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IDENTIFICATION OF OVER-REPRESENTED COMBINATIONS OF TRANSCRIPTION FACTOR BINDING SITES IN SETS OF CO-EXPRESSED GENES

SHAO-SHAN HUANG, DEBRA L. FULTON, DAVID J. ARENILLAS, PAUL PERCO, SHANNAN J. HO SUI, JAMES R. MORTIMER, WYETH W. WASSERMAN
2005 Proceedings of the 4th Asia-Pacific Bioinformatics Conference  
The oPOSSUM analysis system facilitates the interpretation of gene expression data through the analysis of transcription factor binding sites shared by sets of co-expressed genes.  ...  We introduce a new set of analysis algorithms for the study of the combinatorial properties of transcription factor binding sites shared by sets of co-expressed genes.  ...  Acknowledgments We thank Andrew Kwon for annotation of the muscle reference collections.  ... 
doi:10.1142/9781860947292_0028 fatcat:ojgcxmfmorfvhiho6uqnmlqydm

Identification of Transcription Factor Binding Sites Upstream of Human Genes Regulated by the Phosphatidylinositol 3-Kinase and MEK/ERK Signaling Pathways

John W. Tullai, Michael E. Schaffer, Steven Mullenbrock, Simon Kasif, Geoffrey M. Cooper
2004 Journal of Biological Chemistry  
Binding sites for 18 computationally predicted transcription factors were over-represented in the four groups of co-expressed genes compared with the background sequences (p < 0.01).  ...  We have taken an integrated approach in which expression profiling has been combined with the use of small molecule inhibitors and computational analysis of transcription factor binding sites to characterize  ...  Acknowledgments-We thank Ulla Hansen, Zhiping Weng, and Stan Letovsky for helpful discussions and critical review of the article.  ... 
doi:10.1074/jbc.m309260200 pmid:14769801 fatcat:ywebcw4hyrgall544ip4ngue7e

Recent advances in computational promoter analysis in understanding the transcriptional regulatory network

Ping Qiu
2003 Biochemical and Biophysical Research Communications - BBRC  
In this review, current computational approaches for understanding the transcriptional regulatory network, including promoter prediction, transcription factor binding site identification, combinatorial  ...  regulatory elements prediction, and transcription factor target gene identification, are discussed.  ...  I apologize for those wonderful works that have not been cited by the review due to the limit of space.  ... 
doi:10.1016/j.bbrc.2003.08.052 pmid:12963016 fatcat:ssdhqwzrh5hb5cz67euj23l7i4

GPMiner: an integrated system for mining combinatorial cis-regulatory elements in mammalian gene group

Tzong-Yi Lee, Wen-Chi Chang, Justin Hsu, Tzu-Hao Chang, Dray-Ming Shien
2012 BMC Genomics  
Although numerous computational methods have been developed for predicting transcriptional start sites (TSSs) or transcription factor (TF) binding sites (TFBSs), they lack annotations for do not consider  ...  Results: This work identifies TSSs and regulatory features in a promoter sequence, and recognizes co-occurrence of cis-regulatory elements in co-expressed genes using a novel system.  ...  prediction specificity > 70% Transcription factor (TF) binding site TRANSFAC public release 7.0 [46] Storing the experimentally verified transcription factors, their genomic binding sites and  ... 
doi:10.1186/1471-2164-13-s1-s3 pmid:22369687 pmcid:PMC3587379 fatcat:xi4guhr4hbbypn2sjpb2pjrkf4

In Silico Identification of Regulatory Elements in Promoters [chapter]

Vikrant Nain, Shakti Sahi, Polumetla Ananda
2011 Computational Biology and Applied Bioinformatics  
It can be used for detection of significant transcription factor binding sites from comparative genomics data or for detection of combinations of binding sites in sets of co expressed/co regulated genes  ...  Pscan Pscan is a software tool that scans a set of sequences (e.g. promoters) from co-regulated or co-expressed genes with motifs describing the binding specificity of known transcription factors (Zambelli  ...  , and correlate huge data sets of complex information.  ... 
doi:10.5772/22230 fatcat:wcruf4x7bvcsbaszaknsiejuxy

A NOVEL STRATEGY TO SEARCH CONSERVED TRANSCRIPTION FACTOR BINDING SITES AMONG COEXPRESSING GENES IN HUMAN

YOSUKE HATANAKA, MASAO NAGASAKI, RUI YAMAGUCHI, TAKESHI OBAYASHI, KAZUYUKI NUMATA, ANDRÉ FUJITA, TEPPEI SHIMAMURA, YOSHINORI TAMADA, SEIYA IMOTO, KENGO KINOSHITA, KENTA NAKAI, SATORU MIYANO
2008 Genome Informatics Series  
We report various transcription factor binding sites (TFBSs) conserved among co-expressed genes in human promoter region using expression and genomic data.  ...  Assuming similar promoter structure induces similar transcriptional regulation, hence induces similar expression profile, we compared the promoter structure similarities between co-expressed genes.  ...  Then, examination of the promoter region of genes in the same expression pattern group and look for common sequence motifs , namely transcriptional regulatory sites (transcription factor binding sites)  ... 
doi:10.11234/gi1990.20.212 fatcat:7u6ytvdovbcjndidvdmoyhyv5e

RgS-Miner: A Biological Data Warehousing, Analyzing and Mining System for Identifying Transcriptional Regulatory Sites in Human Genome [chapter]

Yi-Ming Sun, Hsien-Da Huang, Jorng-Tzong Horng, Shir-Ly Huang, Ann-Ping Tsou
2004 Lecture Notes in Computer Science  
We present an integrated system, namely RgS-Miner, to predict transcriptional regulatory sites and detect co-occurrence of these regulatory sites.  ...  Recently, biological databases and analytical methods have become available for analyzing gene expression and transcriptional regulatory sequences.  ...  Acknowledgements The authors would like to thank the National Science Council of the Republic of China for financially supporting this research under Contract No. NSC93-3112-B-008-002. Prof.  ... 
doi:10.1007/978-3-540-30075-5_72 fatcat:lnntr6t64rf6hdzyzplubuwpbe

oPOSSUM: identification of over-represented transcription factor binding sites in co-expressed genes

S. J. Ho Sui
2005 Nucleic Acids Research  
promoters with statistical methods for identification of sites over-represented in a set of co-expressed genes.  ...  Similar methods for the identification of over-represented transcription factor binding sites (TFBSs) have been successful in yeast, but extension to human genomics has largely proved ineffective.  ...  This work was supported by the CIHR/MSF Strategic Training Program in Bioinformatics, the National Science and Engineering Research Council of Canada (NSERC) and Merck-Frosst, as well as a grant from the  ... 
doi:10.1093/nar/gki624 pmid:15933209 pmcid:PMC1142402 fatcat:3xqtwlnowbgmjhf3pw2zrin7ay

PathoPlant(R): a platform for microarray expression data to analyze co-regulated genes involved in plant defense responses

L. Bulow, M. Schindler, R. Hehl
2007 Nucleic Acids Research  
Plants react to pathogen attack by expressing specific proteins directed toward the infecting pathogens. This involves the transcriptional activation of specific gene sets.  ...  New web tools enable identification of plant genes regulated by specific stimuli. Sets of genes coregulated by multiple stimuli can be displayed as well.  ...  Conflict of interest statement. None declared.  ... 
doi:10.1093/nar/gkl835 pmid:17099232 pmcid:PMC1669748 fatcat:hofoan6cqrddfaj43kriimhpe4

Transcriptional programs: Modelling higher order structure in transcriptional control

John E Reid, Sascha Ott, Lorenz Wernisch
2009 BMC Bioinformatics  
It simultaneously predicts which genes are co-regulated and which sets of transcription factors cooperate to achieve this co-regulation.  ...  The method is independent of prior specification of training sets of genes, for example, via gene expression data. The analysis is based on known binding motifs.  ...  Acknowledgements We thank Georgy Koentges for many stimulating discussions about TFBS search techniques and the cooperative effects of transcription factors.  ... 
doi:10.1186/1471-2105-10-218 pmid:19607663 pmcid:PMC2725141 fatcat:h6gvr7ttjrcctf5denypsnh6wu

oPOSSUM: integrated tools for analysis of regulatory motif over-representation

Shannan J. Ho Sui, Debra L. Fulton, David J. Arenillas, Andrew T. Kwon, Wyeth W. Wasserman
2007 Nucleic Acids Research  
The identification of over-represented transcription factor binding sites from sets of co-expressed genes provides insights into the mechanisms of regulation for diverse biological contexts. oPOSSUM, an  ...  combinations of motifs in human and mouse genes, has been integrated with the original oPOSSUM system.  ...  (2) address the detection of over-represented sets of TFBSs in the promoters of a set of co-expressed genes.  ... 
doi:10.1093/nar/gkm427 pmid:17576675 pmcid:PMC1933229 fatcat:vcu2fhohdvdenlw5opvswxdemi

PlantPAN: Plant promoter analysis navigator, for identifying combinatorial cis-regulatory elements with distance constraint in plant gene groups

Wen-Chi Chang, Tzong-Yi Lee, Hsien-Da Huang, His-Yuan Huang, Rong-Long Pan
2008 BMC Genomics  
Therefore, a tool for detecting the co-regulation of transcription factors in a group of gene promoters is required.  ...  , enabling the co-occurrence of combinatorial transcription factor binding sites (TFBSs) within a defined distance (20 bp to 200 bp) to be identified.  ...  Acknowledgements The authors would like to thank the National Science Council of the Republic of China, Taiwan  ... 
doi:10.1186/1471-2164-9-561 pmid:19036138 pmcid:PMC2633311 fatcat:5ul4oiycbvaslkom5kppnphyf4

Integrating genomic data to predict transcription factor binding

Dustin T Holloway, Mark Kon, Charles DeLisi
2005 Genome Informatics Series  
Gene expression takes into account the idea that when the gene expression profiles of a transcription factor and a potential target gene are correlated, then it is more likely that the gene is a genuine  ...  Transcription factor binding sites (TFBS) in gene promoter regions are often predicted by using position specific scoring matrices (PSSMs), which summarize sequence patterns of experimentally determined  ...  D m n ) represent a set of TF motif frequencies for gene m, over n transcription factors (n=104).  ... 
pmid:16362910 fatcat:nopywrbj3nbxfpyuo7gprqh77m

Bound to Succeed: Transcription Factor Binding-site Prediction and Its Contribution to Understanding Virulence and Environmental Adaptation in Bacterial Plant Pathogens

Surya Saha, Magdalen Lindeberg
2013 Molecular Plant-Microbe Interactions  
Prediction of transcription factor binding sites represents an important tool for  ...  Bacterial plant pathogens rely on a battalion of transcription factors to fine-tune their response to changing environmental conditions and marshal the genetic resources required for successful pathogenesis  ...  RpoN-dependent gene expression relies on enhancer binding proteins, co-expression of which is required for induction.  ... 
doi:10.1094/mpmi-04-13-0090-cr pmid:23802990 fatcat:wq7pgpu2x5g45kniwxcpqnvgtu

Systematic identification of mammalian regulatory motifs' target genes and functions

Jason B Warner, Anthony A Philippakis, Savina A Jaeger, Fangxue Sherry He, Jolinta Lin, Martha L Bulyk
2008 Nature Methods  
factors whose DNA binding specificities are known and a set of genes that the transcription factors may regulate 2,3,7,8 , or on the computational identification of 'motif dictionaries' 9-12 .  ...  The ability to screen many gene sets with many motifs or motif combinations allows us to tackle the difficulty in a priori identification of co-regulated gene sets.  ...  The ability to screen many gene sets with many motifs or motif combinations allows us to tackle the difficulty in a priori identification of co-regulated gene sets.  ... 
doi:10.1038/nmeth.1188 pmid:18311145 pmcid:PMC2708972 fatcat:y2h7pgfuungvdclmgovitlfbju
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