Reconstruction of enhancer-target networks in 935 samples of human primary cells, tissues and cell lines
Qin Cao, Christine Anyansi, Xihao Hu, Liangliang Xu, Lei Xiong, Wenshu Tang, Myth T.S. Mok, Chao Cheng, Xiaodan Fan, Mark Gerstein, Alfred S.L. Cheng and Kevin Y. Yip
The following tables provide the enhancer-target networks inferred by JEME from the ENCODE+Roadmap and FANTOM5 samples in CSV format. Both the original LASSO predictions described in the paper and additional predictions based on Elastic Net are provided. All coordinates are based on the hg19 human reference genome. In each file, each line corresponds to an enhancer-target pair, where:
The first field is the location of the enhancer (0-based, left-close, right-open)
The second field is the list of transcripts sharing the TSS separated by %
The third field is the confidence score of the enhancer-target connection, with a higher score indicating a more confident prediction
The following links provide the source code of the programs used in the calling of enhancer targets and identifying cancer genes in hepatocellular carcinoma (HCC).