The cistrome refers to "the set of cis-acting targets of a trans-acting factor on a genome-wide scale, also known as the in vivo genome-wide location of transcription factor binding-sites or histone modifications". Here we build integrative analysis pipelines (Cistrome) to help experimental biologists, and conduct efficient data integration to better mine the hidden biological insights from publicly available high throughput data.
An integrative and reproducible bioinformatics data analysis platform based on Galaxy open source framework. Besides standard Galaxy functions, Cistrome has 29 ChIP-chip- and ChIP-seq-specific tools in three major categories, from preliminary peak calling and correlation analyses to downstream genome feature association, gene expression analyses, and motif discovery.
A new portal to browser public ChIP-seq and DNase-seq datasets. Besides providing a comprehensive knowledgebase of all of the publicly available ChIP-Seq and DNase-Seq data in mouse and human, it also provides functions to analysis and visualize these datasets.
A comprehensive resource for predicted transcription factor (TF) targets and enhancer profiles in cancers. The prediction was from integrative analysis of TCGA expression profiles and public ChIP-seq profiles.
TIMER (Tumor IMmune Estimation Resource) s a comprehensive resource for systematical analysis of immune infiltrates across diverse cancer types. The abundances of six immune infiltrates (B cells, CD4+ T cells, CD8+ T cells, Neutrphils, Macrophages and Dendritic cells) are estimated by our statistical method, which is validated using pathological estimations.
A tool developed for high-throughput, rational sgRNA design in CRISPR screen experiment.
This application focus on the whole genome sgRNA design in human and mouse, with accessing both the efficiency and the specificity score. It also have the epigenome browser as a visualization tool for users to identify each of the sgRNA with genome features overlapping like DHS, SNP.
A new sequence model for predicting sgRNA efficiency for CRISPR knockout or CRISPRi/a by systematically assessing the DNA sequence features that contribute to single guide RNA (sgRNA) efficiency in CRISPR-based screens.
Binding and Expression Target Analysis (BETA) is a software package that integrates ChIP-seq of transcription factors or chromatin regulators with differential gene expression data to infer direct target genes
A knowledgebase on chromatin modifying enzymes and chromatin remodelers. All the chromatin regulators (CR) which possess ChIP-seq data are divided into four categories: reader, writer, eraser and remodeler. Then their basic information and their ChIP-seq data are collected and analysed.
A curated database of 88 nuclear receptor cistrome data sets and other associated high-throughput data sets including 121 collaborating factor cistromes, 94 epigenomes, and 319 transcriptomes. All the ChIP_chip/seq peak regions are annotated with enriched HRE and co-regulator motifs. A list of predicted hormone response genes from integration of nuclear receptor ChIP_chip/seq data and differential expression data is also readily available to the users.
CaSNP is a comprehensive collection of copy number alteration (CNA) from SNP arrays. It collects 11,485 Affymetrix SNP arrays of 34 different cancer types in 105 studies to profile the genome-wide CNA and SNP in each. This includes all the cancer SNP profiles using Affymetrix SNP arrays (10K to 6.0) with raw data from GEO, with additional arrays from the TCGA consortium and a few individual publications.