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Two novel qualitative transcriptional signatures robustly applicable to non‐research‐oriented colorectal cancer samples with low‐quality RNA
- Source :
- Journal of Cellular and Molecular Medicine
- Publication Year :
- 2021
- Publisher :
- Wiley, 2021.
-
Abstract
- Currently, due to the low quality of RNA caused by degradation or low abundance, the accuracy of gene expression measurements by transcriptome sequencing (RNA‐seq) is very challenging for non‐research‐oriented clinical samples, majority of which are preserved in hospitals or tissue banks worldwide with complete pathological information and follow‐up data. Molecular signatures consisting of several genes are rarely applied to such samples. To utilize these resources effectively, 45 stage II non‐research‐oriented samples which were formalin‐fixed paraffin‐embedded (FFPE) colorectal carcinoma samples (CRC) using RNA‐seq have been analysed. Our results showed that although gene expression measurements were significantly affected, most cancer features, based on the relative expression orderings (REOs) of gene pairs, were well preserved. We then developed two REO‐based signatures, which consisted of 136 gene pairs for early diagnosis of CRC, and 4500 gene pairs for predicting post‐surgery relapse risk of stage II and III CRC. The performance of our signatures, which included hundreds or thousands of gene pairs, was more robust for non‐research‐oriented clinical samples, compared to that of two published concise REO‐based signatures. In conclusion, REO‐based signatures with relatively more gene pairs could be robustly applied to non‐research‐oriented CRC samples.
- Subjects :
- 0301 basic medicine
transcriptional signature
Transcription, Genetic
Colorectal cancer
colorectal cancer
Computational biology
Stage ii
Biology
03 medical and health sciences
0302 clinical medicine
relative expression orderings
Databases, Genetic
Gene expression
Biomarkers, Tumor
medicine
non‐research‐oriented clinical samples
Humans
Protein Interaction Maps
Relapse risk
low‐quality RNA
Gene
Base Sequence
Gene Expression Profiling
RNA
Cancer
Original Articles
Cell Biology
medicine.disease
Transcriptome Sequencing
Gene Expression Regulation, Neoplastic
Early Diagnosis
030104 developmental biology
030220 oncology & carcinogenesis
Molecular Medicine
Original Article
Colorectal Neoplasms
Transcriptome
Subjects
Details
- ISSN :
- 15824934 and 15821838
- Volume :
- 25
- Database :
- OpenAIRE
- Journal :
- Journal of Cellular and Molecular Medicine
- Accession number :
- edsair.doi.dedup.....eb35353ff7353ca208f3fc516dfc7ba7