ArticleFrontiers in oncology2020
Gene Co-expression Is Distance-Dependent in Breast Cancer.
Article in Frontiers in oncology, 2020. 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.
- Epigenetic and immunological alterations in umbilical cord blood of overweight/obese women with gestational diabetes mellitus: insights into DNA methylation signatures and immune cell dysregulation.BMC pregnancy and childbirth · 2026Article
- Loss of long-range co-expression is a common feature in cancer.NPJ systems biology and applications · 2026Article
- Patient-specific gene co-expression networks reveal novel subtypes and predictive biomarkers in lung adenocarcinoma.NPJ systems biology and applications · 2025Article
- Integration of chromosome conformation and gene expression networks reveals regulatory mechanisms in triple negative breast cancer.Frontiers in cell and developmental biology · 2025Article
- Single-Sample Networks Reveal Intra-Cytoband Co-Expression Hotspots in Breast Cancer Subtypes.International journal of molecular sciences · 2024Article
- Coordinated inflammation and immune response transcriptional regulation in breast cancer molecular subtypes.Frontiers in immunology · 2024Article
- Gene co-expression networks reveal sex-biased differences in musculoskeletal ageing.Frontiers in aging · 2024Article
- The network structure of hematopoietic cancers.Scientific reports · 2023Article
- Multiscale network modeling reveals the gene regulatory landscape driving cancer prognosis in 32 cancer types.Genome research · 2023Article
- Pseudogenes in Cancer: State of the Art.Cancers · 2023Review
- CNVs in 8q24.3 do not influence gene co-expression in breast cancer subtypes.Frontiers in genetics · 2023Article
- Methylation-related genes involved in renal carcinoma progression.Frontiers in genetics · 2023Article
- The Breast Cancer Protein Co-Expression Landscape.Cancers · 2022Article
- Functional impact of multi-omic interactions in breast cancer subtypes.Frontiers in genetics · 2022Article
- The Role of Copy Number Variants in Gene Co-Expression Patterns for Luminal B Breast Tumors.Frontiers in genetics · 2022Article
- Oncogenic Role of miR-217 During Clear Cell Renal Carcinoma Progression.Frontiers in oncology · 2022Article
- k-core genes underpin structural features of breast cancer.Scientific reports · 2021Article
- Gene Co-Expression in Breast Cancer: A Matter of Distance.Frontiers in oncology · 2021Article
- Modularity in Biological Networks.Frontiers in genetics · 2021Review
- Similarities and Differences in Gene Expression Networks Between the Breast Cancer Cell Line Michigan Cancer Foundation-7 and Invasive Human Breast Cancer Tissues.Frontiers in artificial intelligence · 2021Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Breast carcinomas are characterized by anomalous gene regulatory programs. As is well-known, gene expression programs are able to shape phenotypes. Hence, the understanding of gene co-expression may shed light on the underlying mechanisms behind the transcriptional regulatory programs affecting tumor development and evolution. For instance, in breast cancer, there is a clear loss of inter-chromosomal (trans-) co-expression, compared with healthy tissue. At the same time cis- (intra-chromosomal) interactions are favored in breast tumors. In order to have a deeper understanding of regulatory phenomena in cancer, here, we constructed Gene Co-expression Networks by using TCGA-derived RNA-seq whole-genome samples corresponding to the four breast cancer molecular subtypes, as well as healthy tissue. We quantify the cis-/trans- co-expression imbalance in all phenotypes. Additionally, we measured the association between co-expression and physical distance between genes, and characterized the ratio of intra/inter-cytoband interactions per phenotype. We confirmed loss of trans- co-expression in all molecular subtypes. We also observed that gene cis- co-expression decays abruptly with distance in all tumors in contrast with healthy tissue. We observed co-expressed gene hotspots, that tend to be connected at cytoband regions, and coincide accurately with already known copy number altered regions, such as Chr17q12, or Chr8q24.3 for all subtypes. Our methodology recovered different alterations already reported for specific breast cancer subtypes, showing how co-expression network approaches might help to capture distinct events that modify the cell regulatory program.
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