An example of analyzing an autoimmune disease locus by pathway analysis approaches. (A) Expression levels of protein-coding transcripts (FAM213B, MMEL1) and lncRNA genes (RP3-395 M20.8, RP3-395 M20.7, RP3-395 M20.9, RP13-436 F16.1) located in the MMEL1 locus associated with four AIDs. The arrows pinpoint the data for RP3-395 M20.9. (B) Genes co-expressed with RP3-395 M20.9 are grouped in five differently colored segments corresponding to the pathways predicted by GeneNetwork. (C) The top 10 Gene Ontology (GO) biological processes predicted to be associated with the genes co-expressed with RP3-395 M20.9 are shown. (D) This schema shows a hypothetical mechanism of action of RP3-395 M20.9. The disease-associated SNP is located between protein-coding gene A (tumor necrosis factor receptor superfamily, member 14 (TNFRSF14, HVEM)) and lncRNA 1 (RP3-395 M20.9). This SNP only affects RP3-395 M20.9 directly. Two protein-coding genes (tumor necrosis factor beta/lymphotoxin alpha (TNFb/LTA) on chromosome 6, and UBASH3A on chromosome 21) and one lncRNA (LINC00158 on chromosome 21) are co-expressed with RP3-395 M20.9, which could be due to trans-regulation of these genes by RP3-395 M20.9. A hypothetical cis-effect of lncRNA 1 (RP3-395 M20.9) on protein-coding gene TNFRSF14/HVEM in the same locus on chromosome 1 is also mentioned.