ArticleBMC genomics2013
Coexpression analysis of large cancer datasets provides insight into the cellular phenotypes of the tumour microenvironment.
Article in BMC genomics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers, 1 of them a synthesis that pooled it.
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Who cites it
21 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Gene Network Rewiring to Study Melanoma Stage Progression and Elements Essential for Driving Melanoma.PloS one · 2015Pooled it
- 25 Years of Cancer Immunoediting: Dendritic Cells and Macrophages Filled the Missing Gap.Cancers · 2026Review
- Transcriptomic signatures of host immune responses in aphthous ulcers, the earliest lesions of Crohn's disease, suggest that bacterial uptake, rather than global dysbiosis, is the initiating factor.Immunology and cell biology · 2025Article
- Association analysis of melanophilin (Archives animal breeding · 2023Article
- Detection of key mRNAs in liver tissue of hepatocellular carcinoma patients based on machine learning and bioinformatics analysis.MethodsX · 2023Article
- Generation and network analysis of an RNA-seq transcriptional atlas for the rat.NAR genomics and bioinformatics · 2022Article
- Network analysis of transcriptomic diversity amongst resident tissue macrophages and dendritic cells in the mouse mononuclear phagocyte system.PLoS biology · 2020Article
- The Adaptive and Innate Immune Cell Landscape of Uterine Leiomyosarcomas.Scientific reports · 2020Article
- Assembly of a parts list of the human mitotic cell cycle machinery.Journal of molecular cell biology · 2019Article
- Optimal pathways involved in the treatment of sevoflurane or propofol for patients undergoing coronary artery bypass graft surgery.Experimental and therapeutic medicine · 2019Article
- Combination of novel and public RNA-seq datasets to generate an mRNA expression atlas for the domestic chicken.BMC genomics · 2018Article
- Classification of gene signatures for their information value and functional redundancy.NPJ systems biology and applications · 2018Article
- A high resolution atlas of gene expression in the domestic sheep (Ovis aries).PLoS genetics · 2017Article
- Differential co-expression analysis reveals a novel prognostic gene module in ovarian cancer.Scientific reports · 2017Article
- Prediction of optimal gene functions for osteosarcoma using network-based- guilt by association method based on gene oncology and microarray profile.Journal of bone oncology · 2017Article
- Modulation of macrophage antitumor potential by apoptotic lymphoma cells.Cell death and differentiation · 2017Article
- Derivation of marker gene signatures from human skin and their use in the interpretation of the transcriptional changes associated with dermatological disorders.The Journal of pathology · 2017Article
- Extensive rewiring of epithelial-stromal co-expression networks in breast cancer.Genome biology · 2015Article
- A null model for Pearson coexpression networks.PloS one · 2015Article
- The Many Alternative Faces of Macrophage Activation.Frontiers in immunology · 2015Review
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
backgroundBiopsies taken from individual tumours exhibit extensive differences in their cellular composition due to the inherent heterogeneity of cancers and vagaries of sample collection. As a result genes expressed in specific cell types, or associated with certain biological processes are detected at widely variable levels across samples in transcriptomic analyses. This heterogeneity also means that the level of expression of genes expressed specifically in a given cell type or process, will vary in line with the number of those cells within samples or activity of the pathway, and will therefore be correlated in their expression.
resultsUsing a novel 3D network-based approach we have analysed six large human cancer microarray datasets derived from more than 1,000 individuals. Based upon this analysis, and without needing to isolate the individual cells, we have defined a broad spectrum of cell-type and pathway-specific gene signatures present in cancer expression data which were also found to be largely conserved in a number of independent datasets.
conclusionsThe conserved signature of the tumour-associated macrophage is shown to be largely-independent of tumour cell type. All stromal cell signatures have some degree of correlation with each other, since they must all be inversely correlated with the tumour component. However, viewed in the context of established tumours, the interactions between stromal components appear to be multifactorial given the level of one component e.g. vasculature, does not correlate tightly with another, such as the macrophage.
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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.