Leveraging Models of Cell Regulation and GWAS Data in Integrative Network-based Association Studies

Overview

Journal Nat Genet

Specialty Genetics

Date 2012 Jul 28

PMID 22836096

Citations 140

Authors

Andrea Califano

Atul J Butte

Stephen Friend

Trey Ideker

Eric Schadt

Affiliations

Soon will be listed here.

Citing Articles

Multi-tissue network analysis reveals the effect of JNK inhibition on dietary sucrose-induced metabolic dysfunction in rats.

Yang H, Zhang C, Kim W, Shi M, Kiliclioglu M, Bayram C Elife. 2025; 13.

PMID: 39932177 PMC: 11813226. DOI: 10.7554/eLife.98427.

Toxicogenomics Approaches to Address Toxicity and Carcinogenicity in the Liver.

Pandiri A, Auerbach S, Stevens J, Blomme E Toxicol Pathol. 2024; 51(7-8):470-481.

PMID: 38288963 PMC: 11014763. DOI: 10.1177/01926233241227942.

Genome-Wide Genetic Associations Prioritize Evaluation of Causal Mechanisms of Atherosclerotic Disease Risk.

Quertermous T, Li D, Weldy C, Ramste M, Sharma D, Monteiro J Arterioscler Thromb Vasc Biol. 2024; 44(2):323-327.

PMID: 38266112 PMC: 10857784. DOI: 10.1161/ATVBAHA.123.319480.

A multi-layered network model identifies Akt1 as a common modulator of neurodegeneration.

Na D, Lim D, Hong J, Lee H, Cho D, Yu M Mol Syst Biol. 2023; 19(12):e11801.

PMID: 37984409 PMC: 10698508. DOI: 10.15252/msb.202311801.

Integrative genetic and genomic networks identify microRNA associated with COPD and ILD.

Pavel A, Garrison C, Luo L, Liu G, Taub D, Xiao J Sci Rep. 2023; 13(1):13076.

PMID: 37567908 PMC: 10421936. DOI: 10.1038/s41598-023-39751-w.

References

Birtwistle M, Hatakeyama M, Yumoto N, Ogunnaike B, Hoek J, Kholodenko B . Ligand-dependent responses of the ErbB signaling network: experimental and modeling analyses. Mol Syst Biol. 2007; 3:144. PMC: 2132449. DOI: 10.1038/msb4100188. View

Zeggini E, Scott L, Saxena R, Voight B, Marchini J, Hu T . Meta-analysis of genome-wide association data and large-scale replication identifies additional susceptibility loci for type 2 diabetes. Nat Genet. 2008; 40(5):638-45. PMC: 2672416. DOI: 10.1038/ng.120. View

Kinzler K, Vogelstein B . Landscaping the cancer terrain. Science. 1998; 280(5366):1036-7. DOI: 10.1126/science.280.5366.1036. View

Pandey G, Zhang B, Chang A, Myers C, Zhu J, Kumar V . An integrative multi-network and multi-classifier approach to predict genetic interactions. PLoS Comput Biol. 2010; 6(9). PMC: 2936518. DOI: 10.1371/journal.pcbi.1000928. View

Subramanian A, Tamayo P, Mootha V, Mukherjee S, Ebert B, Gillette M . Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A. 2005; 102(43):15545-50. PMC: 1239896. DOI: 10.1073/pnas.0506580102. View

Hardy J, Singleton A . Genomewide association studies and human disease. N Engl J Med. 2009; 360(17):1759-68. PMC: 3422859. DOI: 10.1056/NEJMra0808700. View

Akavia U, Litvin O, Kim J, Sanchez-Garcia F, Kotliar D, Causton H . An integrated approach to uncover drivers of cancer. Cell. 2010; 143(6):1005-17. PMC: 3013278. DOI: 10.1016/j.cell.2010.11.013. View

Chen G, Thomas D . Using biological knowledge to discover higher order interactions in genetic association studies. Genet Epidemiol. 2010; 34(8):863-78. DOI: 10.1002/gepi.20542. View

Emilsson V, Thorleifsson G, Zhang B, Leonardson A, Zink F, Zhu J . Genetics of gene expression and its effect on disease. Nature. 2008; 452(7186):423-8. DOI: 10.1038/nature06758. View

10.

Faust K, Dupont P, Callut J, van Helden J . Pathway discovery in metabolic networks by subgraph extraction. Bioinformatics. 2010; 26(9):1211-8. PMC: 2859126. DOI: 10.1093/bioinformatics/btq105. View

11.

di Bernardo D, Thompson M, Gardner T, Chobot S, Eastwood E, Wojtovich A . Chemogenomic profiling on a genome-wide scale using reverse-engineered gene networks. Nat Biotechnol. 2005; 23(3):377-83. DOI: 10.1038/nbt1075. View

12.

Zhong H, Beaulaurier J, Lum P, Molony C, Yang X, MacNeil D . Liver and adipose expression associated SNPs are enriched for association to type 2 diabetes. PLoS Genet. 2010; 6(5):e1000932. PMC: 2865508. DOI: 10.1371/journal.pgen.1000932. View

13.

Calvano S, Xiao W, Richards D, Felciano R, Baker H, Cho R . A network-based analysis of systemic inflammation in humans. Nature. 2005; 437(7061):1032-7. DOI: 10.1038/nature03985. View

14.

Chautard E, Thierry-Mieg N, Ricard-Blum S . Interaction networks: from protein functions to drug discovery. A review. Pathol Biol (Paris). 2008; 57(4):324-33. DOI: 10.1016/j.patbio.2008.10.004. View

15.

Narayanan M, Vetta A, Schadt E, Zhu J . Simultaneous clustering of multiple gene expression and physical interaction datasets. PLoS Comput Biol. 2010; 6(4):e1000742. PMC: 2855327. DOI: 10.1371/journal.pcbi.1000742. View

16.

Luscombe N, Babu M, Yu H, Snyder M, Teichmann S, Gerstein M . Genomic analysis of regulatory network dynamics reveals large topological changes. Nature. 2004; 431(7006):308-12. DOI: 10.1038/nature02782. View

17.

Birney E, Stamatoyannopoulos J, Dutta A, Guigo R, Gingeras T, Margulies E . Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 2007; 447(7146):799-816. PMC: 2212820. DOI: 10.1038/nature05874. View

18.

Marko N, Quackenbush J, Weil R . Why is there a lack of consensus on molecular subgroups of glioblastoma? Understanding the nature of biological and statistical variability in glioblastoma expression data. PLoS One. 2011; 6(7):e20826. PMC: 3145641. DOI: 10.1371/journal.pone.0020826. View

19.

Zien A, Kuffner R, Zimmer R, Lengauer T . Analysis of gene expression data with pathway scores. Proc Int Conf Intell Syst Mol Biol. 2000; 8:407-17. View

20.

Zhu J, Chen Y, Leonardson A, Wang K, Lamb J, Emilsson V . Characterizing dynamic changes in the human blood transcriptional network. PLoS Comput Biol. 2010; 6(2):e1000671. PMC: 2820517. DOI: 10.1371/journal.pcbi.1000671. View