ArticleBioinformatics (Oxford, England)2023
GPGPS: a robust prognostic gene pair signature of glioma ensembling IDH mutation and 1p/19q co-deletion.
Article in Bioinformatics (Oxford, England), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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11 citing papers in PubMed, 19 citations in OpenAlex.
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- MFAP4 is a novel prognostic biomarker in glioma correlating with immunotherapy resistance and ferroptosis.Frontiers in pharmacology · 2025Article
- PAGE-based transfer learning from single-cell to bulk sequencing enhances model generalization for sepsis diagnosis.Briefings in bioinformatics · 2024Article
- Deep learning model to discriminate diverse infection types based on pairwise analysis of host gene expression.iScience · 2024Article
- Histone demethylase KDM4B accelerates the progression of glioblastoma via the epigenetic regulation of MYC stability.Clinical epigenetics · 2023Article
- Diagnostic Prediction of portal vein thrombosis in chronic cirrhosis patients using data-driven precision medicine model.Briefings in bioinformatics · 2023Article
- MrGPS: an m6A-related gene pair signature to predict the prognosis and immunological impact of glioma patients.Briefings in bioinformatics · 2023Article
- Co-expression module analysis reveals high expression homogeneity for both coding and non-coding genes in sepsis.BMC genomics · 2023Article
- bvnGPS: a generalizable diagnostic model for acute bacterial and viral infection using integrative host transcriptomics and pretrained neural networks.Bioinformatics (Oxford, England) · 2023Article
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Authors and funding
10 authors at 2 institutions in 2 countries.
Funding
Abstract
motivationMany studies have shown that IDH mutation and 1p/19q co-deletion can serve as prognostic signatures of glioma. Although these genetic variations affect the expression of one or more genes, the prognostic value of gene expression related to IDH and 1p/19q status is still unclear.
resultsWe constructed an ensemble gene pair signature for the risk evaluation and survival prediction of glioma based on the prior knowledge of the IDH and 1p/19q status. First, we separately built two gene pair signatures IDH-GPS and 1p/19q-GPS and elucidated that they were useful transcriptome markers projecting from corresponding genome variations. Then, the gene pairs in these two models were assembled to develop an integrated model named Glioma Prognostic Gene Pair Signature (GPGPS), which demonstrated high area under the curves (AUCs) to predict 1-, 3- and 5-year overall survival (0.92, 0.88 and 0.80) of glioma. GPGPS was superior to the single GPSs and other existing prognostic signatures (avg AUC = 0.70, concordance index = 0.74). In conclusion, the ensemble prognostic signature with 10 gene pairs could serve as an independent predictor for risk stratification and survival prediction in glioma. This study shed light on transferring knowledge from genetic alterations to expression changes to facilitate prognostic studies. AVAILABILITY AND IMPLEMENTATION: Codes are available at https://github.com/Kimxbzheng/GPGPS.git. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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