ArticleScientific reports2017
RNA-Seq based genome-wide analysis reveals loss of inter-chromosomal regulation in breast cancer.
Article in Scientific reports, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers, 1 of them a synthesis that pooled it.
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Who cites it
34 citing papers in PubMed, 1 synthesis or guideline pooled it, 57 citations in OpenAlex.
- Unveiling the Link Between Inflammation and Adaptive Immunity in Breast Cancer.Frontiers in immunology · 2019Pooled it
- Loss of long-range co-expression is a common feature in cancer.NPJ systems biology and applications · 2026Article
- Pseudogene Coexpression Networks Reveal a Robust Prognostic Signature for Pediatric B-ALL Survival.Cancer research communications · 2026Article
- Patient-specific gene co-expression networks reveal novel subtypes and predictive biomarkers in lung adenocarcinoma.NPJ systems biology and applications · 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
- Pseudogenes in Cancer: State of the Art.Cancers · 2023Review
- Methylation-related genes involved in renal carcinoma progression.Frontiers in genetics · 2023Article
- CNVs in 8q24.3 do not influence gene co-expression in breast cancer subtypes.Frontiers in genetics · 2023Article
- The Breast Cancer Protein Co-Expression Landscape.Cancers · 2022Article
- Oncogenic Role of miR-217 During Clear Cell Renal Carcinoma Progression.Frontiers in oncology · 2022Article
- The Role of Copy Number Variants in Gene Co-Expression Patterns for Luminal B Breast Tumors.Frontiers in genetics · 2022Article
- Spatial variation in gene expression of Tasmanian devil facial tumors despite minimal host transcriptomic response to infection.BMC genomics · 2021Article
- Gene Co-Expression in Breast Cancer: A Matter of Distance.Frontiers in oncology · 2021Article
- An Information Theoretical Multilayer Network Approach to Breast Cancer Transcriptional Regulation.Frontiers in genetics · 2021Article
- Luminal A Breast Cancer Co-expression Network: Structural and Functional Alterations.Frontiers in genetics · 2021Article
- Loss of Long Distance Co-Expression in Lung Cancer.Frontiers in genetics · 2021Article
- Modularity in Biological Networks.Frontiers in genetics · 2021Review
Corrections and comments
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Authors and funding
4 authors at 3 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Breast cancer is a complex heterogeneous disease. Common hallmark features of cancer can be found. Their origin may be traced back to their intricate relationships governing regulatory programs during the development of this disease. To unveil distinctive features of the transcriptional regulation program in breast cancer, a pipeline for RNA-seq analysis in 780 breast cancer and 101 healthy breast samples, at gene expression and network level, was implemented. Inter-chromosomal relationships between genes resulted strikingly scarce in a cancer network, in comparison to its healthy counterpart. We suggest that inter-chromosomal regulation loss may be a novel feature in breast cancer. Additional evidence was obtained by independent validation in microarray and Hi-C data as well as supplementary computational analyses. Functional analysis showed upregulation in processes related to cell cycle and division; while migration, adhesion and cell-to-cell communication, were downregulated. Both the BRCA1 DNA repairing signalling and the Estrogen-mediated G1/S phase entry pathways were found upregulated. In addition, a synergistic underexpression of the γ-protocadherin complex, located at Chr5q31 is also shown. This region has previously been reported to be hypermethylated in breast cancer. These findings altogether provide further evidence for the central role of transcriptional regulatory programs in shaping malignant phenotypes.
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