ArticleNucleic acids research2012
Gene network inference and visualization tools for biologists: application to new human transcriptome datasets.
Article in Nucleic acids research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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Who cites it
37 citing papers in PubMed.
- An essential gene signature of breast cancer metastasis reveals targetable pathways.Breast cancer research : BCR · 2024Article
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- Pan-cancer molecular subtypes of metastasis reveal distinct and evolving transcriptional programs.Cell reports. Medicine · 2023Article
- Co-Expression Analysis of Airway Epithelial Transcriptome in Asthma Patients with Eosinophilic vs. Non-Eosinophilic Airway Infiltration.International journal of molecular sciences · 2023Article
- bulkAnalyseR: an accessible, interactive pipeline for analysing and sharing bulk multi-modal sequencing data.Briefings in bioinformatics · 2023Article
- FABP4 Controls Fat Mass Expandability (Adipocyte Size and Number) through Inhibition of CD36/SR-B2 Signalling.International journal of molecular sciences · 2023Article
- Atlas of regulated target genes of transcription factors (ART-TF) in human ES cells.BMC bioinformatics · 2022Article
- Accurate determination of causalities in gene regulatory networks by dissecting downstream target genes.Frontiers in genetics · 2022Article
- Review
- ESDN inhibits melanoma progression by blocking E-selectin expression in endothelial cells via STAT3.Cancer letters · 2021Article
- An order independent algorithm for inferring gene regulatory network using quantile value for conditional independence tests.Scientific reports · 2021Article
- IFNγ, and to a Lesser Extent TNFα, Provokes a Sustained Endothelial Costimulatory Phenotype.Frontiers in immunology · 2021Article
- Environmental Impact on Male (In)Fertility via Epigenetic Route.Journal of clinical medicine · 2020Review
- Oxidized phospholipids regulate amino acid metabolism through MTHFD2 to facilitate nucleotide release in endothelial cells.Nature communications · 2018Article
- Dual regulation of Stat1 and Stat3 by the tumor suppressor protein PML contributes to interferon α-mediated inhibition of angiogenesis.The Journal of biological chemistry · 2017Article
- Data-driven reverse engineering of signaling pathways using ensembles of dynamic models.PLoS computational biology · 2017Article
- Past Roadblocks and New Opportunities in Transcription Factor Network Mapping.Trends in genetics : TIG · 2016Review
- Information theoretic approaches for inference of biological networks from continuous-valued data.BMC systems biology · 2016Article
- Inferring gene targets of drugs and chemical compounds from gene expression profiles.Bioinformatics (Oxford, England) · 2016Article
- Integrating Transcriptomic and Proteomic Data Using Predictive Regulatory Network Models of Host Response to Pathogens.PLoS computational biology · 2016Article
Corrections and comments
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Authors and funding
19 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Gene regulatory networks inferred from RNA abundance data have generated significant interest, but despite this, gene network approaches are used infrequently and often require input from bioinformaticians. We have assembled a suite of tools for analysing regulatory networks, and we illustrate their use with microarray datasets generated in human endothelial cells. We infer a range of regulatory networks, and based on this analysis discuss the strengths and limitations of network inference from RNA abundance data. We welcome contact from researchers interested in using our inference and visualization tools to answer biological questions.
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Registered trials
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