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Fig. 6 | Genome Medicine

Fig. 6

From: Long noncoding RNAs expressed in human hepatic stellate cells form networks with extracellular matrix proteins

Fig. 6

lncRNAs discovered in HSCs form networks with ECM proteins. a Schematic of co-expression analysis. Expression of all protein-coding genes as well as the lncRNAs expressed in HSCs were analyzed in HSCs, 37 primary tissues, and six ENCODE cell lines. Co-expression analysis (Spearman coefficient >0.7) identified five main subnetworks. Only subnetwork A contained HSC identity lncRNAs. Subnetwork A was divided into nine main clusters. Only three clusters (red) contained more than one HSC identity lncRNA. Gene ontology (GO) analysis was performed to identify the most enriched categories for each of these three clusters. The extracellular matrix was significantly enriched in cluster II. The top GO categories identified for cluster I (b), cluster II (c), and cluster IV (d) are shown. The -log10 p values are displayed on the x-axis. e The protein-coding genes from cluster I that are contained in the GO category of nucleotide binding are displayed along with all HSC lncRNAs contained in cluster I that are connected to the nucleotide-binding protein-coding genes by one edge (gray lines). mRNAs (blue) and lncRNAs (red) are represented as circles. f The protein-coding genes from cluster II that are contained in the GO category of ECM are displayed along with all HSC lncRNAs contained in cluster II that are connected to the ECM proteins by one edge. g The entire network for cluster IV is displayed, including all protein-coding genes and HSC lncRNA genes. This cluster contains multiple HOX genes (dark green circles) and lncRNAs associated with HOX genes (HOX lncRNA, light green circles). h The HSC identity lncRNAs and the ECM proteins in cluster II that are connected by one edge are shown. HSC identity lncRNAs were defined as occupied by SMAD3, associated with super-enhancers, and restricted in expression to HSCs. i Two super-enhancers regulate genes encoding mRNAs and lncRNAs in cluster IV. Genes encoding mRNAs and lncRNAs located within a super-enhancer and connected by one edge are shown for two super-enhancers

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