http://bioinformatics.ca/links_directory/tag/genetic-transcriptionhttp://bioinformatics.ca/links_directory/tag/genetic-transcription/feed en http://tap.med.utoronto.ca/mts/Global survey of organ and organelle protein expression in mouse: combined proteomic and transcriptomic profiling. This molecular compendium, fully accessible via a searchable web-browser interface, serves as a reliable reference of the expressed tissue and organelle proteomes of a leading model mammal.13425Tue, 14 May 2013 13:20:23 -0400 http://genome.ufl.edu/mapperdbThe MAPPER Database contains putative Transcription Factor Binding Sites (TFBSs) located in the upstream sequences of genes from the human, mouse and D.melanogaster genomes.13366Fri, 17 May 2013 22:20:38 -0400 http://www.polygenicpathways.co.ukThe datasets list genes, environmental risk factors and autoantibodies in a number of polygenic diseases and provide KEGG pathway analysis etched out by susceptibility genes. Host/pathogen interactions are also characterised for herpes simplex, helicobacter pylori and the HIV-1/AIDS virus.12756Mon, 13 May 2013 23:20:26 -0400 http://comparative-legumes.org/The Legume Information System enables productive applied and basic research in the legumes by relating data from multiple crop and model species, and by helping researchers traverse among various data types.12652Fri, 17 May 2013 22:50:38 -0400 http://bioinfo.townsend.yale.edu/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.12246Sun, 12 May 2013 06:10:21 -0400 http://www.dsimb.inserm.fr/dsimb_tools/mitgene/MitoGenesisDB focuses on the dynamic of mitochondrial protein formation through global mRNA analyses. Three main parameters confer a global view of mitochondrial biogenesis: (i) time-course of mRNA production in highly synchronized yeast cell cultures, (ii) microarray analyses of mRNA localization that define translation sites and (iii) mRNA transcription rate and stability which characterize genes that are more dependent on post-transcriptional regulation processes. MitoGenesisDB integrates and establishes cross-comparisons between these data. Several model organisms can be analyzed via orthologous relationships between interspecies genes.11936Sat, 18 May 2013 04:00:31 -0400 http://cbrc.kaust.edu.sa/tcof/TcoF is a database that facilitates the exploration of proteins involved in the regulation of transcription in humans by binding to regulatory DNA regions (transcription factors) and proteins involved in the regulation of transcription in humans by interacting with transcription factors and not binding to regulatory DNA regions (transcription co-factors). Proteins can be searched by a variety of identifiers or predefined sets of proteins can be viewed. 11900Wed, 15 May 2013 09:50:18 -0400 http://www.yeastract.comThe YEAst Search for Transcriptional Regulators And Consensus Tracking (YEASTRACT) is a curated repository of regulatory associations between transcription factors (TF) and target genes in Saccharomyces cerevisiae. YEASTRACT includes DISCOVERER, a set of tools that can be used to identify complex motifs found to be over-represented in the promoter regions of co-regulated genes. EASTRACT allows the identification of documented or potential transcription regulators of a given gene and of documented or potential regulons for each transcription factor. It also renders possible the comparison between DNA motifs and the transcription factor binding sites described in the literature. YEASTRACT provides a set of queries to search and retrieve important biological information from the gathered data and to predict transcription regulation networks in yeast from data emerging from gene-by-gene analysis or global approaches. 11893Fri, 17 May 2013 15:00:14 -0400 http://regulondb.ccg.unam.mx/RegulonDB is a reference database of Escherichia coli K-12. Transcriptional regulation is now part of a unit that initiates with the signal and continues with the signal transduction to the core of regulation, modifying expression of the affected target genes responsible for the response. RegulonDB has summaries for every transcription factor (TF) and TF-binding sites with internal symmetry. In addition to data from the literature, we have incorporated our own information on transcription start sites (TSSs) and transcriptional units (TUs), obtained by using high-throughput whole-genome sequencing technologies. A new portable drawing tool for genomic features is also now available, as well as new ways to download the data, including web services, files for several relational database manager systems and text files including BioPAX format.11848Wed, 15 May 2013 10:20:34 -0400 http://fantom.gsc.riken.jp/4/The Functional Annotation Of the Mammalian Genome (FANTOM) is a database for the transcriptional network that regulates macrophage differentiation. Data comes from cap analysis of gene expression (CAGE), sequencing mRNA 5'-ends with a second-generation sequencer to quantify promoter activities even in the absence of gene annotation. Additional genome-wide experiments complement the setup including short RNA sequencing, microarray gene expression profiling on large-scale perturbation experiments and ChIP-chip for epigenetic marks and transcription factors.11802Thu, 16 May 2013 08:00:21 -0400 http://www.mrc-lmb.cam.ac.uk/genomes/FlyTF/old_index.htmlFlyTF 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.11687Wed, 15 May 2013 21:50:21 -0400 http://www.cancergenetics.med.ohio-state.edu/The website of the Ohio State University Human Cancer Genetics Bioinformatics group. This site has many resources, including databases of promoters and transcription factors, software tools to predict potential P53 consensus binding sites and to predict first exon and promoter regions and a software toolkit for developing web-based applications to view genomic data.11283Thu, 16 May 2013 04:00:26 -0400 http://bayesweb.wadsworth.org/phyloscan/Phyloscan is a web server that locates transcription regulating binding sites by exploiting binding site evolutionary conservation and repeats in promoter regions. Mixed aligned and unaligned sequence data may be used.10637Sat, 18 May 2013 01:20:43 -0400 http://web.bioinformatics.cicbiogune.es/microRNA/miRanalyzer is a web server tool for the analysis of high throughput sequencing experiments for microRNAs. Users input a list of unique reads and copy number. The tool detects all known microRNA sequences annotated in miRBase, finds perfect matches in other libraries of transcribed sequences and predicts new microRNAs. Alignments are based on Bowtie and differences between plant and animal microRNAs are accounted for in prediction.10593Fri, 17 May 2013 19:00:12 -0400 http://berry.engin.umich.edu/oligoarray2_1/OligoArray is free software that computes gene specific oligonucleotides for genome-scale oligonucleotide microarray construction. A database of pre-designed oligonucleotide microarray probes for organisms with a fully sequenced genome can be found at http://berry.engin.umich.edu/oligoarraydb/index.html10510Wed, 15 May 2013 07:30:28 -0400 http://bioinformatics.wustl.edu/webTools/portalModule/PromoterSearch.doPromoter Analysis Pipeline (PAP) can identify potential transcriptional regulators for sets of co-expressed genes and identify potential regulatory targets of transcription factors.10428Wed, 15 May 2013 15:30:23 -0400 http://jbirc.jbic.or.jp/tact/Transcriptome Auto-annotation Conducting Tool (TACT) is an automated tool for conducting functional annotation of transcripts that integrates sequence similarity searches and functional motif predictions. TACT was originally developed as an automatic annotation pipeline for the Human Full-length cDNA Annotation Invitational (H-Inv) project.10291Wed, 15 May 2013 11:30:23 -0400 http://its2.bioapps.biozentrum.uni-wuerzburg.de/The Internal Transcribed Spacer 2 Database (ITS2) includes a homology based RNA structure prediction algorithm which allows the detection and secondary structure prediction of ITS2 sequences. This resource also contains more than 25,000 pre-calculated secondary structures for currently known ITS2 sequences that can be searched and browsed via taxonomy.10290Sun, 12 May 2013 08:00:14 -0400 http://www.scripps.edu/mb/barbas/zfdesign/zfdesignhome.phpZinc Finger Tools provides several tools for selecting zinc finger protein target sites and for designing the proteins that will target them.10224Sat, 18 May 2013 02:00:15 -0400 http://cubic.bioc.columbia.edu/services/NORSp/NORSp (predictor of NOn-Regular Secondary Structure) is a tool for predicting disordered regions in proteins.10178Thu, 16 May 2013 11:20:28 -0400 http://bips.u-strasbg.fr/PipeAlign/PipeAlign takes one or more protein sequences as input and analyzes them in a five-step process during which searches for sequence homologues, analyses of multiple sequence alignments, and hierarchical relationships between protein subfamilies are performed.10177Sat, 18 May 2013 00:20:54 -0400 http://bioportal.weizmann.ac.il/~lapidotm/rMotif/html/rMotif provides tools for the discovery of de-novo, fully, or partially characterized regulatory motifs including transcription factor binding sites (TFBS).10164Fri, 17 May 2013 15:10:36 -0400 http://bussemaker.bio.columbia.edu/reduce/REDUCE uses a motif-based regression method for the identification of TFBS (transcription factor binding sites) from microarray data in yeast, worm and fly. A free registration is required.10143Fri, 17 May 2013 08:00:12 -0400 http://rsat.ccb.sickkids.ca/Regulatory Sequence Analysis Tools (RSAT) detects regulatory signals in non-coding sequences; tools include sequence retrieval, pattern discovery, pattern matching, genome-scale pattern matching, feature-map drawing, random sequence generation and other utilities. Tools may be accessed separately or connected to other tools. As well, the tools are available as web services for integration into programmatic work flows. New tools incorporated include an automated sequence retrieval from EnsEMBL, motif comparison and motif quality tools, and the capacity to process ChIP-sequence data.10112Fri, 17 May 2013 01:40:25 -0400 http://visant.bu.edu/VisANT is an integrative visual analysis tool for biological networks and pathways that contains modules for querying and integrating KEGG pathways with expression data. VisANT is java-based, and can be run as a java applet, as a java web application, or downloaded and run locally. New functions in VisANT 3.5 allow determination of over-representation and expression enrichment.10070Mon, 13 May 2013 20:00:07 -0400 http://www.cbs.dtu.dk/services/OligoWiz2/OligoWiz 2.0 is a client for microarray probe design that allows for the integration of sequence annotations, probe quality parameters, and the placement of multiple probes per transcript.10017Fri, 17 May 2013 06:20:29 -0400 http://hscl.cimr.cam.ac.uk/TFBScluster_genome_portal.htmlTFBScluster is a web tool designed to identify clusters of transcription factor binding sites (TFBSs) conserved in mammalian and mouse genomes. By entering a specified range of TFBS, you can retrieve a list of SWISS-PROT characterized genes to which the clusters are localized.9895Fri, 17 May 2013 04:00:14 -0400 http://robotics.stanford.edu/~xsliu/MDscan/Server designed to pinpoint protein-DNA interaction sites at the base pair level. Uses ChIP-array data, word enumeration and position-specific weight matrix updating to search for motifs representing these interaction sites.9870Wed, 15 May 2013 06:40:16 -0400 http://jaspar.cgb.ki.se/cgi-bin/jaspar_db.plJASPAR is a non-redundant, curated collection of transcription factor binding profiles. Each profile is generated from published, experimentally defined eukaryotic transcription factor binding sites.9802Wed, 15 May 2013 14:00:20 -0400 http://genes.mit.edu/GENSCAN.htmlIdentification of complete gene structures in genomic DNA.9492Thu, 16 May 2013 10:00:29 -0400 http://cpc.cbi.pku.edu.cn/programs/run_cpc.jspCPC (Coding Potential Calculator) distinguishes protein-coding from non-coding RNAs based on the sequence features of the input transcripts.9381Mon, 13 May 2013 09:10:12 -0400 http://compareprospector.stanford.edu/Server which attempts to identify any motifs related to genes predicted to share regulatory elements. It alters Gibbs sampling through biasing searches towards conserved sequences across multiple species.9367Mon, 13 May 2013 19:00:12 -0400 http://zlab.bu.edu/CARRIE-webServer which analyzes microarray and promoter sequence data associated with a response to a specific stimulus. After analysis a potential transcriptional regulatory network is created. CARRIE also determines which transcription factors were likely involved in regulation and which genes they regulated.9302Fri, 17 May 2013 21:20:27 -0400 http://robotics.stanford.edu/~xsliu/BioProspector/Server which scans upstream of genes in the same gene expression cluster for regulatory sequence motifs using a Gibbs sampling strategy. The Markov background model is used for non-motif bases, improving specificity of predicted motif locations.9289Sun, 12 May 2013 20:20:10 -0400 http://statgen.ncsu.edu/asg/The Alternative Splicing Gallery (ASG) takes an identifier such as an EnsEMBL gene ID or a RefSeq ID as input, and provides a graph mapping splice events to transcript information. The user can also view GO information for the record, and select one or more exons and download the resulting sequence. ASG also links out to other alternative splicing databases like ProSplicer.9228Sat, 18 May 2013 02:00:36 -0400