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TRANSFAC(R): transcriptional regulation, from patterns to profiles

V. Matys
2003 Nucleic Acids Research  
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

E. Wingender
2001 Nucleic Acids Research  
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

E. Wingender
2000 Nucleic Acids Research  
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

V. Matys
2006 Nucleic Acids Research  
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

T. Heinemeyer, X. Chen, H. Karas, A. E. Kel, O. V. Kel, I. Liebich, T. Meinhardt, I. Reuter, F. Schacherer, E. Wingender
1999 Nucleic Acids Research  
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

E. Wingender
2008 Briefings in Bioinformatics  
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

Alejandro Tapia, Cristian Vilos, Juan Marín, Horacio B Croxatto, Luigi Devoto
2011 Reproductive Biology and Endocrinology  
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

Elena Zaslavsky, German Nudelman, Susanna Marquez, Uri Hershberg, Boris M Hartmann, Juilee Thakar, Stuart C Sealfon, Steven H Kleinstein
2013 BMC Bioinformatics  
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

Chia-Hung Chien, Yi-Fan Chiang-Hsieh, Ann-Ping Tsou, Shun-Long Weng, Wen-Chi Chang, Hsien-Da Huang
2014 BioMed Research International  
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

Ramkrishna Mitra, Jingchun Sun, Min Zhao, Zhongming Zhao
2013 BMC Bioinformatics  
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

Jesper Ryge, Ole Winther, Jacob Wienecke, Albin Sandelin, Ann-Charlotte Westerdahl, Hans Hultborn, Ole Kiehn
2010 BMC Genomics  
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

Carlos Riveros, Drew Mellor, Kaushal S. Gandhi, Fiona C. McKay, Mathew B. Cox, Regina Berretta, S. Yahya Vaezpour, Mario Inostroza-Ponta, Simon A. Broadley, Robert N. Heard, Stephen Vucic, Graeme J. Stewart (+6 others)
2010 PLoS ONE  
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

K. D. MacIsaac, D. B. Gordon, L. Nekludova, D. T. Odom, J. Schreiber, D. K. Gifford, R. A. Young, E. Fraenkel
2005 Bioinformatics  
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

A.E. Kel
2003 Nucleic Acids Research  
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

E. Zaslavsky, U. Hershberg, J. Seto, A. M. Pham, S. Marquez, J. L. Duke, J. G. Wetmur, B. R. tenOever, S. C. Sealfon, S. H. Kleinstein
2010 Journal of Immunology  
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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