TissueNexus is a compendium of 49 tissue-/cell line-specific functional gene networks (FGNs) for humans. In an FGN, a node represents a gene, and the edge weight connecting represents the probability that two genes take participate in the same biological process or pathway. These networks were built by integrating heterogeneous functional genomic data which are dominantly tissue-specific RNA-seq gene expression using the state-of-the-art XGBoost algorithm. A total of 1,326 RNA-seq datasets involving 41,324 samples have been integrated for these networks.