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The expression level of small non‐coding RNA s derived from the first exon of protein‐coding genes is predictive of cancer status
Author(s) -
Zovoilis Athanasios,
Mungall Andrew J,
Moore Richard,
Varhol Richard,
Chu Andy,
Wong Tina,
Marra Marco,
Jones Steven JM
Publication year - 2014
Publication title -
embo reports
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 4.584
H-Index - 184
eISSN - 1469-3178
pISSN - 1469-221X
DOI - 10.1002/embr.201337950
Subject(s) - gene , exon , genetics , rna , biology , gene expression , coding (social sciences) , computational biology , mathematics , statistics
Small non‐coding RNA s (sm RNA s) are known to be significantly enriched near the transcriptional start sites of genes. However, the functional relevance of these sm RNA s remains unclear, and they have not been associated with human disease. Within the cancer genome atlas project ( TCGA ), we have generated small RNA datasets for many tumor types. In prior cancer studies, these RNA s have been regarded as transcriptional “noise,” due to their apparent chaotic distribution. In contrast, we demonstrate their striking potential to distinguish efficiently between cancer and normal tissues and classify patients with cancer to subgroups of distinct survival outcomes. This potential to predict cancer status is restricted to a subset of these sm RNA s, which is encoded within the first exon of genes, highly enriched within CpG islands and negatively correlated with DNA methylation levels. Thus, our data show that genome‐wide changes in the expression levels of small non‐coding RNA s within first exons are associated with cancer.