> Tag > Links tagged with 'transcription factors'

Links tagged with 'transcription factors'

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FANTOM - Functional Annotation of MouseDatabase Content

http://www.gsc.riken.go.jp/e/FANTOM/ [open in a new window]

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Model Organisms > Mouse and Rat

Functional annotations for RIKEN full-length cDNA clones.

links directory index: 3
TitlePublication YearGoogle Scholar Citation Count
Integrated analysis of the genome and the transcriptome by FANTOM20043
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tagsalgorithms animals chromosome mapping database management systems documentation genome mice phylogeny proteome sequence alignment sequence analysis systems integration transcription factors

FatiGOplusTool Content

http://www.fatigo.org/ [open in a new window]

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DNA > Annotations
Expression > Gene Regulation
Expression > Transcript Expression Analysis
Protein > Networks & Interactions, Pathways and Enzymes

FatiGOplus is a tool for the functional profiling of genome-scale experiments oriented to the interpretation of microarray experiments. As part of the Babelomics suite, FatiGOplus finds differential distributions of biological terms (GO, KEGG pathways, Interpro motifs, Transfac motifs, CisRed motifs, etc.) between two groups of genes.

links directory index: 1322
TitlePublication YearGoogle Scholar Citation Count
FatiGO +: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments2007150
BABELOMICS: a systems biology perspective in the functional annotation of genome-scale experiments2006215
BABELOMICS: a suite of web tools for functional annotation and analysis of groups of genes in high-throughput experiments2005204
FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes2004753
NAR Web Server Issue 2007
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tagsalgorithms amino acid motifs animals artificial intelligence binding sites chromosome mapping computational biology dna sequence analysis gene expression profiling genes genetic databases genomics humans mice oligonucleotide array sequence analysis phylogeny programming languages rats sequence alignment systems biology systems integration transcription factors

Filamentous Fungal Gene Expression Database (FFGED)Database Content

http://bioinfo.townsend.yale.edu/ [open in a new window]

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Expression > Databases
Model Organisms > Databases

The filamentous fungal gene expression database (FFGED) is a user-friendly management of gene expression data, which are assorted into experimental metadata, experimental design, raw data, normalized details, and analysis results. FFGED functions as a collective and collaborative platform, by connecting each experiment with similar related experiments made public by other users, and correlating diverse gene expression levels under multiple experimental designs within different experiments.

This content is being maintained by Jeffrey P. Townsend.

links directory index: 158
TitlePublication YearGoogle Scholar Citation Count
Transcriptional profiling of cross pathway control in Neurospora crassa and comparative analysis of the Gcn4 and CPC1 regulons200741
Enabling a community to dissect an organism: overview of the Neurospora functional genomics project200764
Long-oligomer microarray profiling in Neurospora crassa reveals the transcriptional program underlying biochemical and physiological events of conidial germination200553
NAR Web Server Issue 2005
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tagsalgorithms amitrole animals base sequence basic-leucine zipper transcription factors bayes theorem ChIP-seq chromosome mapping cluster analysis computational biology computer graphics database management systems dictyostelium dna-binding proteins enzyme inhibitors experimental design expressed sequence tags fungal dna fungal gene expression regulation fungal genes fungal genome fungal proteins fungal spores gene deletion gene expression gene expression profiling gene library genetic databases genetic models genetic promoter regions genetic techniques genetic transcription genomics internet messenger rna microarray molecular sequence data mutation neurospora neurospora crassa northern blotting nucleic acid databases oligonucleotide array sequence analysis oligonucleotide probes phenotype regulon related experiments reproducibility of results rna-seq saccharomyces cerevisiae saccharomyces cerevisiae proteins sequence alignment single nucleotide polymorphism software statistical models systems integration transcription factors user-computer interface ustilago

FlyFactorSurveyDatabase Content

http://pgfe.umassmed.edu/TFDBS/ [open in a new window]

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Model Organisms > Databases

FlyFactorSurvey is a database of DNA binding specificities for Drosophila transcription factors (TFs) determined using the bacterial one-hybrid system. The database provides to recognition motifs and position weight matrices for TFs. Search tools and flat file downloads are provided to retrieve binding site information (as sequences, matrices and sequence logos) for individual TFs, groups of TFs or for all TFs with characterized binding specificities. Linked analysis tools allow users to identify motifs within our database that share similarity to a query matrix or to view the distribution of occurrences of an individual motif throughout the Drosophila genome.

links directory index: 9
TitlePublication YearGoogle Scholar Citation Count
FlyFactorSurvey: a database of Drosophila transcription factor binding specificities determined using the bacterial one-hybrid system20119
NAR Database Issue 2011
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external linksLink on Wikipedia
tagsanimals bacteria binding sites drosophila drosophila proteins genetic databases transcription factors transcriptional regulatory elements two-hybrid system techniques

FlyTFDatabase Content

http://www.mrc-lmb.cam.ac.uk/genomes/FlyTF/old_index.html [open in a new window]

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Model Organisms > Databases

FlyTF is a database of computationally predicted and/or experimentally verified site-specific transcription factors (TFs) in the fruit fly Drosophila melanogaster. This database contains information on the manual curation of 1052 FlyBase identifiers, which are putative site-specific transcription factors, based on FlyBase/Gene Ontology annotation or the DBD Transcription Factor Database.

links directory index: 12
TitlePublication YearGoogle Scholar Citation Count
FlyTF: improved annotation and enhanced functionality of the Drosophila transcription factor database201012
NAR Database Issue 2010
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tagsanimals computational biology dna drosophila melanogaster drosophila proteins genetic databases genetic transcription nucleic acid databases protein databases tertiary protein structure transcription factors

FooterTool Content

http://biodev.hgen.pitt.edu/Footer/ [open in a new window]

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DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

Footer is a tool for identifying highly-probable binding sites of known transcription factors using phylogenetic footprinting principles to analyse two homologous DNA sequences.

links directory index: 26
TitlePublication YearGoogle Scholar Citation Count
FOOTER: a web tool for finding mammalian DNA regulatory regions using phylogenetic footprinting200526
NAR Web Server Issue 2005
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tagsalgorithms animals binding sites dna footprinting dna sequence analysis gene expression regulation genetic promoter regions mammals phylogeny transcription factors

GBrowseTool Content

http://gmod.org/wiki/Gbrowse [open in a new window]

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DNA > Annotations

GBrowse is a combination of database and interactive web pages for manipulating and displaying annotations on genomes.

links directory index: 727
TitlePublication YearGoogle Scholar Citation Count
The generic genome browser: a building block for a model organism system database2002727
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tagsanimals database management systems diptera drosophila melanogaster drosophila proteins genetic databases genome transcription factors

Genome SurveyorTool Content

http://veda.cs.uiuc.edu/gs [open in a new window]

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Expression > Gene Regulation
Model Organisms > Fly

Genome Surveyor is a tool for discovery and analysis of cis-regulatory elements and transcription factors in Drosphila built on the GBrowse genome browser.

links directory index: 3
TitlePublication YearGoogle Scholar Citation Count
Genome Surveyor 2.0: cis-regulatory analysis in Drosophila20113
NAR Web Server Issue 2011
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tagsanimals binding sites drosophila drosophila melanogaster insect genome transcription factors transcriptional regulatory elements

HHpredTool Content

http://protevo.eb.tuebingen.mpg.de/hhpred [open in a new window]

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Protein > 3-D Structure Comparison
Protein > 3-D Structure Prediction
Sequence Comparison > Similarity Searching and Classification

Based on the comparison of profile HMMs, HHpred takes a protein sequence or multiple sequence alignment as input and searches for remote homologues in an assortment of databases such as PDB, SMART and Pfam. The user can select either a local or global alignment method, and the search results can be used to generate 3D structural models.

links directory index: 539
TitlePublication YearGoogle Scholar Citation Count
The HHpred interactive server for protein homology detection and structure prediction2005539
NAR Web Server Issue 2005
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tagsamino acid sequence homology bacterial proteins markov chains protein conformation protein databases protein sequence analysis sequence alignment transcription factors

HLungDBDatabase Content

http://www.megabionet.org/bio/hlung/ [open in a new window]

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Human Genome > Databases

The human lung cancer database (HLungDB) is a database with the integration of the lung cancer-related genes, proteins and miRNAs together with the corresponding clinical information. Currently, we have collected 2585 genes and 212 miRNA with the experimental evidences involved in the different stages of lung carcinogenesis through text mining. The results from analysis of transcription factor-binding motifs, the promoters and the SNP sites for each gene are also included. Genes with epigenetic regulation were also included.

links directory index: 7
TitlePublication YearGoogle Scholar Citation Count
HLungDB: an integrated database of human lung cancer research20107
NAR Database Issue 2010
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tagsamino acid motifs computational biology gene regulatory networks genetic databases genetic epigenesis humans lung neoplasms micrornas neoplastic cell transformation nucleic acid databases protein databases transcription factors

iCRTool Content

http://210.212.215.199/icr/index.html [open in a new window]

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DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Protein > Networks & Interactions, Pathways and Enzymes

Identify Conserved targets of a Regulon (iCR) predicts regulatory binding sites based on conservation across multiple species. The user provides an ungapped multiple sequence alignment representing the regulatory binding site. iCR reports back with predicted binding sites that are conserved and highlights the downstream co-regulated genes.

links directory index: 48
TitlePublication YearGoogle Scholar Citation Count
iCR: a web tool to identify conserved targets of a regulatory protein across the multiple related prokaryotic species20064
PredictRegulon: a web server for the prediction of the regulatory protein binding sites and operons in prokaryote genomes200444
NAR Web Server Issue 2006
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tags5' flanking region bacterial genome bacterial proteins binding sites dna-binding proteins genomics mycobacterium tuberculosis nucleic acid regulatory sequences operon prokaryotic cells regulon sequence alignment serine endopeptidases transcription factors transcriptional regulatory elements

JASPARTool Content

http://jaspar.cgb.ki.se/cgi-bin/jaspar_db.pl [open in a new window]

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DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

JASPAR is a non-redundant, curated collection of transcription factor binding profiles. Each profile is generated from published, experimentally defined eukaryotic transcription factor binding sites.

links directory index: 716
TitlePublication YearGoogle Scholar Citation Count
JASPAR: an open-access database for eukaryotic transcription factor binding profiles2004716
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tagsanimals base sequence binding sites computational biology dna eukaryotic cells genetic transcription humans molecular sequence data nucleic acid databases response elements transcription factors

JASPARDatabase Content

http://jaspar.cgb.ki.se [open in a new window]

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DNA > Databases
Expression > Databases

JASPAR is an open-access database of matrix profiles describing the DNA-binding patterns of transcription factors (TFs) and other proteins interacting with DNA in a sequence-specific manner. The database now holds 457 non-redundant, curated profiles. The new entries include the first batch of profiles derived from ChIP-seq and ChIP-chip whole-genome binding experiments, and 177 yeast TF binding profiles. Classification of TF families has been improved by adopting a new DNA-binding domain nomenclature. A curated catalog of mammalian TFs is provided, extending the use of the JASPAR profiles to additional TFs belonging to the same structural family.

links directory index: 119
TitlePublication YearGoogle Scholar Citation Count
JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles2010119
NAR Database Issue 2010
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tagsalgorithms animals chromatin immunoprecipitation computational biology fungal proteins genetic databases genome humans nucleic acid databases protein binding protein databases transcription factors

MAPPER2 DatabaseDatabase Content

http://genome.ufl.edu/mapperdb [open in a new window]

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DNA > Databases
Expression > Gene Regulation
Model Organisms > Databases
Model Organisms > Fly
Model Organisms > Mouse and Rat

The MAPPER Database contains putative Transcription Factor Binding Sites (TFBSs) located in the upstream sequences of genes from the human, mouse and D.melanogaster genomes.

links directory index: 192
TitlePublication YearGoogle Scholar Citation Count
The MAPPER2 Database: a multi-genome catalog of putative transcription factor binding sites.20120
MAPPER: a search engine for the computational identification of putative transcription factor binding sites in multiple genomes2005132
The MAPPER database: a multi-genome catalog of putative transcription factor binding sites200560
NAR Web Server Issue 2005
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tagsalgorithms animals base sequence binding sites cell cycle proteins computational biology drosophila melanogaster gene expression regulation gene library genetic databases genetic promoter regions genetic transcription genome genomics humans markov chains mice molecular evolution nucleic acid databases programming languages protein binding protein databases sequence alignment transcription factors

MatchTool Content

http://www.gene-regulation.com/pub/programs.html#match [open in a new window]

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DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

Match is a weight matrix-based tool which searches for putative transcription factor binding sites (TFBS) in DNA sequences. Registration at the site is free and is required to use Match.

links directory index: 591
TitlePublication YearGoogle Scholar Citation Count
MATCH: A tool for searching transcription factor binding sites in DNA sequences2003591
NAR Web Server Issue 2003
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tagsalgorithms binding sites dna sequence analysis nucleic acid regulatory sequences transcription factors

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