TargetFinder: searching annotated sequence databases for target genes of transcription factors (original) (raw)
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MATCHTM: a tool for searching transcription factor binding sites in DNA sequences
Nucleic Acids Research, 2003
Match TM is a weight matrix-based tool for searching putative transcription factor binding sites in DNA sequences. Match TM is closely interconnected and distributed together with the TRANSFAC 1 database. 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. Several sets of optimised matrix cutoff 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 cutoff values. Furthermore a number of tissue-specific profiles are provided that were compiled by the TRANSFAC 1
PromoterSweep: a tool for identification of transcription factor binding sites
Theoretical Chemistry Accounts, 2010
There are many tools available for the prediction of potential promoter regions and the transcription factor binding sites (TFBS) harboured by them. Unfortunately, these tools cannot really avoid the prediction of vast amounts of false positives, the greatest problem in promoter analysis. The combination of different methods and algorithms has shown an improvement in prediction accuracy for similar biological problems such as gene prediction. The web-tool presented here uses this approach to perform an exhaustive integrative analysis, identification and annotation of potential promoter regions. The combination of methods employed includes searches in different experimental promoter databases to identify promoter regions and their orthologs, use of TFBS databases and search tools, and a phylogenetic footprinting strategy, combining multiple alignment of genomic sequences together with motif discovery tools that were tested previously in order to get the best method combination. The pipeline is available for academic users at the HUSAR open server http://genius.embnet.dkfz-heidelberg.de/menu/ biounit/open-husar/. It integrates all of this information and identifies among the huge number of TFBS predictions those, which are more likely to be potentially functional.
xFITOM: a generic GUI tool to search for transcription factor binding sites
Bioinformation, 2010
Locating transcription factor binding sites in genomic sequences is a key step in deciphering transcription networks. Currently available software for site search is mostly server-based, limiting the range and flexibility of this type of analysis. xFITOM is a fully customizable program for locating binding sites in genomic sequences written in C++. Through an easy-to-use interface, xFITOM that allows users an unprecedented degree of flexibility in site search. Among other features,it enables users to define motifs by mixing real sites and IUPAC consensus sequences,to search the annotated sequences of unfinished genomes and to choose among 11 different search algorithms. XFITOM IS AVAILABLE FOR DOWNLOAD AT: http://research.umbc.edu/˜erill.
BioTechniques, 2013
While transcription factor (TF) binding affinity data generated by high-throughput techniques such as ChIP-seq has become increasingly available, a need remains for computational tools, especially for less-studied species and transcription factors. To facilitate and accelerate analyses, we developed LASAGNA-Search, an integrated user-friendly web tool for TF binding site (TFBS) search and visualization that combines existing and novel features. Important features include accepting unaligned variable-length binding sites, a collection of 1726 models, automatic promoter sequence retrieval, visualization in the UCSC Genome Browser, gene regulatory network inference, and visualization based on binding specificities. ®
Bioinformatics, 2014
LASAGNA-Search 2.0 is an integrated webtool for transcription factor (TF) binding site search and visualization. The tool is based on the LASAGNA (Length-Aware Site Alignment Guided by Nucleotide Association) algorithm. It eliminates manual TF model collection and promoter sequence retrieval. Search results can be visualized locally or in the University of California Santa Cruz Genome Browser. Gene regulatory network inference based on the search results offers another way of visualization. A list of TFs and target genes is all a user needs to start using the tool. LASAGNA-Search 2.0 currently offers 1792 TF models and supports 15 species for automatic promoter retrieval and visualization in the University of California Santa Cruz Genome Browser. It is a user-friendly tool designed for non-bioinformaticians and is suitable for research and teaching. We describe important changes made since the initial release. Availability and implementation: LASAGNA-Search 2.0 is freely available without registration at
The MAPPER database: a multi-genome catalog of putative transcription factor binding sites
Nucleic Acids Research, 2004
We describe a comprehensive map of putative transcription factor binding sites (TFBSs) across multiple genomes created using a search method that relies on hidden Markov models built from experimentally determined TFBSs. Using the information in the TRANSFAC and JASPAR databases, we built 1134 models for TFBSs and used them to scan regions 10 kb upstream of the start of the transcript for all known genes in the human, mouse and Drosophila melanogaster genomes. The results, together with homology information on clusters of ortholog genes across the three genomes, were used to create a multiorganism catalog of annotated TFBSs. The catalog can be queried through a web interface accessible at http://bio.chip.org/mapper that allows the identification, visualization and selection of TFBSs occurring in the promoter of a gene of interest and also the common factors predicted to bind across the cluster of orthologs that includes that gene. Alternatively, the interface allows the user to retrieve binding sites for a single transcription factor of interest in a single gene or in all genes of the human, mouse or fruit fly genomes.
The MAPPER2 Database: a multi-genome catalog of putative transcription factor binding sites
Nucleic Acids Research, 2011
The MAPPER 2 Database (http://genome.ufl.edu/ mapperdb) is a component of MAPPER 2 , a webbased system for the analysis of transcription factor binding sites in multiple genomes. The database contains predicted binding sites identified in the promoters of all human, mouse and Drosophila genes using 1017 probabilistic models representing over 600 different transcription factors. In this article we outline the current contents of the database and we describe its web-based user interface in detail. We then discuss ongoing work to extend the database contents to experimental data and to add analysis capabilities. Finally, we provide information about recent improvements to the hardware and software platform that MAPPER 2 is based on.
IMAGE: a new tool for the prediction of transcription factor binding sites
Bioinformatics and biology insights, 2008
IMAGE is an application tool, based on the vector quantization method, aiding the discovery of nucleotidic sequences corresponding to Transcription Factor binding sites. Starting from the knowledge of regulation regions of a number of co-expressed genes, the software is able to predict the occurrence of specific motifs of different lengths (starting from 6 base pairs) with a defined number of punctual mutations.
Interdisciplinary Sciences: Computational Life Sciences, 2016
Transcription factors are transacting proteins that interact with specific nucleotide sequences known as transcription factor binding site (TFBS), and these interactions are implicated in regulation of the gene expression. Regulation of transcriptional activation of a gene often involves multiple interactions of transcription factors with various sequence elements. Identification of these sequence elements is the first step in understanding the underlying molecular mechanism(s) that regulate the gene expression. For in silico identification of these sequence elements, we have developed an online computational tool named transcription factor information system (TFIS) for detecting TFBS for the first time using a collection of JAVA programs and is mainly based on TFBS detection using position weight matrix (PWM). The database used for obtaining position frequency matrices (PFM) is JASPAR and HOCOMOCO, which is an open-access database of transcription factor binding profiles. Pseudo-counts are used while converting PFM to PWM, and TFBS detection is carried out on the basis of percent score taken as threshold value. TFIS is equipped with advanced features such as direct sequence retrieving from NCBI database using gene identification number and accession number, detecting binding site for common TF in a batch of gene sequences, and TFBS detection after generating PWM from known raw binding sequences in addition to general detection methods. TFIS can detect the presence of potential TFBSs in both the directions at the same time. This feature increases its efficiency. And the results for this dual detection are presented in different colors specific to the orientation of the binding site. Results obtained by the TFIS are more detailed and specific to the detected TFs as integration of more informative links from various related web servers are added in the result pages like Gene Ontology, PAZAR database and Transcription Factor Encyclopedia in addition to NCBI and UniProt. Common TFs like SP1, AP1 and NF-KB of the Amyloid beta precursor gene is easily detected using TFIS along with multiple binding sites. In another scenario of embryonic developmental process, TFs of the FOX family (FOXL1 and FOXC1) were also identified. TFIS is platform-independent which is publicly available along with its support and documentation at http://tfistool.appspot.com and http:// www.bioinfoplus.com/tfis/. TFIS is licensed under the GNU General Public License, version 3 (GPL-3.0).
TF Target Mapper: A BLAST search tool for the identification of Transcription Factor target genes
BMC Bioinformatics, 2006
Background: In the current era of high throughput genomics a major challenge is the genome-wide identification of target genes for specific transcription factors. Chromatin immunoprecipitation (ChIP) allows the isolation of in vivo binding sites of transcription factors and provides a powerful tool for examining gene regulation. Crosslinked chromatin is immunoprecipitated with antibodies against specific transcription factors, thus enriching for sequences bound in vivo by these factors in the immunoprecipitated DNA. Cloning and sequencing the immunoprecipitated sequences allows identification of transcription factor target genes. Routinely, thousands of such sequenced clones are used in BLAST searches to map their exact location in the genome and the genes located in the vicinity. These genes represent potential targets of the transcription factor of interest. Such bioinformatics analysis is very laborious if performed manually and for this reason there is a need for developing bioinformatic tools to automate and facilitate it.