Tissue-specific regulatory circuits reveal variable modular perturbations across complex diseases
Open accessAbstract
Mapping perturbed molecular circuits that underlie complex diseases remains a great challenge. We developed a comprehensive resource of 394 cell type- and tissue-specific gene regulatory networks for human, each specifying the genome-wide connectivity among transcription factors, enhancers, promoters and genes. Integration with 37 genome-wide association studies (GWASs) showed that disease-associated genetic variants--including variants that do not reach genome-wide significance--often perturb regulatory modules that are highly specific to disease-relevant cell types or tissues. Our resource opens the door to systematic analysis of regulatory programs across hundreds of human cell types and tissues (http://regulatorycircuits.org).
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Marbach et al. overlaid GWAS results onto tissue-specific regulatory networks and identified modules enriched for genetic variants in each disease.
“They then overlaid the GWAS results of diseases onto tissue-specific regulatory networks in the disease-relevant tissues and identified modules particularly enriched for genetic variants in each disease.”
From Multi-omics approaches to disease (2017) · cites this paper as [79]
Marbach and colleagues combined genomics, epigenomics, and transcriptomics to elucidate tissue-specific regulatory circuits in 394 human cell types.
“For example, Marbach and colleagues [79] combined genomics, epigenomics, and transcriptomics to elucidate tissue-specific regulatory circuits in 394 human cell types.”
From Multi-omics approaches to disease (2017) · cites this paper as [79]
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“80 and used by the popular DAPPLE tool11 probabilistically integrates evidence from diverse sources, including MINT, BIND, IntAct, KEGG annotated protein-protein interactions (PPrel), KEGG Enzymes involved in neighboring steps (ECrel), Reactome and others; (2) Entrez GeneRIF (gene reference into function) includes pro…”
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Computational tools for inferring transcription factor activity
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Self-citationTranscription Factor and lncRNA Regulatory Networks Identify Key Elements in Lung Adenocarcinoma
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- Authors
- Marbach, D., Lamparter, D., Quon, G., Kellis, M., Kutalik, Z., & Bergmann, S.
- Affiliations
- SIB Swiss Institute of Bioinformatics (CH)
- Broad Institute (US)
- Corresponding author
- Marbach, Daniel
- Venue
- Nature Methods
- Published
- 2016-03-07
- Volume
- 13
- Issue
- 4
- Pages
- 366-370
- ISSN
- 1548-7091 (ISSN-L)
- 1548-7105
- PMC
- PMC4967716
- OpenAlex
- W2295275561
- Cited by
- 326
- References
- 86
- Citations by year
- 2026: 13 · 2025: 14 · 2024: 29 · 2023: 24 · 2022: 39 · 2021: 39 · 2020: 50 · 2019: 40 · 2018: 40 · 2017: 25 · 2016: 12
- FWCI
- 20.44
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Methods (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- DSpace@MIT (Massachusetts Institute of Technology) (submittedVersion, cc-by-nc)
- eScholarship (California Digital Library) (submittedVersion)
- IRIS (submittedVersion)
- SERVAL (Université de Lausanne) (submittedVersion)
- PMC
- Funders
- National Science Foundation
- Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (51RTP0_151019, 143914, 151019, 31003A, 152724, 310030)
- Fondation Leenaards
- National Institute of Mental Health (R01MH109978)
- National Human Genome Research Institute (R01HG008155, R01HG004037)
- National Institute of General Medical Sciences (R01GM113708)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Keywords
- gene regulatory networks, tissue-specific gene regulation, cell type-specific gene regulation, complex diseases, disease-associated variants, regulatory modules, transcription factors, enhancers, promoter, genome-wide association study, regulatory circuits
- MeSH terms
- Brain Diseases, Humans, Organ Specificity, Promoter Regions, Genetic, Transcription Factors, Genetic Variation, Genome, Human, Cell Lineage, Computational Biology, Protein Interaction Mapping, Gene Regulatory Networks, Genome-Wide Association Study, Epigenomics
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Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
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