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Comprehensive landscape of subtype-specific coding and non-coding RNA transcripts in breast cancer
| Content Provider | Semantic Scholar |
|---|---|
| Author | Vu, Trung Nghia Pramana, Setia Calza, Stefano Suo, Chen Lee, Donghwan Pawitan, Yudi |
| Copyright Year | 2016 |
| Abstract | Molecular classification of breast cancer into clinically relevant subtypes helps improve prognosis and adjuvant-treatment decisions. The aim of this study is to provide a better characterization of the molecular subtypes by providing a comprehensive landscape of subtype-specific isoforms including coding, long non-coding RNA and microRNA transcripts. Isoform-level expression of all coding and non-coding RNAs is estimated from RNA-sequence data of 1168 breast samples obtained from The Cancer Genome Atlas (TCGA) project. We then search the whole transcriptome systematically for subtype-specific isoforms using a novel algorithm based on a robust quasi-Poisson model. We discover 5451 isoforms specific to single subtypes. A total of 27% of the subtype-specific isoforms have better accuracy in classifying the intrinsic subtypes than that of their corresponding genes. We find three subtype-specific miRNA and 707 subtype-specific long non-coding RNAs. The isoforms from long non-coding RNAs also show high performance for separation between Luminal A and Luminal B subtypes with an AUC of 0.97 in the discovery set and 0.90 in the validation set. In addition, we discover 1500 isoforms preferentially co-expressed in two subtypes, including 369 isoforms co-expressed in both Normal-like and Basal subtypes, which are commonly considered to have distinct ER-receptor status. Finally, analyses at protein level reveal four subtype-specific proteins and two subtype co-expression proteins that successfully validate results from the isoform level. |
| Starting Page | 68851 |
| Ending Page | 68863 |
| Page Count | 13 |
| File Format | PDF HTM / HTML |
| Alternate Webpage(s) | http://www.oncotarget.com/index.php?journal=oncotarget&op=download&page=article&path%5B%5D=11998&path%5B%5D=39062 |
| PubMed reference number | 27634900 |
| Alternate Webpage(s) | https://doi.org/10.18632/oncotarget.11998 |
| DOI | 10.18632/oncotarget.11998 |
| Journal | Oncotarget |
| Volume Number | 7 |
| Language | English |
| Access Restriction | Open |
| Subject Keyword | Area Under Curve Classification Long Intergenic Non-Protein Coding RNA Mammary Neoplasms MicroRNAs Pharmaceutical Adjuvants Phenobarbital Protein Isoforms RNA, Untranslated Subtype (attribute) The Cancer Genome Atlas Transcript Transcriptome algorithm non-T, non-B childhood acute lymphoblastic leukemia |
| Content Type | Text |
| Resource Type | Article |
