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TRANSFAC(R): transcriptional regulation, from patterns to profiles
2003
Nucleic Acids Research
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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 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 ...
ACKNOWLEDGEMENTS We would like to thank all present and former members of BIOBASE GmbH and the AG Bioinformatics at the German Research Centre for Biotechnology (GBF) for contributing to this work in various ...
doi:10.1093/nar/gkg108
pmid:12520026
pmcid:PMC165555
fatcat:3hjrkzoaxnhafl2mfo2qhtv52a
The TRANSFAC system on gene expression regulation
2001
Nucleic Acids Research
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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. ...
Altogether, these distinct database modules constitute the TRANSFAC system. ...
ACKNOWLEDGEMENTS The authors are indebted to H. Hermjakob (EBI) for his help in establishing links between TRANSFAC, S/MARt DB and TRANSPATH. We also acknowledge the generous help granted by T. ...
doi:10.1093/nar/29.1.281
pmid:11125113
pmcid:PMC29801
fatcat:u3d65o47wbbfpggwzo6pfrdjoa
TRANSFAC: an integrated system for gene expression regulation
2000
Nucleic Acids Research
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TRANSFAC is a database on transcription factors, their genomic binding sites and DNA-binding profiles (http://transfac.gbf.de/TRANSFAC/ ). ...
of scaffold/matrix attached regions (S/MARs) and the proteins binding to them. ...
ACKNOWLEDGEMENTS The authors are indebted to M. Ashburner (EBI) for regularly providing the links to FlyBase. We also gladly acknowledge the generous help granted by T. Takai-Igarashi and T. ...
doi:10.1093/nar/28.1.316
pmid:10592259
pmcid:PMC102445
fatcat:c4um2wfgdzhylowqzpagcwt2cq
TRANSFAC(R) and its module TRANSCompel(R): transcriptional gene regulation in eukaryotes
2006
Nucleic Acids Research
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The TRANSFAC Ò database on transcription factors, their binding sites, nucleotide distribution matrices and regulated genes as well as the complementing database TRANSCompel Ò on composite elements have ...
factors (by courtesy of DATF, Database of Arabidopsis Transcription Factors) has to be stressed. ...
ACKNOWLEDGEMENTS We like to thank Prof Jingchu Luo, Dr Anyuan Guo and colleagues from Peking University, Center for Bioinformatics, for providing the DATF data and Dr Casey Bergman and colleagues from ...
doi:10.1093/nar/gkj143
pmid:16381825
pmcid:PMC1347505
fatcat:p7armsmw6rgnnpeo3uyrat2mwe
Expanding the TRANSFAC database towards an expert system of regulatory molecular mechanisms
1999
Nucleic Acids Research
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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. ...
ACKNOWLEDGEMENTS The authors are indebted to H. Hermjakob (EBI, Hinxton, UK) for his support in establishing TRANSFAC-links to the EMBL data library and to the SwissProt database, and to M. ...
doi:10.1093/nar/27.1.318
pmid:9847216
pmcid:PMC148171
fatcat:fjpblo3scrcv7fhpt75ttmc7vy
The TRANSFAC project as an example of framework technology that supports the analysis of genomic regulation
2008
Briefings in Bioinformatics
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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 ...
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. ...
These data are required when expanding the scope from mere transcriptional networks to comprehensive gene regulation networks, since it became clear during the last years that the post-transcriptional ...
doi:10.1093/bib/bbn016
pmid:18436575
fatcat:5umimjlklvfx3nuuchv5gpkuoa
Bioinformatic detection of E47, E2F1 and SREBP1 transcription factors as potential regulators of genes associated to acquisition of endometrial receptivity
2011
Reproductive Biology and Endocrinology
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Results: We found 40 up-and 21 down-regulated transcripts in the CERTL. ...
The objective of this work was to perform a research synthesis of available gene expression profiles related to acquisition of endometrial receptivity for embryo implantation, in order to gain insights ...
)), to regulate transcription. ...
doi:10.1186/1477-7827-9-14
pmid:21272326
pmcid:PMC3040129
fatcat:mxa2l74exbcepplxvgk2smqbby
Reconstruction of regulatory networks through temporal enrichment profiling and its application to H1N1 influenza viral infection
2013
BMC Bioinformatics
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TIDAL infers 12 transcription factors and 32 regulatory connections that drive the antiviral response to influenza. ...
Conclusions: We apply TIDAL to reconstruct the transcriptional programs activated in monocyte-derived human dendritic cells in response to influenza and measles infections. ...
Duke for generating the transcription factor target data. ...
doi:10.1186/1471-2105-14-s6-s1
pmid:23734902
pmcid:PMC3633009
fatcat:lzvynnkxobcfbm6jdmdcjdvxxe
Large-Scale Investigation of Human TF-miRNA Relations Based on Coexpression Profiles
2014
BioMed Research International
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In this study, a large-scale investigation of novelcis- andtrans-elements was undertaken to further determine TF-miRNA regulatory relations, which are necessary to unravel the transcriptional regulation ...
The computational pipeline was successfully established to filter redundancy due to short sequence motifs for TFBS pattern search. ...
Acknowledgments Thanks are due to Pei-Wen Jiang for the assistance of programming and system maintenance and to Hsi-Yuan Huang for experience sharing in expression profile analysis. ...
doi:10.1155/2014/623078
pmid:24995316
pmcid:PMC4068100
fatcat:7bea2kubcjhtpiypyshi5vylyq
Identifying transcription factor and microRNA mediated synergetic regulatory networks in lung cancer
2013
BMC Bioinformatics
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To find the regulation of TF to genes or miRNAs, we explored the TFs and their binding profiles from the TRANSFAC Professional database. ...
It has been demonstrated that, at the network level, the transcriptional regulation by transcription factors (TFs) and post-transcriptional regulation by microRNAs (miR-NAs) are tightly coupled. ...
Acknowledgements We would like to thank the members in Bioinformatics and Systems Medicine Laboratory for their valuable discussion in this project. ...
doi:10.1186/1471-2105-14-s17-a14
pmcid:PMC3853118
fatcat:t2xs5onbanfk7kzldumxa7jvsu
Transcriptional regulation of gene expression clusters in motor neurons following spinal cord injury
2010
BMC Genomics
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to alter the transcriptional response to prevent the motor neurons from entering a state of hyper-excitability. ...
Here we examine the dynamic transcriptional response of motor neurons to spinal cord injury as it evolves over time to unravel common gene expression patterns and their underlying regulatory mechanisms ...
obtained from JASPAR [39] or TRANSFAC [40] . ...
doi:10.1186/1471-2164-11-365
pmid:20534130
pmcid:PMC2900267
fatcat:crmrrnoodfe7hc36ucdzq6ug3e
A Transcription Factor Map as Revealed by a Genome-Wide Gene Expression Analysis of Whole-Blood mRNA Transcriptome in Multiple Sclerosis
2010
PLoS ONE
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We investigate the possibility that this network could be mapped using microarray technologies and contemporary bioinformatics methods on a dataset derived from whole blood in 99 untreated MS patients ...
One of the reasons is that there are several clinical subtypes of MS and transcription factors that may be involved in one subtype may not be in others. ...
These higher-level regulatory sequences -which effectively identify 'regulators of regulators' -were obtained by TRANSFAC profiling the coding genes of transcription factors corresponding to key sequences ...
doi:10.1371/journal.pone.0014176
pmid:21152067
pmcid:PMC2995726
fatcat:5dogckkm2vedxisu5a6n2lxe6e
A hypothesis-based approach for identifying the binding specificity of regulatory proteins from chromatin immunoprecipitation data
2005
Bioinformatics
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Motivation:Genome-widechromatin-immunoprecipitation(ChIP-chip) detects binding of transcriptional regulators to DNA in vivo at low resolution. ...
Motif discovery algorithms can be used to discover sequence patterns in the bound regions that may be recognized by the immunoprecipitated protein. ...
and is consistent with the domain structure of the transcriptional regulator. ...
doi:10.1093/bioinformatics/bti815
pmid:16332710
fatcat:kdinksdfkjhtbhxzmmpoft4jca
MATCHTM: a tool for searching transcription factor binding sites in DNA sequences
2003
Nucleic Acids Research
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In particular, Match TM uses the matrix library collected in TRANSFAC 1 and therefore provides the possibility to search for a great variety of different transcription factor binding sites. ...
Furthermore a number of tissue-specific profiles are provided that were compiled by the TRANSFAC 1 team. ...
To build such profiles groups of transcription factors known to be active in a particular tissue or a process have been collected for each profile with the help of information from the TRANSFAC 1 database ...
doi:10.1093/nar/gkg585
pmid:12824369
pmcid:PMC169193
fatcat:x5wbyuom3vcmdifmgkfcfwjovq
Antiviral Response Dictated by Choreographed Cascade of Transcription Factors
2010
Journal of Immunology
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The network-building approach developed in this study is generally applicable to transcriptional profiling time series. It differs from most current analyses in several important ways. ...
Results To define the transcriptional regulatory network underlying an uninhibited antiviral response, we performed genome-wide transcriptional profiling of human monocyte-derived DCs infected with NDV ...
doi:10.4049/jimmunol.0903453
pmid:20164420
pmcid:PMC2856074
fatcat:oac6hawazfepfb5knl6dxlx26i
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