regions helps identifying targets against methotrexate resistance of colon cancer.
EuPA open proteomics, 2016Co-Authors: Alexander E. Kel, O V Kel-margoulis, Philip Stegmaier, Tagir Valeev, Jeannette Koschmann, Vladimir Poroikov, Edgar WingenderAbstract:Abstract We present an “upstream analysis” strategy for causal analysis of multiple “-omics” data. It analyzes promoters using the TRANSFAC database, combines it with an analysis of the upstream signal transduction pathways and identifies master regulators as potential drug targets for a pathological process. We applied this approach to a complex multi-omics data set that contains transcriptomics, proteomics and epigenomics data. We identified the following potential drug targets against induced resistance of cancer cells towards chemotherapy by methotrexate (MTX): TGFalpha, IGFBP7, alpha9-integrin, and the following chemical compounds: zardaverine and divalproex as well as human metabolites such as nicotinamide N-oxide.
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P-Match: transcription factor binding site search by combining patterns and weight matrices
Nucleic Acids Research, 2005Co-Authors: D Chekmenev, C Haid, Alexander E. KelAbstract:P-Match is a new tool for identifying transcription factor (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 is closely interconnected with the TRANSFAC® database. In particular, P-Match uses the matrix library as well as sets of aligned known TF-binding sites collected in TRANSFAC® and therefore provides the possibility to search for a large variety of different TF binding sites. Using results of extensive tests of recognition accuracy, we selected three sets of optimized cut-off values that minimize either false negatives or false positives, or the sum of both errors. Comparison with the weight matrix approaches such as Match™ tool shows that P-Match generally provides superior recognition accuracy in the area of low false negative errors (high sensitivity). As familiar to the user of Match™, P-Match also allows to save user-specific profiles that include selected subsets of matrices with corresponding TF-binding sites or user-defined cut-off values. Furthermore, a number of tissue-specific profiles are provided that were compiled by the TRANSFAC® team. A public version of the P-Match tool is available at http://www.gene-regulation.com/cgi-bin/pub/programs/pmatch/bin/p-match.cgi.
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matchtm a tool for searching transcription factor binding sites in dna sequences
Nucleic Acids Research, 2003Co-Authors: Alexander E. Kel, Ingmar Reuter, Olga V Kelmargoulis, Ellen Gosling, Evgeny Cheremushkin, Edgar WingenderAbstract:MatchTM is a weight matrix-based tool for searching putative transcription factor binding sites in DNA sequences. MatchTM is closely interconnected and distributed together with the TRANSFAC® database. In particular, MatchTM uses the matrix library collected in TRANSFAC® and therefore provides the possibility to search for a great variety of different transcription factor binding sites. Several sets of optimised matrix cut-off values are built in the system to provide a variety of search modes of different stringency. The user may construct and save his/her specific user profiles which are selected subsets of matrices including default or user-defined cut-off values. Furthermore a number of tissue-specific profiles are provided that were compiled by the TRANSFAC® team. A public version of the MatchTM tool is available at: http://www.gene-regulation.com/pub/programs.html#match. The same program with a different web interface can be found at http://compel.bionet.nsc.ru/Match/Match.html. An advanced version of the tool called MatchTM Professional is available at http://www.biobase.de.
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TRANSFAC®: transcriptional regulation, from patterns to profiles
Nucleic acids research, 2003Co-Authors: V Matys, K Hornischer, Reinhard Hehl, Martin Haubrock, Alexander E. Kel, Ellen Fricke, Robert Geffers, Ellen Gößling, Dagmar Karas, O V Kel-margoulisAbstract:The TRANSFAC 1 database on eukaryotic transcriptional regulation, comprising data on transcription factors, their target genes and regulatory binding sites, has been extended and further developed, both in number of entries and in the scope and structure of the collected data. Structured fields for expression patterns have been introduced for transcription factors from human and mouse, using the CYTOMER 1 database on anatomical structures and developmental stages. The functionality of Match TM , a tool for matrix-based search of transcription factor binding sites, has been enhanced. For instance, the program now comes along with a number of tissue(or state-)specific profiles and new profiles can be created and modified with Match TM Profiler. The GENE table was extended and gained in importance, containing amongst others links to LocusLink, RefSeq and OMIM now. Further, (direct) links between factor and target gene on one hand and between gene and encoded factor on the other hand were introduced. The TRANSFAC 1 public release is available at http://www.gene-regulation.com. For yeast an additional release including the latest data was made available separately as TRANSFAC 1 Saccharomyces Module (TSM) at http://TRANSFAC. gbf.de. For CYTOMER 1 free download versions are available at http://www.biobase.de:8080/index.html.
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Expanding the TRANSFAC database towards an expert system of regulatory molecular mechanisms
Nucleic acids research, 1999Co-Authors: T. Heinemeyer, I Liebich, Xin Chen, Holger Karas, T. Meinhardt, Ingmar Reuter, Frank Schacherer, Alexander E. Kel, O. V. Kel, Edgar WingenderAbstract:TRANSFAC is a database on transcription factors, their genomic binding sites and DNA-binding profiles. In addition to being updated and extended by new features, it has been complemented now by a series of additional database modules. Among them, modules which provide data about signal transduction pathways (TRANSPATH) or about cell types/organs/developmental stages (CYTOMER) are available as well as an updated version of the previously described COMPEL database. The databases are available on the WWW at http://TRANSFAC.gbf.de/
V Matys - One of the best experts on this subject based on the ideXlab platform.
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TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes.
Nucleic acids research, 2006Co-Authors: V Matys, O V Kel-margoulis, EICK FRICKE, I Liebich, A Barre-dirrie, D Chekmenev, Mathias Krull, Sjoerd Op't Land, I. Reuter, K HornischerAbstract: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.
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TRANSFAC superscript and its module transcompel superscript transcriptional gene regulation in eukaryotes
Nucleic Acids Research, 2006Co-Authors: V Matys, I Liebich, D Chekmenev, Mathias Krull, Ingmar Reuter, Olga V Kelmargoulis, Ellen Fricke, Sigrid Land, A Barredirrie, K HornischerAbstract:The TRANSFAC[superscript ®] database on transcription factors, their binding sites, nucleotide distribution matrices and regulated genes as well as the complementing database TRANSCompel[superscript ®] on composite elements have been further enhanced on various levels. A new web interface with different search options and integrated versions of Match[superscript TM] and Patch[superscript TM] provides increased functionality for TRANSFAC[superscript ®]. The list of databases which are linked to the common GENE table of TRANSFAC[superscript ®] and TRANSCompel[superscript ®] has been extended by: Ensembl, UniGene, EntrezGene, HumanPSD[superscript TM] and TRANSPRO[superscript TM]. 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[superscript ®] 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[superscript ®], 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[superscript ®] 7.0 and TRANSCompel[superscript ®] 7.0, are accessible under http://www.gene-regulation.com/pub/databases.html.
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TRANSFAC®: transcriptional regulation, from patterns to profiles
Nucleic acids research, 2003Co-Authors: V Matys, K Hornischer, Reinhard Hehl, Martin Haubrock, Alexander E. Kel, Ellen Fricke, Robert Geffers, Ellen Gößling, Dagmar Karas, O V Kel-margoulisAbstract:The TRANSFAC 1 database on eukaryotic transcriptional regulation, comprising data on transcription factors, their target genes and regulatory binding sites, has been extended and further developed, both in number of entries and in the scope and structure of the collected data. Structured fields for expression patterns have been introduced for transcription factors from human and mouse, using the CYTOMER 1 database on anatomical structures and developmental stages. The functionality of Match TM , a tool for matrix-based search of transcription factor binding sites, has been enhanced. For instance, the program now comes along with a number of tissue(or state-)specific profiles and new profiles can be created and modified with Match TM Profiler. The GENE table was extended and gained in importance, containing amongst others links to LocusLink, RefSeq and OMIM now. Further, (direct) links between factor and target gene on one hand and between gene and encoded factor on the other hand were introduced. The TRANSFAC 1 public release is available at http://www.gene-regulation.com. For yeast an additional release including the latest data was made available separately as TRANSFAC 1 Saccharomyces Module (TSM) at http://TRANSFAC. gbf.de. For CYTOMER 1 free download versions are available at http://www.biobase.de:8080/index.html.
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The TRANSFAC system on gene expression regulation.
Nucleic acids research, 2001Co-Authors: Edgar Wingender, V Matys, I Liebich, Mathias Krull, Xin Chen, Reinhard Hehl, Ellen Fricke, Robert Geffers, Holger Michael, R. OhnhäuserAbstract:The TRANSFAC database on transcription factors and their DNA-binding sites and profiles (http:// www.gene-regulation.de/) has been quantitatively extended and supplemented by a number of modules. These modules give information about pathologically relevant mutations in regulatory regions and transcription factor genes (PathoDB), scaffold/matrix attached regions (S/MARt DB), signal transduction (TRANSPATH) and gene expression sources (CYTOMER). Altogether, these distinct database modules constitute the TRANSFAC system. They are accompanied by a number of program routines for identifying potential transcription factor binding sites or for localizing individual components in the regulatory network of a cell.
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TRANSFAC: an integrated system for gene expression regulation
Nucleic acids research, 2000Co-Authors: Edgar Wingender, V Matys, I Liebich, Xin Chen, Reinhard Hehl, Holger Karas, T. Meinhardt, M. Prüß, Ingmar Reuter, Frank SchachererAbstract:TRANSFAC is a database on transcription factors, their genomic binding sites and DNA-binding profiles (http://TRANSFAC.gbf.de/TRANSFAC/ ). Its content has been enhanced, in particular by information about training sequences used for the construction of nucleotide matrices as well as by data on plant sites and factors. Moreover, TRANSFAC has been extended by two new modules: PathoDB provides data on pathologically relevant mutations in regulatory regions and transcription factor genes, whereas S/MARt DB compiles features of scaffold/matrix attached regions (S/MARs) and the proteins binding to them. Additionally, the databases TRANSPATH, about signal transduction, and CYTOMER, about organs and cell types, have been extended and are increasingly integrated with the TRANSFAC data sources.
I Liebich - One of the best experts on this subject based on the ideXlab platform.
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TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes.
Nucleic acids research, 2006Co-Authors: V Matys, O V Kel-margoulis, EICK FRICKE, I Liebich, A Barre-dirrie, D Chekmenev, Mathias Krull, Sjoerd Op't Land, I. Reuter, K HornischerAbstract: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.
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TRANSFAC superscript and its module transcompel superscript transcriptional gene regulation in eukaryotes
Nucleic Acids Research, 2006Co-Authors: V Matys, I Liebich, D Chekmenev, Mathias Krull, Ingmar Reuter, Olga V Kelmargoulis, Ellen Fricke, Sigrid Land, A Barredirrie, K HornischerAbstract:The TRANSFAC[superscript ®] database on transcription factors, their binding sites, nucleotide distribution matrices and regulated genes as well as the complementing database TRANSCompel[superscript ®] on composite elements have been further enhanced on various levels. A new web interface with different search options and integrated versions of Match[superscript TM] and Patch[superscript TM] provides increased functionality for TRANSFAC[superscript ®]. The list of databases which are linked to the common GENE table of TRANSFAC[superscript ®] and TRANSCompel[superscript ®] has been extended by: Ensembl, UniGene, EntrezGene, HumanPSD[superscript TM] and TRANSPRO[superscript TM]. 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[superscript ®] 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[superscript ®], 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[superscript ®] 7.0 and TRANSCompel[superscript ®] 7.0, are accessible under http://www.gene-regulation.com/pub/databases.html.
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The TRANSFAC system on gene expression regulation.
Nucleic acids research, 2001Co-Authors: Edgar Wingender, V Matys, I Liebich, Mathias Krull, Xin Chen, Reinhard Hehl, Ellen Fricke, Robert Geffers, Holger Michael, R. OhnhäuserAbstract:The TRANSFAC database on transcription factors and their DNA-binding sites and profiles (http:// www.gene-regulation.de/) has been quantitatively extended and supplemented by a number of modules. These modules give information about pathologically relevant mutations in regulatory regions and transcription factor genes (PathoDB), scaffold/matrix attached regions (S/MARt DB), signal transduction (TRANSPATH) and gene expression sources (CYTOMER). Altogether, these distinct database modules constitute the TRANSFAC system. They are accompanied by a number of program routines for identifying potential transcription factor binding sites or for localizing individual components in the regulatory network of a cell.
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TRANSFAC: an integrated system for gene expression regulation
Nucleic acids research, 2000Co-Authors: Edgar Wingender, V Matys, I Liebich, Xin Chen, Reinhard Hehl, Holger Karas, T. Meinhardt, M. Prüß, Ingmar Reuter, Frank SchachererAbstract:TRANSFAC is a database on transcription factors, their genomic binding sites and DNA-binding profiles (http://TRANSFAC.gbf.de/TRANSFAC/ ). Its content has been enhanced, in particular by information about training sequences used for the construction of nucleotide matrices as well as by data on plant sites and factors. Moreover, TRANSFAC has been extended by two new modules: PathoDB provides data on pathologically relevant mutations in regulatory regions and transcription factor genes, whereas S/MARt DB compiles features of scaffold/matrix attached regions (S/MARs) and the proteins binding to them. Additionally, the databases TRANSPATH, about signal transduction, and CYTOMER, about organs and cell types, have been extended and are increasingly integrated with the TRANSFAC data sources.
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Expanding the TRANSFAC database towards an expert system of regulatory molecular mechanisms
Nucleic acids research, 1999Co-Authors: T. Heinemeyer, I Liebich, Xin Chen, Holger Karas, T. Meinhardt, Ingmar Reuter, Frank Schacherer, Alexander E. Kel, O. V. Kel, Edgar WingenderAbstract:TRANSFAC is a database on transcription factors, their genomic binding sites and DNA-binding profiles. In addition to being updated and extended by new features, it has been complemented now by a series of additional database modules. Among them, modules which provide data about signal transduction pathways (TRANSPATH) or about cell types/organs/developmental stages (CYTOMER) are available as well as an updated version of the previously described COMPEL database. The databases are available on the WWW at http://TRANSFAC.gbf.de/
Ingmar Reuter - One of the best experts on this subject based on the ideXlab platform.
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TRANSFAC superscript and its module transcompel superscript transcriptional gene regulation in eukaryotes
Nucleic Acids Research, 2006Co-Authors: V Matys, I Liebich, D Chekmenev, Mathias Krull, Ingmar Reuter, Olga V Kelmargoulis, Ellen Fricke, Sigrid Land, A Barredirrie, K HornischerAbstract:The TRANSFAC[superscript ®] database on transcription factors, their binding sites, nucleotide distribution matrices and regulated genes as well as the complementing database TRANSCompel[superscript ®] on composite elements have been further enhanced on various levels. A new web interface with different search options and integrated versions of Match[superscript TM] and Patch[superscript TM] provides increased functionality for TRANSFAC[superscript ®]. The list of databases which are linked to the common GENE table of TRANSFAC[superscript ®] and TRANSCompel[superscript ®] has been extended by: Ensembl, UniGene, EntrezGene, HumanPSD[superscript TM] and TRANSPRO[superscript TM]. 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[superscript ®] 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[superscript ®], 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[superscript ®] 7.0 and TRANSCompel[superscript ®] 7.0, are accessible under http://www.gene-regulation.com/pub/databases.html.
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matchtm a tool for searching transcription factor binding sites in dna sequences
Nucleic Acids Research, 2003Co-Authors: Alexander E. Kel, Ingmar Reuter, Olga V Kelmargoulis, Ellen Gosling, Evgeny Cheremushkin, Edgar WingenderAbstract:MatchTM is a weight matrix-based tool for searching putative transcription factor binding sites in DNA sequences. MatchTM is closely interconnected and distributed together with the TRANSFAC® database. In particular, MatchTM uses the matrix library collected in TRANSFAC® and therefore provides the possibility to search for a great variety of different transcription factor binding sites. Several sets of optimised matrix cut-off values are built in the system to provide a variety of search modes of different stringency. The user may construct and save his/her specific user profiles which are selected subsets of matrices including default or user-defined cut-off values. Furthermore a number of tissue-specific profiles are provided that were compiled by the TRANSFAC® team. A public version of the MatchTM tool is available at: http://www.gene-regulation.com/pub/programs.html#match. The same program with a different web interface can be found at http://compel.bionet.nsc.ru/Match/Match.html. An advanced version of the tool called MatchTM Professional is available at http://www.biobase.de.
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TRANSFAC: an integrated system for gene expression regulation
Nucleic acids research, 2000Co-Authors: Edgar Wingender, V Matys, I Liebich, Xin Chen, Reinhard Hehl, Holger Karas, T. Meinhardt, M. Prüß, Ingmar Reuter, Frank SchachererAbstract:TRANSFAC is a database on transcription factors, their genomic binding sites and DNA-binding profiles (http://TRANSFAC.gbf.de/TRANSFAC/ ). Its content has been enhanced, in particular by information about training sequences used for the construction of nucleotide matrices as well as by data on plant sites and factors. Moreover, TRANSFAC has been extended by two new modules: PathoDB provides data on pathologically relevant mutations in regulatory regions and transcription factor genes, whereas S/MARt DB compiles features of scaffold/matrix attached regions (S/MARs) and the proteins binding to them. Additionally, the databases TRANSPATH, about signal transduction, and CYTOMER, about organs and cell types, have been extended and are increasingly integrated with the TRANSFAC data sources.
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Expanding the TRANSFAC database towards an expert system of regulatory molecular mechanisms
Nucleic acids research, 1999Co-Authors: T. Heinemeyer, I Liebich, Xin Chen, Holger Karas, T. Meinhardt, Ingmar Reuter, Frank Schacherer, Alexander E. Kel, O. V. Kel, Edgar WingenderAbstract:TRANSFAC is a database on transcription factors, their genomic binding sites and DNA-binding profiles. In addition to being updated and extended by new features, it has been complemented now by a series of additional database modules. Among them, modules which provide data about signal transduction pathways (TRANSPATH) or about cell types/organs/developmental stages (CYTOMER) are available as well as an updated version of the previously described COMPEL database. The databases are available on the WWW at http://TRANSFAC.gbf.de/
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Databases on transcriptional regulation: TRANSFAC, TRRD and COMPEL
Nucleic acids research, 1998Co-Authors: T. Heinemeyer, Edgar Wingender, Ingmar Reuter, Henning Hermjakob, Alexander E. Kel, O. V. Kel, Elena V. Ignatieva, E. A. Ananko, O. A. Podkolodnaya, Fedor A. KolpakovAbstract:TRANSFAC, TRRD (Transcription Regulatory Region Database) and COMPEL are databases which store information about transcriptional regulation in eukaryotic cells. The three databases provide distinct views on the components involved in transcription: transcription factors and their binding sites and binding profiles (TRANSFAC), the regulatory hierarchy of whole genes (TRRD), and the structural and functional properties of composite elements (COMPEL). The quantitative and qualitative changes of all three databases and connected programs are described. The databases are accessible via WWW:http://TRANSFAC.gbf.de/TRANSFAC orhttp://www.bionet.nsc.ru/TRRD