Tag: chip-seq

The ENCODE (Encyclopedia of DNA Elements) Consortium is an international collaboration of research groups funded by the National Human Genome Research Institute (NHGRI). The goal of ENCODE is to build a comprehensive parts list of functional elements ...

HOmo sapiens COmprehensive MOdel COllection (HOCOMOCO) v10 provides transcription factor (TF) binding models for 601 human and 396 mouse TFs. In addition to basic mononucleotide position weight matrices (PWMs), HOCOMOCO provides a set of dinucleotide ...

ChIP-Seq, RNA-Seq and DNase-Seq data for haematopoietic and embryonic stem cells

TFBSshape provides DNA shape features for transcription factor binding sites (TFBSs) that in addtion to sequence features, usually in the form of position weight matrices (PWMs), characterize DNA binding specificities of transcription factors (TFs) f ...

Reference human lncRNA sets

Curated database to annotate gene promoters identified from ChIP-seq results. Users can search the database based on gene id/symbol, or by specific tissue/cell type and filter results based on any combination of tissue/cell specificity, Known/Novel, ...

Human Assay-for-Transposase-Accessible Chromatin data

A Multi-Dimensional Omics Database for Apple Co-Expression Networks and Chromatin States. AppleMDO is a multi-dimensional omics database. Users can submit locus IDs to quickly search for co-expression networks, functional modules, chromatin states a ...

DESSO is a deep learning-based framework that can be used to accurately identify both sequence and shape regulatory motifs from the human genome.

An Integrated Correlation Network Database for the Identification of CeRNA Axes in Uveal Melanoma.

A comprehensive database for decoding the regulatory transcription co-factors in human and mouse.

A database of enhancer-associated insertion and deletion variants by analysis of H3K27ac ChIP-Seq. Cancer hallmarks rely on its specific transcriptional programs, which are dysregulated by multiple mechanisms, including genomic aberrations in the DN ...

ChIP-seq-based database of human transcription factor binding sites and the topological arrangements of the proteins bound to them.

ChIP-Atlas is a web service providing both GUI- and API-based data-mining tools to reveal the architecture of the transcription regulatory landscape.

A PROkaryotic Chromatin ImmunoPrecipitation DataBase

A manually curated resource for multi-omics level evidence integration of fibrosis research

A Comprehensive Multi-Omics Association Database of Secondary Growth in Response to Stress in Populus trichocarpa.

MVIP provides a large number of available multi-omics data under viral infection in various species.

CancerCRCdb is a comprehensive database of human core regulatory circuitry.

A database of nucleosome positioning in vivo and nucleosomics of cell-free DNA.

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

ConnecTF is a platform to build gene networks by integrating transcription factor-target gene interactions.

CpGmotifs is a tool to discover DNA motifs associated to CpG methylation events.

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

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 web database for sequence and shape motif analyses and identification.

BART Cancer Database is a web resource designed to display putative transcriptional regulators (TRs) that are responsible for up and downregulation of genes in 15 different cancer types in The Cancer Genome Atlas. BART Cancer uses BART (Binding Analy ...