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The cox-filter method identifies respective subtype-specific lncRNA prognostic signatures for two human cancers
- Source :
- BMC Medical Genomics, Vol 13, Iss 1, Pp 1-10 (2020), BMC Medical Genomics
- Publication Year :
- 2020
- Publisher :
- BMC, 2020.
-
Abstract
- Background The most common histological subtypes of esophageal cancer are squamous cell carcinoma (ESCC) and adenocarcinoma (EAC). It has been demonstrated that non-marginal differences in gene expression and somatic alternation exist between these two subtypes; consequently, biomarkers that have prognostic values for them are expected to be distinct. In contrast, laryngeal squamous cell cancer (LSCC) has a better prognosis than hypopharyngeal squamous cell carcinoma (HSCC). Likewise, subtype-specific prognostic signatures may exist for LSCC and HSCC. Long non-coding RNAs (lncRNAs) hold promise for identifying prognostic signatures for a variety of cancers including esophageal cancer and head and neck squamous cell carcinoma (HNSCC). Methods In this study, we applied a novel feature selection method capable of identifying specific prognostic signatures uniquely for each subtype – the Cox-filter method – to The Cancer Genome Atlas esophageal cancer and HSNCC RNA-Seq data, with the objectives of constructing subtype-specific prognostic lncRNA expression signatures for esophageal cancer and HNSCC. Results By incorporating biological relevancy information, the lncRNA lists identified by the Cox-filter method were further refined. The resulting signatures include genes that are highly related to cancer, such as H19 and NEAT1, which possess perfect prognostic values for esophageal cancer and HNSCC, respectively. Conclusions The Cox-filter method is indeed a handy tool to identify subtype-specific prognostic lncRNA signatures. We anticipate the method will gain wider applications.
- Subjects :
- lcsh:Internal medicine
Esophageal Neoplasms
lcsh:QH426-470
Somatic cell
Esophageal cancer
Kaplan-Meier Estimate
Disease-Free Survival
Long non-coding RNA (lncRNA)
Databases, Genetic
Genetics
medicine
Cox regression model
Humans
RNA, Neoplasm
lcsh:RC31-1245
Genetics (clinical)
Squamous Cell Carcinoma of Head and Neck
Proportional hazards model
business.industry
Gene Expression Profiling
Prognostic signature
Head and neck squamous cell carcinoma (HNSCC)
medicine.disease
Lncrna expression
Head and neck squamous-cell carcinoma
Human genetics
Gene Expression Regulation, Neoplastic
Survival Rate
lcsh:Genetics
Head and Neck Neoplasms
Carcinoma, Squamous Cell
Cancer research
Adenocarcinoma
RNA, Long Noncoding
DNA microarray
business
Research Article
Subjects
Details
- Language :
- English
- ISSN :
- 17558794
- Volume :
- 13
- Issue :
- 1
- Database :
- OpenAIRE
- Journal :
- BMC Medical Genomics
- Accession number :
- edsair.doi.dedup.....b454bd88b91b61db4376a2bafaec45f1