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- W2772030232 abstract "Abstract We studied the transcriptome landscape of skin cutaneous melanoma (SKCM) using 103 primary tumor samples from TCGA, and measured the expression levels of both protein coding genes and non-coding RNAs (ncRNAs). In particular, we emphasized pseudogenes potentially relevant to this cancer. While cataloguing the profiles based on the known biotypes, all the employed RNA-Seq methods generated just a small consensus of significant biotypes. We thus designed an approach to reconcile the profiles from all methods following a simple strategy: we selected genes that were confirmed as differentially expressed by the ensemble predictions obtained in a regression model. The main advantages of this approach are: 1) Selection of a high-confidence gene set identifying relevant pathways; 2) Use of a regression model whose covariates embed all method-driven outcomes to predict an averaged profile; 3) Method-specific assessment of prediction power and significance. Furthermore, the approach can be generalized to any biological system for which noisy RNA-Seq profiles are computed. As our analyses concerned bio-annotations of both high-quality protein coding genes and ncRNAs, we considered the associations between pseudogenes and parental genes (targets). Among the candidate targets that were validated, we identified PINK1, which is studied in patients with Parkinson and cancer (especially melanoma)." @default.
- W2772030232 created "2017-12-22" @default.
- W2772030232 creator A5017664557 @default.
- W2772030232 creator A5033429638 @default.
- W2772030232 creator A5041189368 @default.
- W2772030232 creator A5048314173 @default.
- W2772030232 creator A5070178366 @default.
- W2772030232 creator A5087254915 @default.
- W2772030232 date "2017-12-11" @default.
- W2772030232 modified "2023-09-26" @default.
- W2772030232 title "Ensemble Modeling Approach Targeting Heterogeneous RNA-Seq data: Application to Melanoma Pseudogenes" @default.
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- W2772030232 doi "https://doi.org/10.1038/s41598-017-17337-7" @default.