ArticleOncotarget2017
Robust transcriptional tumor signatures applicable to both formalin-fixed paraffin-embedded and fresh-frozen samples.
Article in Oncotarget, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
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Who cites it
40 citing papers in PubMed.
- Exploring the influence of pre-analytical variables on gene expression measurements and relative expression orderings in cancer research.Scientific reports · 2025Article
- Development of machine learning-based predictors for early diagnosis of hepatocellular carcinoma.Scientific reports · 2024Article
- Identification of cancer risk assessment signature in patients with chronic obstructive pulmonary disease and exploration of the potential key genes.Annals of medicine · 2022Article
- StemSC: a cross-dataset human stemness index for single-cell samples.Stem cell research & therapy · 2022Article
- Hierarchical identification of a transcriptional panel for the histological diagnosis of lung neuroendocrine tumors.Frontiers in genetics · 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
- Identification of a Qualitative Signature for the Diagnosis of Dementia With Lewy Bodies.Frontiers in genetics · 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
- Early Diagnosis of Hepatocellular Carcinoma Using Machine Learning Method.Frontiers in bioengineering and biotechnology · 2020Article
- Qualitative transcriptional signature for predicting pathological response of colorectal cancer to FOLFOX therapy.Cancer science · 2020Article
- A Five-Gene-Pair-Based Prognostic Signature for Predicting the Relapse Risk of Early Stage ER+ Breast Cancer.Frontiers in genetics · 2020Article
- A Qualitative Transcriptional Signature for Predicting CpG Island Methylator Phenotype Status of the Right-Sided Colon Cancer.Frontiers in genetics · 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
- Qualitative Transcriptional Signature for the Pathological Diagnosis of Pancreatic Cancer.Frontiers in molecular biosciences · 2020Article
- A Qualitative Transcriptional Signature for the Risk Assessment of Precancerous Colorectal Lesions.Frontiers in genetics · 2020Article
Corrections and comments
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Authors and funding
11 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Formalin-fixed paraffin-embedded (FFPE) samples represent a valuable resource for clinical researches. However, FFPE samples are usually considered an unreliable source for gene expression analysis due to the partial RNA degradation. In this study, through comparing gene expression profiles between FFPE samples and paired fresh-frozen (FF) samples for three cancer types, we firstly showed that expression measurements of thousands of genes had at least two-fold change in FFPE samples compared with paired FF samples. Therefore, for a transcriptional signature based on risk scores summarized from the expression levels of the signature genes, the risk score thresholds trained from FFPE (or FF) samples could not be applied to FF (or FFPE) samples. On the other hand, we found that more than 90% of the relative expression orderings (REOs) of gene pairs in the FF samples were maintained in their paired FFPE samples and largely unaffected by the storage time. The result suggested that the REOs of gene pairs were highly robust against partial RNA degradation in FFPE samples. Finally, as a case study, we developed a REOs-based signature to distinguish liver cirrhosis from hepatocellular carcinoma (HCC) using FFPE samples. The signature was validated in four datasets of FFPE samples and eight datasets of FF samples. In conclusion, the valuable FFPE samples can be fully exploited to identify REOs-based diagnostic and prognostic signatures which could be robustly applicable to both FF samples and FFPE samples with degraded RNA.
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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.