Tools

Cis-element Atlas (CATlas)

Published:

A web portal for single-cell epigenetic datasets in human and mouse.

You can explore cell clusters and annotations identified from single-cell ATAC-seq, as well as genomic tracks. We also offer the downloading of candidate enhancer linked to putative target genes at cell-type resolution. For detail about the experimental or computational pipeline, please refer to our recent work published on Nature.

We hope you find this data resource useful. Please write us with experiences and suggestions. We would love stories about how people are using it in their work.

RBPgroup

Published:

This web-based database provides the RNA binding sites and regulatory elements.

Crosslinking immunoprecipitation sequencing (CLIP-seq) technologies have enabled researchers to characterize transcriptome-wide binding sites of RNA-binding protein (RBP) with high resolution. We develop a soft-clustering method, RBPgroup, to various CLIP-seq datasets to group together RBPs that specifically bind the same RNA sites. Such combinatorial clustering of RBPs helps interpret CLIP-seq data and suggests functional RNA regulatory elements. website link

Genetic Variants Allelic TF Binding Database (GVATdb)

Published:

A web server for searching SNPs with differential Transcription factors (TF) binding.

This database characterizes the allelic binding of 95,886 common human single nucleotide polymorphisms (SNPs, MAF>1% in Eeuropean and Asian populations) to 270 distinct transcription factors (TFs). The SNPs were chosen from neighboring regions (<=500 kb) of 83 risk loci of type 2 diabetes (T2D) that were identified in several genome wide association studies (GWAS). The data were generated using SNP-SELEX. website link