How Difficult Is Inference of Mammalian Causal Gene Regulatory Networks?

PLoS ONE

Volumn 9, Issue 11, 2014, Pages

  Djordjevic, Djordje ^a,b   Yang, Andrian ^a   Zadoorian, Armella ^a,b   Rungrugeecharoen, Kevin ^a,b   Ho, Joshua W K ^a,b  

^a VICTOR CHANG CARDIAC RESEARCH INSTITUTE   (Australia)

^b UNIVERSITY OF NEW SOUTH WALES   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

CELL POPULATION; DEVELOPMENTAL STAGE; DIAGNOSTIC TEST ACCURACY STUDY; EMBRYO; EXPERIMENTAL MODEL; GENE DISRUPTION; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE OVEREXPRESSION; GENE REGULATORY NETWORK; INFORMATION PROCESSING; KNOCKOUT GENE; MAMMAL; ORGANOGENESIS; SENSITIVITY AND SPECIFICITY; ANIMAL; EMBRYOLOGY; HEART; HEART MUSCLE; METABOLISM; MOUSE; PROTEIN PROTEIN INTERACTION; SIGNAL TRANSDUCTION; TOOTH;

ANIMALS; GENE EXPRESSION REGULATION, DEVELOPMENTAL; GENE REGULATORY NETWORKS; HEART; MICE; MYOCARDIUM; PROTEIN INTERACTION MAPS; SIGNAL TRANSDUCTION; TOOTH;

EID: 84932093797     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0111661     Document Type: Article

References (33)

1. Davidson EH (2006) The regulatory genome: Gene regulatory networks in development and evolution. Amsterdam: Academic Press.
2. Ho JWK (2012) Application of a systems approach to study developmental gene regulation. Biophysical Reviews 4: 245-253.
3. Davidson EH (2010) Emerging properties of animal gene regulatory networks. Nature 468: 911-920.
4. Levine M, Davidson EH (2005) Gene regulatory networks for development. Proceedings of the National Academy of Sciences of the United States of America 102: 4936-4942.
5. Kitano H (2002) Computational systems biology. Nature 420: 206-210.
6. Friedman N, Linial M, Nachman I, Pe'er D (2000) Using Bayesian networks to analyze expression data. Journal of Computational Biology 7: 601-620.
7. Bansal M, Belcastro V, Ambesi-Impiombato A, di Bernardo D (2007) How to infer gene networks from expression profiles. Molecular Systems Biology 3: 78.
8. Wang Y, Penfold CA, Hodgson DA, Gifford ML, Burroughs NJ (2014) Correcting for link loss in causal network inference caused by regulator interference. Bioinformatics.
9. Barzel B, Barabsi AL (2013) Network link prediction by global silencing of indirect correlations. Nature Biotechnology 31: 720725.
10. Glass K, Huttenhower C, Quackenbush J, Yuan GC (2013) Passing messages between biological networks to refine predicted interactions. PLoS ONE 8: E64832.
11. Maathuis MH, Colombo D, Kalisch M, Bhlmann P (2010) Predicting causal effects in large-scale systems from observational data. Nature Methods 7: 247248.
12. Marbach D, Prill RJ, Schaffter T, Mattiussi C, Floreano D, et al. (2010) Revealing strengths and weaknesses of methods for gene network inference. Proceedings of the National Academy of Sciences 107: 6286-6291.
13. Marbach D, Costello JC, Kffner R, Vega NM, Prill RJ, et al. (2012) Wisdom of crowds for robust gene network inference. Nature Methods 9: 796-804.
14. Wagner A (2001) How to reconstruct a large genetic network from n gene perturbations in fewer than n2 easy steps. Bioinformatics 17: 11831197.
15. Markowetz F, Bloch J, Spang R (2005) Non-transcriptional pathway features reconstructed from secondary effects of rna interference. Bioinformatics 21: 40264032.
16. Frhlich H, Tresch A, Beibarth T (2009) Nested effects models for learning signaling networks from perturbation data. Biom J 51: 304323.
17. Frhlich H, Sahin z, Arlt D, Bender C, Beibarth T (2009) Deterministic effects propagation networks for reconstructing protein signaling networks from multiple interventions. BMC Bioinformatics 10: 322.
18. Pinna A, Soranzo N, De La Fuente A (2010) From knockouts to networks: Establishing direct cause-effect relationships through graph analysis. PLoS ONE 5: E12912.
19. Huynh-Thu VA, Irrthum A, Wehenkel L, Geurts P (2010) Inferring regulatory networks from expression data using tree-based methods. PLoS ONE 5: E12776.
20. Margolin AA, Nemenman I, Basso K, Wiggins C, Stolovitzky G, et al. (2006) ARACNE: An algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context. BMC Bioinformatics 7 Suppl 1: S7.
21. Buckingham M, Meilhac S, Zaffran S (2005) Building the mammalian heart from two sources of myocardial cells. Nature Reviews Genetics 6: 826837.
22. Olsen C, Fleming K, Prendergast N, Rubio R, Emmert-Streib F, et al. (2014) Inference and validation of predictive gene networks from biomedical literature and gene expression data. Genomics 103: 329336.
23. O'Connell DJ, Ho JWK, Mammoto T, Turbe-Doan A, O'Connell JT, et al. (2012) A Wnt-Bmp feedback circuit controls intertissue signaling dynamics in tooth organogenesis. Science Signaling 5: Ra4.
24. Smyth GK (2005) Limma: Linear models for microarray data. In: Gentleman R, Carey V, Dudoit S, Irizarry R, Huber W, editors, Bioinformatics and Computational Biology Solutions Using R and Bioconductor, New York: Springer. pp. 397-420.
25. Meyer PE, Lafitte F, Bontempi G (2008) minet: A R/Bioconductor package for inferring large transcriptional networks using mutual information. BMC Bioinformatics 9: 461.
26. Margolin AA, Wang K, Lim WK, Kustagi M, Nemenman I, et al. (2006) Reverse engineering cellular networks. Nature Protocols 1: 662-671.
27. Mora A, Donaldson IM (2011) iRefR: An R package to manipulate the iRefIndex consolidated protein interaction database. BMC Bioinformatics 12: 455.
28. Csardi G, Nepusz T (2006) The igraph software package for complex network research. InterJournal Complex Systems: 1695.
29. Sing T, Sander O, Beerenwinkel N, Lengauer T (2005) ROCR: Visualizing classifier performance in R. Bioinformatics 21: 39403941.
30. Odom DT (2004) Control of pancreas and liver gene expression by hnf transcription factors. Science 303: 13781381.
31. Li TR, White KP (2003) Tissue-specific gene expression and ecdysone-regulated genomic networks in drosophila. Developmental Cell 5: 5972.
32. Rustici G, Kolesnikov N, Brandizi M, Burdett T, Dylag M, et al. (2013) ArrayExpress update - trends in database growth and links to data analysis tools. Nucleic Acids Research 41: D987-D990.
33. Edgar R (2002) Gene Expression Omnibus: NCBI gEnE expression and hybridization array data repository. Nucleic Acids Research 30: 207210.