Fig. 3

Genes that are overexpressed in late and early SSc-PF are distributed throughout the lung network. a The lung network shows functional connections between inflammatory and fibrotic processes. Genes in the largest connected component were clustered into functional modules using community detection. Biological processes associated with the functional modules are in boxes next to the modules. Genes are colored by whether they are overexpressed in late SSc-PF/UIP (red), early SSc-PF/NSIP (blue), both (SSc-PF, purple), or neither (grey). NSIP non-specific interstitial pneumonia, UIP usual interstitial pneumonia. Gene symbols in bold have putative SSc risk polymorphisms. Node (gene) size is determined by degree (number of functional interactions) and edge width is determined by the weight (probability of interaction between pairs of genes). The layout is determined by community membership, the strength of connections between communities, and finally the interactions between individual genes in the network. A fully labeled network is supplied as Additional file 30: Figure S3 and is intended to be viewed digitally. b Quantification of differentially expressed genes in each of the five largest functional modules. c–e Hubs of the consensus lung network; only the first neighbors of the hub that are in the same functional module are shown. c LAMC1 is a hub of the response to TGF-beta module. d NPC2 is a hub of the ECM disassembly, wound healing module. e TNFAIP3 is a hub of the innate immune response, NF-κB signaling, and apoptotic processes module. f Bridges of the consensus lung network. First neighbors of PLAUR, CD44, TNFSF10, and TGFBI are shown