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JASPAR
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Offers a collection of extensively curated, non-redundant profiles collected from published collections of Transcription Factors Binding Sites (TFBS) from multicellular eukaryotes. JASPAR provides a web portal that provides a graphical interface for casual users, enabling browsing and database search functions, as well as basic sequence search functionality for selected profiles. It can also be used for seeking models for specific factors or structural classes, or if experimental evidence is paramount.
AthaMap
Generates a map of predicted transcription factor binding sites (TFBS) and small RNA target sites for the whole Arabidopsis thaliana genome. AthaMap can be used for bioinformatic predictions of putative regulatory sites. Several online web tools are available that address specific questions. Starting with the identification of transcription factor-binding sites (TFBS) in any gene of interest, colocalizing TFBS can be identified as well as common TFBS in a set of user-provided genes. Furthermore, genes can be identified that are potentially targeted by specific transcription factors or small inhibitory RNAs.
CIS-BP / Catalog of Inferred Sequence Binding Preferences
A freely available online database of transcription factor (TF) inferred binding specificities. CIS-BP currently incorporates data from >300 species covering >250 TF families, totaling >160,000 TFs (of which, >65,000 have at least one DNA binding motif). CisBP collects data from >25 sources, including other database such as Transfac, JASPAR, HOCOMOCO, FactorBook, UniProbe, Fly Factor Survey, and dozens of additional publications. In addition to housing these “directly determined” DNA binding motifs, CisBP also includes “inferred” motifs. Inferences are performed by mapping motifs across and within species, using DNA binding domain similarity thresholds established separately for each TF family (see publication for details). In other words, if a mouse TF has a known motif, we can infer its human ortholog’s motif, provided that the ortholog’s DNA binding domain is “similar enough”.
UniPROBE / Universal PBM Resource for Oligonucleotide Binding Evaluation
Gathers data about in vitro DNA binding specificities of proteins. UniPROBE is a database including DNA binding data about more than 500 non-redundant proteins and complexes from various organisms generated by using universal protein-binding microarray (PBM) technology. It provides information related to k-mers, position weight matrices and graphical sequence logos. Searches can be made by text search, similar motifs or by transcription factor (TF) sites.
DBTSS / DataBase of Transcriptional Start Sites
It was originally constructed as a collection of uniquely determined transcriptional start sites (TSSs) in humans and some other species in 2002. Since then, DBTSS has been regularly updated and in recent updates epigenetic information has also been incorporated because such information is useful for characterizing the biological relevance of these TSSs/downstream genes. DBTSS is no longer a mere storage site for TSS information but has evolved into an integrative platform of a variety of genome activity data.
HOCOMOCO / HOmo sapiens COmprehensive MOdel COllection
Provides non-redundant curated binding models. HOCOMOCO is a comprehensive and carefully hand-curated collection of Transcription Factors Binding Sites (TFBS) models with reduced redundancy of model associations to individual transcription factor (TF). This website provides a system of interactive filters making it easier to browse the tables of the collection. To facilitate a practical application, all models are linked to gene and protein databases.
AtcisDB / Arabidopsis cis-regulatory element database
Compiles cis-regulatory information related to Arabidopsis thaliana. AtcisDB gathers data relative to transcription factor binding site information, promoter sequence and related annotations. Searches can be made by gene symbol or locus ID and displays a chart that give access to a gene description, chromosome location, promoter sequence, type and sources as well as information about the regulatory network. The totality of the database can be downloaded in zip format.
TRRD / Transcription Regulatory Regions Database
New
Provides a description of the structure–function organization of transcription regulatory regions of eukaryotic genes. TRRD is a resource that comprises height databases linked with cross-references: TRRDGENES (general gene description), TRRDLCR (locus control regions); TRRDUNITS (regulatory regions: promoters, enhancers, silencers, etc.), TRRDSITES (transcription factor binding sites), TRRDFACTORS (transcription factors), TRRDEXP (expression patterns), TRRDBIB (bibliography) and TRRDSTARTS (transcription initiation starts of gene). It can be useful for researchers involved in several branches of molecular biology, genetics, pharmacology, biotechnology and biomedicine.
ENCODE-motifs
A database that uncovers the molecular basis of TF binding in the human genome based on regulatory motif analysis of all Transcription Factors (TFs) grouped by family. This allows browsing of all known motifs for each factor, curated from TRANSFAC, Jaspar, and Protein Binding Microarray (PBM) experiments, and their enrichment and instances within corresponding TF binding experiments. It also provides a list of novel regulatory motifs discovered by systematic application of several motif discovery tools (including MEME, MDscan, Weeder, AlignACE) and evaluated based on their enrichment relative to control motifs within TF-bound regions. ENCODE-motifs also provides a genome-wide map of regulatory motif instances in the human genome for both known and novel motifs.
ABS / Annotated regulatory Binding Sites
A public database of known binding sites identified in promoters of orthologous vertebrate genes that have been manually curated from bibliography. ABS lists 650 experimental binding sites from 68 transcription factors and 100 orthologous target genes in human, mouse, rat or chicken genome sequences. Computational predictions and promoter alignment information are also provided for each entry. A simple and easy-to-use web interface facilitates data retrieval allowing different views of the information. In addition, the release 1.0 of ABS includes a customizable generator of artificial datasets based on the known sites contained in the collection and an evaluation tool to aid during the training and the assessment of motif-finding programs.
TFBSshape
Provides DNA shape features for transcription factor binding sites (TFBSs) that in addition to sequence features, usually in the form of position weight matrices (PWMs), characterize DNA binding specificities of transcription factors (TFs) from 23 different species. The DNA shape features were visualized in the form of heat maps. Users can download these DNA shape feature data and perform further analysis, for example, to identify which DNA shape feature(s) at which position(s) in the target DNA contribute to the DNA binding specificity of a TF.
SBR-Blood / hematopoietic Systems Biology Repository
Enables the user to conduct cell type correlations with previously published data sets and data sets currently under investigation. By reproducing concepts manually validated in the community, it has been shown to be correct in terms of functionality (using the integrated data to confirm established knowledge) and provides a useful resource for studying epigenetic profile changes during stem cell differentiation. The structure of SBR-Blood makes it highly adaptable and can support different organisms and biological systems. In particular, SBR-Blood is an excellent tool to compare transcription and epigenetic regulation profiles.
BloodChIP
A user friendly database that integrates genome-wide binding profiles of haematopoietic transcription factors in human blood cell types with chromatin accessibility profiles from the Human Epigenome Atlas and corresponding gene expression. An interactive web interface allows users to query BloodChIP and ascertain the relative expression level of their genes across different cell types. Importantly, the user is then able to associate expression levels in these cell fractions with chromatin accessibility and transcription factor binding profiles in primary human HSPCs and other cell types to gain insights into the transcriptional regulation of these genes. The database supports exploration and selection based on either genes or transcription factors of interest. All queries, as well as the complete database, can be exported by the user for further data analysis.
GTRD / Gene Transcription Regulation Database
Contains information on location in genome, structured information about cell lines and experimental conditions extracted from descriptions of corresponding ChIP-seq experiments. GTRD provides: (i) browsing and displaying information; (ii) advanced search possibilities; (iii) integrated genome browser that provides visualization of the GTRD data: read alignments, peaks, clusters, metaclusters and information about gene structures from the Ensembl database and binding sites predicted using position weight matrices from the HOCOMOCO database.
PlantDHS
A plant DNase I hypersensitive site (DHS) database that integrates histone modification, RNA sequencing, nucleosome positioning/occupancy, transcription factor binding sites, and genomic sequence within an easily navigated user interface. DHSs are indicative of all CREs, including promoters, enhancers, silencers, insulators and transcription factor binding sites; all of which play immense roles in global gene expression regulation. PlantDHS provides a platform to predict all CREs associated with individual genes from three model plant species, including Arabidopsis thaliana, Brachypodium distachyon and rice (Oryza sativa). PlantDHS is especially valuable in the detection of distant CREs that are located away from promoters.
CardioSignal
Provides online analysis tools to speeding up hypothesis-driven research in gene regulation. CardioSignal was designed for integration of regulatory information on the transcriptional regulation involved in heart development and cardiac hypertrophy. This database contains 677 cardiac genes from twenty species. Among them are 128 cardiac transcription factors. Of the approximately 179 individual promoters from six species, the database also documented 247 experimentally verified binding sites and 64 cisregulatory modules.
YY1TargetDB
Annotates and organizes YY1-binding loci and target motifs in a systematic way with easy access. YY1TargetDB is a web-based relational database which collects YY1 binding loci from high-throughput experiments (ChIP-Seq or ChIP-on-chip) in 15 cell lines from human and mouse and computationally predicted YY1 and cofactor binding motifs with each locus. In addition to browsing the database, users may retrieve information through two types of searching: Basic and Advanced Search.
TRABAS / Transcription Regulation by ABA Signaling
Enables retrieval of expression data of abscisic acid (ABA) regulated genes in ABA signaling related. TRABAS is an integration of available information related to ABA signaling mediated gene regulation gathered using different independent methods like Massive Parallel Signature Sampling (MPSS), cDNA microarray and Affymetrix arrays. After selection of a gene set using any of the filters, TRABAS can also be used to retrieve expression data for the selected set of genes.
ORegAnno / Open REGulatory ANNOtation database
Obsolete
A resource for curated regulatory annotation. ORegAnno contains information about regulatory regions, transcription factor binding sites, RNA binding sites, regulatory variants, haplotypes, and other regulatory elements. It differentiates itself from other regulatory resources by facilitating crowd-sourced interpretation and annotation of regulatory observations from the literature and highly curated resources. It contains a comprehensive annotation scheme that aims to describe both the elements and outcomes of regulatory events. Moreover, ORegAnno assembles these disparate data sources and annotations into a single, high quality catalogue of curated regulatory information.
DoOP / Database of Orthologous Promoters
Obsolete
Stores eukaryotic promoter sequences. DoOP provides clusters of orthologous putative promoters within the phylum Chordata and kingdom Viridiplantae. The cluster sequences can be a source for a more detailed analysis of possible promoter elements, including transcription factor binding sites (TFBSs). The DoOPSearch tool allows users to search the motif collections of the DoOP database with a program called MOtiF sEarch and EXTension (MOFEXT).
TransfactomeDB
Obsolete
A repository of sequence specificity models and condition-specific regulatory activities for a large number of DNA- and RNA-binding proteins in Saccharomyces cerevisiae. The web interface allows the user to dynamically interact with published microarray data and easily discern otherwise hidden regulatory patterns. TransfactomeDB has the advantages of (i) having a uniform, biophysically motivated representation of sequence specificities in the form of PSAMs; (ii) providing condition-specific regulatory information for each PSAM; and (iii) predicting single-nucleotide TF-binding affinity profiles for arbitrary DNA and RNA sequences.
PreDREM / Predicted DNA REgulatory Motifs
Obsolete
A database of DNA regulatory motifs and motifs modules predicted from DNase I hypersensitive sites in 349 human cell and tissue samples. It contains 845-1325 predicted motifs in each sample, which result in a total of 2684 non-redundant motifs. In comparison with seven large collections of known motifs, more than 84% of the 2684 predicted motifs are similar to the known motifs, and 54-76% of the known motifs are similar to the predicted motifs. PreDREM also stores 43 663-20 13 288 motif modules in each sample, which provide the cofactor motifs of each predicted motif.
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