The human genome contains approximately 20,000 protein-coding genes, representing <2% of the genome [67]. Within the past decade sequencing technologies

have revealed that over 90% of the genome is actively transcribed and includes a collection of antisense and non-coding RNA (ncRNA) selleck transcripts [68] and [69]. ncRNA are transcripts that lack open reading frames and do not typically encode a protein, the best studied of which are miRNA. Similar to gene expression, miRNA signatures can accurately separate histological subtypes and are thought to be as good or even superior to global mRNA expression profiles in their ability to accurately classify NSCLC subtypes [70]. miR-205 has been shown as a highly specific marker for SqCC [71], while in AC, specific miRNAs have been shown to associate with mutation patterns. miR-155 is upregulated exclusively in AC with wildtype EGFR and KRAS, while miR-21 and miR-25 are upregulated

in EGFR mutant AC and miR-495 is up-regulated in KRAS positive AC [72] and [73]. The study of long ncRNAs (lncRNAs) in lung cancer is still an emerging field, and to date no lncRNAs have demonstrated diagnostic or therapeutic potential in lung cancer. However, diagnostic lncRNAs have been identified in other cancer types including prostate and liver cancer [74] and [75] and metastasis-associated lung adenocarcinoma BMS-354825 transcript 1 (MALAT1) is known to be associated with metastasis and poor prognosis in NSCLC, highlighting its potential as a prognostic marker [76]. Based on these and other recent findings, non-coding transcripts may be just as important to tumor biology and therapeutics as protein coding transcripts, underscoring their significance. While the application of single dimensional analyses (expression, copy number, or

mutation studies alone) are informative for identifying disrupted genes, they often overlook genes disrupted at low frequencies and are not capable of distinguishing causal from passenger events [77]. The integration of multiple dimensions of ‘omics data provides a more comprehensive Sirolimus mouse understanding of the genetic mechanisms affecting a tumor as it not only enables the identification of genes with concurrent DNA and expression alterations which are more likely to be driver alterations, but also genes disrupted by multiple mechanisms but at low frequencies by any single mechanism (Fig. 2B and C) [77]. However, gene discovery on its own provides limited information regarding tumor biology. The inclusion of pathway or network analysis (Ingenuity Pathway Analysis, Kyoto Encyclopaedia of Genes and Genomes (KEGG) and Gene Set Enrichment Analysis to name a few) can be a useful tool to provide biological context to a set of alterations and aid in interpreting how they work in conjunction to promote tumorigenesis (Fig. 2B and C).