Tag: gene regulation

JASPAR (http://jaspar.genereg.net) is an open-access database of curated, non-redundant transcription factor (TF)-binding profiles stored as position frequency matrices (PFMs) and TF flexible models (TFFMs) for TFs across multiple species in six taxo ...

Database of RNA interactions in post-transcriptional regulation.

EcoCyc is a model organism database for Escherichia coli K-12 MG1655. EcoCyc curation captures literature-based information on the functions of individual E. coli gene products, metabolic pathways, and regulation of E. coli gene expression. EcoCyc ha ...

This database enables the reliable identification of an individual Interferon Regulated Gene (IRG) or IRG signatures from high-throughput data sets (i.e. microarray, proteomic data etc.). It also assists in identifying regulatory elements, chromosoma ...

YEASTRACT (Yeast Search for Transcriptional Regulators And Consensus Tracking) is a curated repository of more than 48333 regulatory associations between transcription factors (TF) and target genes in Saccharomyces cerevisiae, based on more than 1200 ...

DIANA-LncBase v3.0 (www.microrna.gr/LncBase) is a reference repository with experimentally supported miRNA targets on non-coding transcripts. Its third version provides approximately half a million entries, corresponding to ∼240 000 unique tissue a ...

The Open REGulatory ANNOtation database (ORegAnno) is an open database for the curation of known regulatory elements from scientific literature. Annotation is collected from users worldwide for various biological assays and is automatically cross-ref ...

The Arabidopsis Gene Regulatory Information Server (AGRIS) is a new information resource of Arabidopsis promoter sequences, transcription factors and their target genes. AGRIS currently contains two databases, AtcisDB (Arabidopsis thaliana cis-regula ...

PRODORIC is a comprehensive database about gene regulation and gene expression in prokaryotes. It includes a manually curated and unique collection of transcription factor binding sites.

TransmiR is a database for transcription factor-microRNA regulations, which is free for academic usage.

PAZAR is a software framework for the construction and maintenance of regulatory sequence data annotations; a framework which allows multiple boutique databases to function independently within a larger system (or information mall). The goal of PAZAR ...

ScerTF is a database of position weight matrices (PWMs) for transcription factors in Saccharomyces species. It identifies a single matrix for each TF that best predicts in vivo data, providing metrics related to the performance of that matrix in accu ...

Polymorphic miRNA-mediated gene regulation in vertebrates

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Gene regulation in bacteriophages

SilkDB is a database of the integrated genome resource for the silkworm, Bombyx mori. This database provides access to not only genomic data including functional annotation of genes, gene products and chromosomal mapping, but also extensive biologica ...

HMM-based Identification of TF Footprints

EXPath is a database resource that collects and utilizes expression profiles derived from microarray under various conditions to infer metabolic pathways for six model plants: Arabidopsis thaliana, Oryza sativa, Zea mays, Solanum lycopersicum, Glycin ...

A database of curated mutual regulation between miRNAs and epigenetic modifications.

Three-dimensional (3D) chromatin structure is an emerging paradigm for understanding gene regulation mechanisms. Hi-C (high-throughput chromatin conformation capture), a method to detect long-range chromatin interactions, allows extensive genome-wide ...

EpiRegio is a resource of Regulatory EleMents (REMs) associated to protein coding, and non-protein coding genes. For a detailed documentation, please read our documentation.

a tool for analyzing putative transcription factor binding sites in salmonid genomes | SalMotifDB: cis-regulatory motif database for salmonids | We're getting there, it's worth the wait

A database of gene expression patterns in the Drosophila terminalia. An Atlas of Transcription Factors Expressed in Male Pupal Terminalia of Drosophila melanogaster.

YEASTRACT+ combines the existing database information of all yeast species, providing bioinformatics tools for the prediction and visualization of gene and genomic regulation based on orthologous regulatory associations described for other yeast spec ...

Gene expression regulation database curated by mining abstracts from literature. Gene Expression Regulation Database. Gene Expression Regulation Database (GREDB) has been developed to facilitate systems-level analyses that will provide insights int ...

CONREL is a genome browser that allows for the exploration of consensus regulatory elements at different levels of abstraction. The total binding affinity of transcription factors on whole consensus region sequences is here fully exploited to charact ...

A comprehensive web-atlas for p53, p63, and cell cycle-dependent gene regulation.

Comparative transcriptomics and co-expression database for bacterial pathogens.

A dbEmbryo multi-omics database for analyses of synergistic regulation in early mammalian embryo development.

A Knowledgebase of RAG Regulators.

A positive miRNA-target regulations database.

A database of enhancer mediated feed-forward loops for human and mouse.

A search tool for finding variants from specific chromosome coordinates. It is possible to integrate the results in NGS pipeline.

ERMer: A serverless platform for navigating, analyzing, and visualizing Escherichiacoli regulatory landscape through graph database.

An integrated resource for human miRNA-Transcription Factor-Target Gene coregulatory networks and associated Feed Forward Loops. Defence Institute of Physiology and Allied Science. miRNA and Transcription Factors (TFs) are fundamental transcription ...

A comprehensive database for regulations of human transcription factors and their targets. Transcription factors (TFs) as key regulators could modulate the expression of target genes by binding to specific DNA sequences of their promoter(s) or enhan ...

A Database of Regulatory SNPs for Agricultural Animal Species.

A framework for the annotation and prioritization of non-coding regulatory variants in whole-genome sequencing. Genomic Regulatory Elements ENcyclopedia. This is the home of the GREEN-DB and companion tools (GREEN-VARAN). Genomic Regulatory Elemen ...