ChIPBase v2.0 is designed for studying transcription factor binding sites and motifs, and decoding transcriptional regulatory networks of non-coding RNAs (lncRNAs, miRNAs, snoRNAs, tRNAs...) and protein-coding genes (PCGs) from ~~10,200 ChIP-seq data (ChIP-seq, ChIP-exo, MNChIP-seq) in 10 speices (Human, Mouse, Fruitfly, Worm, A. Thaliana (plant), Yeast, Rat, Zebrafish, X. tropicalis, Chicken).
We identified thousands of Binding Motif Matrices and their binding sites from ChIP-seq data of transcription factors and predicted millions of transcriptional regulatory relationships between transcription factors and genes.
We constructed Regulator module to predict hundreds of transcription factors that were involved in or affected transcription of ncRNAs (lncRNAs, miRNAs, snoRNAs, tRNAs...) and protein-coding genes.
Moreover, we built a web-based tool, Co-Expression, to explore the co-expression patterns between transcription factors and various types of genes by integrating the gene expression profiles of ~10,000 tumor samples (TCGA) and ~9,100 normal tissues or cell lines.
ChIPBase also provides a ChIP-Function tool and a genome browser to predict functions of diverse genes and visualize various ChIP-seq data. This study will greatly expand our understanding of the transcriptional regulations of ncRNAs and protein-coding genes.
ChIPBase paper is available athttp://nar.oxfordjournals.org/content/early/2016/10/20/nar.gkw965.full
ChIPBase is freely available at http://rna.sysu.edu.cn/chipbase/.