ArticleOncotarget2017
Circumvent the uncertainty in the applications of transcriptional signatures to tumor tissues sampled from different tumor sites.
Article in Oncotarget, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed, 48 citations in OpenAlex.
- Exploring the influence of pre-analytical variables on gene expression measurements and relative expression orderings in cancer research.Scientific reports · 2025Article
- Identification of cancer risk assessment signature in patients with chronic obstructive pulmonary disease and exploration of the potential key genes.Annals of medicine · 2022Article
- Prognostic value of a microRNA-pair signature in laryngeal squamous cell carcinoma patients.European archives of oto-rhino-laryngology : official journal of the European Federation of Oto-Rhino-Laryngological Societies (EUFOS) : affiliated with the German Society for Oto-Rhino-Laryngology - Head and Neck Surgery · 2022Article
- Identification of the origin of brain metastases based on the relative methylation orderings of CpG sites.Epigenetics · 2021Article
- Stratification of patients with clear cell renal cell carcinoma to facilitate drug repositioning.iScience · 2021Article
- Two novel qualitative transcriptional signatures robustly applicable to non-research-oriented colorectal cancer samples with low-quality RNA.Journal of cellular and molecular medicine · 2021Article
- A qualitative transcriptional signature for determining the grade of colorectal adenocarcinoma.Cancer gene therapy · 2020Article
- A qualitative transcriptional signature to reclassify histological grade of ER-positive breast cancer patients.BMC genomics · 2020Article
- A qualitative transcriptional signature for predicting the biochemical recurrence risk of prostate cancer patients after radical prostatectomy.The Prostate · 2020Article
- Article
- A Qualitative Transcriptional Signature for the Risk Assessment of Precancerous Colorectal Lesions.Frontiers in genetics · 2020Article
- Early Diagnosis of Hepatocellular Carcinoma Using Machine Learning Method.Frontiers in bioengineering and biotechnology · 2020Article
- Qualitative Transcriptional Signature for the Pathological Diagnosis of Pancreatic Cancer.Frontiers in molecular biosciences · 2020Article
- A Qualitative Transcriptional Signature for Predicting CpG Island Methylator Phenotype Status of the Right-Sided Colon Cancer.Frontiers in genetics · 2020Article
- A Five-Gene-Pair-Based Prognostic Signature for Predicting the Relapse Risk of Early Stage ER+ Breast Cancer.Frontiers in genetics · 2020Article
- Qualitative transcriptional signature for predicting pathological response of colorectal cancer to FOLFOX therapy.Cancer science · 2020Article
- A Qualitative Transcriptional Signature for Predicting Extreme Resistance of ER-Negative Breast Cancer to Paclitaxel, Doxorubicin, and Cyclophosphamide Neoadjuvant Chemotherapy.Frontiers in molecular biosciences · 2020Article
- A qualitative transcriptional signature for the histological reclassification of lung squamous cell carcinomas and adenocarcinomas.BMC genomics · 2019Article
- A qualitative transcriptional signature for predicting microsatellite instability status of right-sided Colon Cancer.BMC genomics · 2019Article
- A qualitative transcriptional signature for the early diagnosis of colorectal cancer.Cancer science · 2019Article
Corrections and comments
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Authors and funding
11 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The expression measurements of thousands of genes are correlated with the proportions of tumor epithelial cell (PTEC) in clinical samples. Thus, for a tumor diagnostic or prognostic signature based on a summarization of expression levels of the signature genes, the risk score for a patient may dependent on the tumor tissues sampled from different tumor sites with diverse PTEC for the same patient. Here, we proposed that the within-samples relative expression orderings (REOs) based gene pairs signatures should be insensitive to PTEC variations. Firstly, by analysis of paired tumor epithelial cell and stromal cell microdissected samples from 27 cancer patients, we showed that above 80% of gene pairs had consistent REOs between the two cells, indicating these REOs would be independent of PTEC in cancer tissues. Then, by simulating tumor tissues with different PTEC using each of the 27 paired samples, we showed that about 90% REOs of gene pairs in tumor epithelial cells were maintained in tumor samples even when PTEC decreased to 30%. Especially, the REOs of gene pairs with larger expression differences in tumor epithelial cells tend to be more robust against PTEC variations. Finally, as a case study, we developed a gene pair signature which could robustly distinguish colorectal cancer tissues with various PTEC from normal tissues. We concluded that the REOs-based signatures were robust against PTEC variations.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.