ArticlePLoS computational biology2015
Extensive decoupling of metabolic genes in cancer.
Article in PLoS computational biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed, 44 citations in OpenAlex.
- Exploring the relationship between metabolism and immune microenvironment in breast cancer bone metastasis based on metabolic pathways.PloS one · 2026Article
- Multistate Gene Cluster Switches Determine the Adaptive Mitochondrial and Metabolic Landscape of Breast Cancer.Cancer research · 2024Article
- Gene regulatory networks in disease and ageing.Nature reviews. Nephrology · 2024Review
- Exploring the relationship between metabolism and immune microenvironment in osteosarcoma based on metabolic pathways.Journal of biomedical science · 2024Article
- Transformation to ischaemia tolerance of frog brain function corresponds to dynamic changes in mRNA co-expression across metabolic pathways.Proceedings. Biological sciences · 2022Article
- m1A methylation modification patterns and metabolic characteristics in hepatocellular carcinoma.BMC gastroenterology · 2022Article
- Multi-Omics Integrative Analysis of Lung Adenocarcinoma: AnFrontiers in medicine · 2022Article
- Convergent network effects along the axis of gene expression during prostate cancer progression.Genome biology · 2020Article
- Differential Co-Expression Analyses Allow the Identification of Critical Signalling Pathways Altered during Tumour Transformation and Progression.International journal of molecular sciences · 2020Review
- Identification of lncRNA-associated differential subnetworks in oesophageal squamous cell carcinoma by differential co-expression analysis.Journal of cellular and molecular medicine · 2020Article
- Defining a metabolic landscape of tumours: genome meets metabolism.British journal of cancer · 2020Review
- Pan-cancer analysis of transcriptional metabolic dysregulation using The Cancer Genome Atlas.Nature communications · 2018Article
- Molecular Characterization and Clinical Relevance of Metabolic Expression Subtypes in Human Cancers.Cell reports · 2018Article
- A Landscape of Metabolic Variation across Tumor Types.Cell systems · 2018Article
- Race Disparities in the Contribution of miRNA Isoforms and tRNA-Derived Fragments to Triple-Negative Breast Cancer.Cancer research · 2018Article
- Pediatric Sarcoma Data Forms a Unique Cluster Measured via the Earth Mover's Distance.Scientific reports · 2017Article
- Oncodomains: A protein domain-centric framework for analyzing rare variants in tumor samples.PLoS computational biology · 2017Article
- Differential Coexpression Analysis Reveals Extensive Rewiring of Arabidopsis Gene Coexpression in Response to Pseudomonas syringae Infection.Scientific reports · 2016Article
- Tissue-specific and convergent metabolic transformation of cancer correlates with metastatic potential and patient survival.Nature communications · 2016Article
- Independent and core pathways in oncogenic KRAS signaling.Expert review of proteomics · 2016Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Tumorigenesis requires the re-organization of metabolism to support malignant proliferation. We examine how the altered metabolism of cancer cells is reflected in the rewiring of co-expression patterns among metabolic genes. Focusing on breast and clear-cell kidney tumors, we report the existence of key metabolic genes which act as hubs of differential co-expression, showing significantly different co-regulation patterns between normal and tumor states. We compare our findings to those from classical differential expression analysis, and counterintuitively observe that the extent of a gene's differential co-expression only weakly correlates with its differential expression, suggesting that the two measures probe different features of metabolism. Focusing on this discrepancy, we use changes in co-expression patterns to highlight the apparent loss of regulation by the transcription factor HNF4A in clear cell renal cell carcinoma, despite no differential expression of HNF4A. Finally, we aggregate the results of differential co-expression analysis into a Pan-Cancer analysis across seven distinct cancer types to identify pairs of metabolic genes which may be recurrently dysregulated. Among our results is a cluster of four genes, all components of the mitochondrial electron transport chain, which show significant loss of co-expression in tumor tissue, pointing to potential mitochondrial dysfunction in these tumor types.
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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.