ArticleBMC bioinformatics2015
A network model for angiogenesis in ovarian cancer.
Article in BMC bioinformatics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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Who cites it
38 citing papers in PubMed, 73 citations in OpenAlex.
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- Circulating Blood Prognostic Biomarker Signatures for Hemorrhagic Cerebral Cavernous Malformations (CCMs).International journal of molecular sciences · 2024Article
- Current and future directions in network biology.Bioinformatics advances · 2024Article
- Integration of Single-Cell RNA-Sequencing and Network Analysis to Investigate Mechanisms of Drug Resistance.Methods in molecular biology (Clifton, N.J.) · 2023Article
- gpuZoo: Cost-effective estimation of gene regulatory networks using the Graphics Processing Unit.NAR genomics and bioinformatics · 2022Article
- Connections for Matters of the Heart: Network Medicine in Cardiovascular Diseases.Frontiers in cardiovascular medicine · 2022Review
- Constructing gene regulatory networks using epigenetic data.NPJ systems biology and applications · 2021Article
- Transcription factor network analysis based on single cell RNA-seq identifies that Trichostatin-a reverses docetaxel resistance in prostate Cancer.BMC cancer · 2021Article
- Regulatory Network of PD1 Signaling Is Associated with Prognosis in Glioblastoma Multiforme.Cancer research · 2021Article
- Gene Targeting in Disease Networks.Frontiers in genetics · 2021Article
- Placental Gene Co-expression Network for Maternal Plasma Lipids Revealed Enrichment of Inflammatory Response Pathways.Frontiers in genetics · 2021Article
- Molecular networks in Network Medicine: Development and applications.Wiley interdisciplinary reviews. Systems biology and medicine · 2020Review
- PUMA: PANDA Using MicroRNA Associations.Bioinformatics (Oxford, England) · 2020Article
- Sex Differences in Gene Expression and Regulatory Networks across 29 Human Tissues.Cell reports · 2020Article
- Generating Ensembles of Gene Regulatory Networks to Assess Robustness of Disease Modules.Frontiers in genetics · 2020Article
Corrections and comments
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Authors and funding
5 authors at 4 institutions in 2 countries.
Funding
Abstract
backgroundWe recently identified two robust ovarian cancer subtypes, defined by the expression of genes involved in angiogenesis, with significant differences in clinical outcome. To identify potential regulatory mechanisms that distinguish the subtypes we applied PANDA, a method that uses an integrative approach to model information flow in gene regulatory networks.
resultsWe find distinct differences between networks that are active in the angiogenic and non-angiogenic subtypes, largely defined by a set of key transcription factors that, although previously reported to play a role in angiogenesis, are not strongly differentially-expressed between the subtypes. Our network analysis indicates that these factors are involved in the activation (or repression) of different genes in the two subtypes, resulting in differential expression of their network targets. Mechanisms mediating differences between subtypes include a previously unrecognized pro-angiogenic role for increased genome-wide DNA methylation and complex patterns of combinatorial regulation.
conclusionsThe models we develop require a shift in our interpretation of the driving factors in biological networks away from the genes themselves and toward their interactions. The observed regulatory changes between subtypes suggest therapeutic interventions that may help in the treatment of ovarian cancer.
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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.