ArticleOncotarget2016
Differential expression analysis for individual cancer samples based on robust within-sample relative gene expression orderings across multiple profiling platforms.
Article in Oncotarget, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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Who cites it
36 citing papers in PubMed.
- Integration of multi-omics data uncovers novel germline susceptibility candidates in early-onset colorectal cancer.European journal of human genetics : EJHG · 2026Article
- Exploring the influence of pre-analytical variables on gene expression measurements and relative expression orderings in cancer research.Scientific reports · 2025Article
- Excavation of gene markers associated with pancreatic ductal adenocarcinoma based on interrelationships of gene expression.IET systems biology · 2024Article
- RankCompV3: a differential expression analysis algorithm based on relative expression orderings and applications in single-cell RNA transcriptomics.BMC bioinformatics · 2024Article
- A pyroptosis-related lncRNA-based prognostic index for hepatocellular carcinoma by relative expression orderings.Translational cancer research · 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
- 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
- Metabolism-Related Gene Pairs to Predict the Clinical Outcome and Molecular Characteristics of Early Hepatocellular Carcinoma.Cancers · 2022Article
- Transcriptomic Portraits and Molecular Pathway Activation Features of Adult Spinal Intramedullary Astrocytomas.Frontiers in oncology · 2022Article
- The prognostic and clinical significance of IFI44L aberrant downregulation in patients with oral squamous cell carcinoma.BMC cancer · 2021Article
- A transcriptional signature detects homologous recombination deficiency in pancreatic cancer at the individual level.Molecular therapy. Nucleic acids · 2021Article
- Article
- Long non-coding RNA pairs to assist in diagnosing sepsis.BMC genomics · 2021Article
- Transcriptomic analysis identifies organ-specific metastasis genes and pathways across different primary sites.Journal of translational medicine · 2021Article
- Identification of Genes Universally Differentially Expressed in Gastric Cancer.BioMed research international · 2021Article
- PenDA, a rank-based method for personalized differential analysis: Application to lung cancer.PLoS computational biology · 2020Article
- A qualitative transcriptional signature to reclassify histological grade of ER-positive breast cancer patients.BMC genomics · 2020Article
- Early Diagnosis of Pancreatic Ductal Adenocarcinoma by Combining Relative Expression Orderings With Machine-Learning Method.Frontiers in cell and developmental biology · 2020Article
- Qualitative transcriptional signature for predicting pathological response of colorectal cancer to FOLFOX therapy.Cancer science · 2020Article
- Early Diagnosis of Hepatocellular Carcinoma Using Machine Learning Method.Frontiers in bioengineering and biotechnology · 2020Article
Corrections and comments
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Authors and funding
12 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The highly stable within-sample relative expression orderings (REOs) of gene pairs in a particular type of human normal tissue are widely reversed in the cancer condition. Based on this finding, we have recently proposed an algorithm named RankComp to detect differentially expressed genes (DEGs) for individual disease samples measured by a particular platform. In this paper, with 461 normal lung tissue samples separately measured by four commonly used platforms, we demonstrated that tens of millions of gene pairs with significantly stable REOs in normal lung tissue can be consistently detected in samples measured by different platforms. However, about 20% of stable REOs commonly detected by two different platforms (e.g., Affymetrix and Illumina platforms) showed inconsistent REO patterns due to the differences in probe design principles. Based on the significantly stable REOs (FDR<0.01) for normal lung tissue consistently detected by the four platforms, which tended to have large rank differences, RankComp detected averagely 1184, 1335 and 1116 DEGs per sample with averagely 96.51%, 95.95% and 94.78% precisions in three evaluation datasets with 25, 57 and 58 paired lung cancer and normal samples, respectively. Individualized pathway analysis revealed some common and subtype-specific functional mechanisms of lung cancer. Similar results were observed for colorectal cancer. In conclusion, based on the cross-platform significantly stable REOs for a particular normal tissue, differentially expressed genes and pathways in any disease sample measured by any of the platforms can be readily and accurately detected, which could be further exploited for dissecting the heterogeneity of cancer.
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