Uncovering and characterizing splice variants associated with survival in lung cancer patients
Fig 1
Workflow for generating multi-granularity graphs (MGGs).
Using the NEEP method significant splice variants were calculated, utilizing clinical data, the complementary-DNA reference library, and RNA-Seq data from Ensembl and TCGA. Multi-granular graphs were constructed for known protein-protein interactions from BioGRID, mapped from Ensembl to at least one significant splice variant. Domains were predicted for each splice variant using HMMER3 [16] and Pfam [17]. Gained and ghost domains were identified in splice variants associated with survival. Final MGGs represent potential lost or gained protein interactions associated with patient survival.