Networks in Caenorhabditis elegans

Current Opinion in Genetics and Development

Volumn 21, Issue 6, 2011, Pages 787-798

  Gunsalus, Kristin C ^a,b   Rhrissorrakrai, Kahn ^a  

^a NEW YORK UNIVERSITY   (United States)

^b NEW YORK UNIVERSITY ABU DHABI   (United Arab Emirates)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; MICRORNA; TRANSCRIPTION FACTOR;

ASSAY; CAENORHABDITIS ELEGANS; CHROMATIN IMMUNOPRECIPITATION; DEVELOPMENTAL BIOLOGY; EMBRYO DEVELOPMENT; FEEDBACK SYSTEM; FUNCTIONAL GENOMICS; GENE EXPRESSION; GENE MAPPING; GENETIC DATABASE; GENETIC MODEL; GENETIC REGULATION; GENETIC VARIABILITY; HIGH THROUGHPUT SCREENING; MOLECULAR BIOLOGY; MOLECULAR DYNAMICS; MOLECULAR GENETICS; MOLECULAR INTERACTION; MORPHOGENESIS; NETWORK BIOLOGY; NONHUMAN; ORTHOLOGY; PARASITE DEVELOPMENT; PHENOTYPE; PRIORITY JOURNAL; PROTEIN DNA INTERACTION; PROTEIN MOTIF; PROTEIN PROTEIN INTERACTION; PROTEIN RNA BINDING; PROTEOMICS; REVIEW; RNA INTERFERENCE; RNA SEQUENCE; SYSTEMS BIOLOGY; TRANSCRIPTION REGULATION;

ANIMALS; CAENORHABDITIS ELEGANS; CAENORHABDITIS ELEGANS PROTEINS; GENE REGULATORY NETWORKS; GENES, HELMINTH; MODELS, BIOLOGICAL; PHENOTYPE; RNA PROCESSING, POST-TRANSCRIPTIONAL; SYSTEMS BIOLOGY; TRANSCRIPTION, GENETIC;

ANIMALIA; CAENORHABDITIS ELEGANS; NEMATODA;

EID: 81955164148     PISSN: 0959437X     EISSN: 18790380     Source Type: Journal    
DOI: 10.1016/j.gde.2011.10.003     Document Type: Review

References (118)

1. Goh K.I., Cusick M.E., Valle D., Childs B., Vidal M., Barabasi A.L. The human disease network. Proc Natl Acad Sci U S A 2007, 104:8685-8690.
2. Barabasi A.L., Oltvai Z.N. Network biology: understanding the cell's functional organization. Nat Rev Genet 2004, 5:101-113.
3. Han J.D., Dupuy D., Bertin N., Cusick M.E., Vidal M. Effect of sampling on topology predictions of protein-protein interaction networks. Nat Biotechnol 2005, 23:839-844.
4. Felix M.A., Wagner A. Robustness and evolution: concepts, insights and challenges from a developmental model system. Heredity 2008, 100:132-140.
5. Masel J., Siegal M.L. Robustness: mechanisms and consequences. Trends Genet 2009, 25:395-403.
6. Gillis J., Pavlidis P. The impact of multifunctional genes on guilt by association analysis. PloS One 2011, 6:e17258.
7. Han J.D., Bertin N., Hao T., Goldberg D.S., Berriz G.F., Zhang L.V., Dupuy D., Walhout A.J., Cusick M.E., Roth F.P., et al. Evidence for dynamically organized modularity in the yeast protein-protein interaction network. Nature 2004, 430:88-93.
8. Hartwell L.H., Hopfield J.J., Leibler S., Murray A.W. From molecular to modular cell biology. Nature 1999, 402:C47-C52.
9. Spirin V., Mirny L.A. Protein complexes and functional modules in molecular networks. Proc Natl Acad Sci U S A 2003, 100:12123-12128.
10. Costanzo M., Baryshnikova A., Myers C.L., Andrews B., Boone C. Charting the genetic interaction map of a cell. Curr Opin Biotechnol 2011, 22:66-74.
11. Milo R., Shen-Orr S., Itzkovitz S., Kashtan N., Chklovskii D., Alon U. Network motifs: simple building blocks of complex networks. Science 2002, 298:824-827.
12. Zhang L.V., King O.D., Wong S.L., Goldberg D.S., Tong A.H., Lesage G., Andrews B., Bussey H., Boone C., Roth F.P. Motifs, themes and thematic maps of an integrated Saccharomyces cerevisiae interaction network. J Biol 2005, 4:6.
13. Veeramani B., Bader J.S. Metabolic flux correlations, genetic interactions, and disease. J Comput Mol Cell Biol 2009, 16:291-302.
14. Madar A., Bonneau R. Learning global models of transcriptional regulatory networks from data. Methods Mol Biol 2009, 541:181.
15. Van Nostrand EL, Kim SK: Systems Biology of C. elegans. Curr Opin Genet Dev 2011 (this issue).
16. Li S., Armstrong C.M., Bertin N., Ge H., Milstein S., Boxem M., Vidalain P.O., Han J.D., Chesneau A., Hao T., et al. A map of the interactome network of the metazoan C. elegans. Science 2004, 303:540-543.
17. Simonis N., Rual J.F., Carvunis A.R., Tasan M., Lemmens I., Hirozane-Kishikawa T., Hao T., Sahalie J.M., Venkatesan K., Gebreab F., et al. Empirically controlled mapping of the Caenorhabditis elegans protein-protein interactome network. Nat Methods 2009, 6:47-54.
18. Lamesch P., Milstein S., Hao T., Rosenberg J., Li N., Sequerra R., Bosak S., Doucette-Stamm L., Vandenhaute J., Hill D.E., et al. C. elegans ORFeome version 3.1: increasing the coverage of ORFeome resources with improved gene predictions. Genome Res 2004, 14:2064-2069.
19. Salehi-Ashtiani K., Lin C., Hao T., Shen Y., Szeto D., Yang X., Ghamsari L., Lee H., Fan C., Murray R.R., et al. Large-scale RACE approach for proactive experimental definition of C. elegans ORFeome. Genome Res 2009, 19:2334-2342.
20. Schrimpf S.P., Weiss M., Reiter L., Ahrens C.H., Jovanovic M., Malmstrom J., Brunner E., Mohanty S., Lercher M.J., Hunziker P.E., et al. Comparative functional analysis of the Caenorhabditis elegans and Drosophila melanogaster proteomes. PLoS Biol 2009, 7:e48.
21. Merrihew G.E., Davis C., Ewing B., Williams G., Kall L., Frewen B.E., Noble W.S., Green P., Thomas J.H., MacCoss M.J. Use of shotgun proteomics for the identification, confirmation, and correction of C. elegans gene annotations. Genome Res 2008, 18:1660-1669.
22. Allen M.A., Hillier L.W., Waterston R.H., Blumenthal T. A global analysis of C. elegans trans-splicing. Genome Res 2011, 21:255-264.
23. Gerstein M.B., Lu Z.J., Van Nostrand E.L., Cheng C., Arshinoff B.I., Liu T., Yip K.Y., Robilotto R., Rechtsteiner A., Ikegami K., et al. Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. Science 2010, 330:1775-1787.
24. Hillier L.W., Reinke V., Green P., Hirst M., Marra M.A., Waterston R.H. Massively parallel sequencing of the polyadenylated transcriptome of C. elegans. Genome Res 2009, 19:657-666.
25. Jan C.H., Friedman R.C., Ruby J.G., Bartel D.P. Formation, regulation and evolution of Caenorhabditis elegans 3' UTRs. Nature 2011, 469:97-101.
26. Mangone M., Manoharan A.P., Thierry-Mieg D., Thierry-Mieg J., Han T., Mackowiak S.D., Mis E., Zegar C., Gutwein M.R., Khivansara V., et al. The landscape of C. elegans 3' UTRs. Science 2010, 329:432-435.
27. Boxem M., Maliga Z., Klitgord N., Li N., Lemmens I., Mana M., de Lichtervelde L., Mul J.D., van de Peut D., Devos M., et al. A protein domain-based interactome network for C. elegans early embryogenesis. Cell 2008, 134:534-545.
28. Dreze M., Charloteaux B., Milstein S., Vidalain P.O., Yildirim M.A., Zhong Q., Svrzikapa N., Romero V., Laloux G., Brasseur R., et al. 'Edgetic' perturbation of a C. elegans BCL2 ortholog. Nat Methods 2009, 6:843-849.
29. Cheeseman I.M., Niessen S., Anderson S., Hyndman F., Yates J.R., Oegema K., Desai A. A conserved protein network controls assembly of the outer kinetochore and its ability to sustain tension. Genes Dev 2004, 18:2255-2268.
30. Skop A.R., Liu H., Yates H., Meyer B.J., Heald R. Dissection of the mammalian midbody proteome reveals conserved cytokinesis mechanisms. Science 2004, 305:61-66.
31. Giaever G., Chu A.M., Ni L., Connelly C., Riles L., Veronneau S., Dow S., Lucau-Danila A., Anderson K., Andre B., et al. Functional profiling of the Saccharomyces cerevisiae genome. Nature 2002, 418:387-391.
32. Rual J.F., Ceron J., Koreth J., Hao T., Nicot A.S., Hirozane-Kishikawa T., Vandenhaute J., Orkin S.H., Hill D.E., van den Heuvel S., et al. Toward improving Caenorhabditis elegans phenome mapping with an ORFeome-based RNAi library. Genome Res 2004, 14:2162-2168.
33. Kamath R.S., Fraser A.G., Dong Y., Poulin G., Durbin R., Gotta M., Kanapin A., Le Bot N., Moreno S., Sohrmann M., et al. Systematic functional analysis of the Caenorhabditis elegans genome using RNAi. Nature 2003, 421:231-237.
34. Simmer F., Moorman C., van der Linden A.M., Kuijk E., van den Berghe P.V., Kamath R.S., Fraser A.G., Ahringer J., Plasterk R.H. Genome-wide RNAi of C. elegans using the hypersensitive rrf-3 strain reveals novel gene functions. PLoS Biol 2003, 1:E12.
35. Sönnichsen B., Koski L., Walsh A., Marshall P., Neumann F., Brehm M., Alleaume A-M., Bettencourt P., Cassin E., Hewitson M., et al. Full-genome RNAi profiling of early embryogenesis in Caenorhabditis elegans. Nature 2005, 434:462-469.
36. Mani R., St Onge R.P., Hartman J.L.t., Giaever G., Roth F.P. Defining genetic interaction. Proc Natl Acad Sci U S A 2008, 105:3461-3466.
37. Costanzo M., Baryshnikova A., Bellay J., Kim Y., Spear E.D., Sevier C.S., Ding H., Koh J.L., Toufighi K., Mostafavi S., et al. The genetic landscape of a cell. Science 2010, 327:425-431.
38. Boone C: Genetic networks. Curr Opin Genet Dev 2011 (this issue).
39. Kamath R.S., Ahringer J. Genome-wide RNAi screening in Caenorhabditis elegans. Methods 2003, 30:313-321.
40. O'Rourke S.M., Dorfman M.D., Carter J.C., Bowerman B. Dynein modifiers in C. elegans: light chains suppress conditional heavy chain mutants. PLoS Genet 2007, 3:e128.
41. Dorfman M., Gomes J.E., O'Rourke S., Bowerman B. Using RNA interference to identify specific modifiers of a temperature-sensitive, embryonic-lethal mutation in the Caenorhabditis elegans ubiquitin-like Nedd8 protein modification pathway E1-activating gene rfl-1. Genetics 2009, 182:1035-1049.
42. Frische E.W., Pellis-van Berkel W., van Haaften G., Cuppen E., Plasterk R.H., Tijsterman M., Bos J.L., Zwartkruis F.J. RAP-1 and the RAL-1/exocyst pathway coordinate hypodermal cell organization in Caenorhabditis elegans. EMBO J 2007, 26:5083-5092.
43. Baugh L.R., Wen J.C., Hill A.A., Slonim D.K., Brown E.L., Hunter C.P. Synthetic lethal analysis of Caenorhabditis elegans posterior embryonic patterning genes identifies conserved genetic interactions. Genome Biol 2005, 6:R45.
44. Byrne A.B., Weirauch M.T., Wong V., Koeva M., Dixon S.J., Stuart J.M., Roy P.J. A global analysis of genetic interactions in Caenorhabditis elegans. J Biol 2007, 6:8.
45. Lehner B., Crombie C., Tischler J., Fortunato A., Fraser A.G. Systematic mapping of genetic interactions in Caenorhabditis elegans identifies common modifiers of diverse signaling pathways. Nat Genet 2006, 38:896-903.
46. Badano J.L., Katsanis N. Beyond Mendel: an evolving view of human genetic disease transmission. Nat Rev Genet 2002, 3:779-789.
47. Tischler J., Lehner B., Fraser A.G. Evolutionary plasticity of genetic interaction networks. Nat Genet 2008, 40:390-391.
48. Green R.A., Kao H.L., Audhya A., Arur S., Mayers J.R., Fridolfsson H.N., Schulman M., Schloissnig S., Niessen S., Laband K., et al. A high-resolution C. elegans essential gene network based on phenotypic profiling of a complex tissue. Cell 2011, 145:470-482.
49. Gunsalus K.C., Ge H., Schetter A.J., Goldberg D.S., Han J.D., Hao T., Berriz G.F., Bertin N., Huang J., Chuang L.S., et al. Predictive models of molecular machines involved in Caenorhabditis elegans early embryogenesis. Nature 2005, 436:861-865.
50. Piano F., Schetter A.J., Morton D.G., Gunsalus K.C., Reinke V., Kim S.K., Kemphues K.J. Gene clustering based on rnai phenotypes of ovary-enriched genes in C. elegans. Curr Biol 2002, 12:1959-1964.
51. Niu W., Lu Z.J., Zhong M., Sarov M., Murray J.I., Brdlik C.M., Janette J., Chen C., Alves P., Preston E., et al. Diverse transcription factor binding features revealed by genome-wide ChIP-seq in C. elegans. Genome Res 2011, 21:245-254.
52. Arda H.E., Taubert S., MacNeil L.T., Conine C.C., Tsuda B., Van Gilst M., Sequerra R., Doucette-Stamm L., Yamamoto K.R., Walhout A.J. Functional modularity of nuclear hormone receptors in a Caenorhabditis elegans metabolic gene regulatory network. Mol Syst Biol 2010, 6:367.
53. Deplancke B., Mukhopadhyay A., Ao W., Elewa A.M., Grove C.A., Martinez N.J., Sequerra R., Doucette-Stamm L., Reece-Hoyes J.S., Hope I.A., et al. A gene-centered C. elegans protein-DNA interaction network. Cell 2006, 125:1193-1205.
54. Martinez N.J., Ow M.C., Barrasa M.I., Hammell M., Sequerra R., Doucette-Stamm L., Roth F.P., Ambros V.R., Walhout A.J. A C. elegans genome-scale microRNA network contains composite feedback motifs with high flux capacity. Genes Dev 2008, 22:2535-2549.
55. Vermeirssen V., Barrasa M.I., Hidalgo C.A., Babon J.A., Sequerra R., Doucette-Stamm L., Barabasi A.L., Walhout A.J. Transcription factor modularity in a gene-centered C. elegans core neuronal protein-DNA interaction network. Genome Res 2007, 17:1061-1071.
56. Baugh L.R., Hill A.A., Claggett J.M., Hill-Harfe K., Wen J.C., Slonim D.K., Brown E.L., Hunter C.P. The homeodomain protein PAL-1 specifies a lineage-specific regulatory network in the C. elegans embryo. Development 2005, 132:1843-1854.
57. Yanai I., Baugh L.R., Smith J.J., Roehrig C., Shen-Orr S.S., Claggett J.M., Hill A.A., Slonim D.K., Hunter C.P. Pairing of competitive and topologically distinct regulatory modules enhances patterned gene expression. Mol Syst Biol 2008, 4:163.
58. Reece-Hoyes J.S., Deplancke B., Shingles J., Grove C.A., Hope I.A., Walhout A.J. A compendium of Caenorhabditis elegans regulatory transcription factors: a resource for mapping transcription regulatory networks. Genome Biol 2005, 6:R110.
59. Mangan S., Alon U. Structure and function of the feed-forward loop network motif. Proc Natl Acad Sci U S A 2003, 100:11980-11985.
60. Nelson M.D., Zhou E., Kiontke K., Fradin H., Maldonado G., Martin D., Shah K., Fitch D.H. A bow-tie genetic architecture for morphogenesis suggested by a genome-wide RNAi screen in Caenorhabditis elegans. PLoS Genet 2011, 7:e1002010.
61. Raj A., Rifkin S.A., Andersen E., van Oudenaarden A. Variability in gene expression underlies incomplete penetrance. Nature 2010, 463:913-918.
62. Bergman A., Siegal M.L. Evolutionary capacitance as a general feature of complex gene networks. Nature 2003, 424:549-552.
63. Levy S.F., Siegal M.L. Network hubs buffer environmental variation in Saccharomyces cerevisiae. PLoS Biol 2008, 6:e264.
64. Bhardwaj N., Kim P.M., Gerstein M.B. Rewiring of transcriptional regulatory networks: hierarchy, rather than connectivity, better reflects the importance of regulators. Sci Signal 2010, 3:ra79.
65. Luscombe N.M., Babu M.M., Yu H., Snyder M., Teichmann S.A., Gerstein M. Genomic analysis of regulatory network dynamics reveals large topological changes. Nature 2004, 431:308-312.
66. Liu T., Rechtsteiner A., Egelhofer T.A., Vielle A., Latorre I., Cheung M.S., Ercan S., Ikegami K., Jensen M., Kolasinska-Zwierz P., et al. Broad chromosomal domains of histone modification patterns in C. elegans. Genome Res 2011, 21:227-236.
67. Nakamura A., Seydoux G. Less is more: specification of the germline by transcriptional repression. Development 2008, 135:3817-3827.
68. Bartel D.P. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 2004, 116:281-297.
69. Bartel D.P. MicroRNAs: target recognition and regulatory functions. Cell 2009, 136:215-233.
70. Rajewsky N. microRNA target predictions in animals. Nat Genet 2006, 38(Suppl.):S8-S13.
71. van der Burgt A., Fiers M.W., Nap J.P., van Ham R.C. In silico miRNA prediction in metazoan genomes: balancing between sensitivity and specificity. BMC Genomic 2009, 10:204.
72. Chung W.J., Agius P., Westholm J.O., Chen M., Okamura K., Robine N., Leslie C.S., Lai E.C. Computational and experimental identification of mirtrons in Drosophila melanogaster and Caenorhabditis elegans. Genome Res 2011, 21:286-300.
73. Friedlander M.R., Chen W., Adamidi C., Maaskola J., Einspanier R., Knespel S., Rajewsky N. Discovering microRNAs from deep sequencing data using miRDeep. Nat Biotechnol 2008, 26:407-415.
74. Zhang L., Ding L., Cheung T.H., Dong M.Q., Chen J., Sewell A.K., Liu X., Yates J.R., Han M. Systematic identification of C. elegans miRISC proteins, miRNAs, and mRNA targets by their interactions with GW182 proteins AIN-1 and AIN-2. Mol Cell 2007, 28:598-613.
75. Kato M., de Lencastre A., Pincus Z., Slack F.J. Dynamic expression of small non-coding RNAs, including novel microRNAs and piRNAs/21U-RNAs, during Caenorhabditis elegans development. Genome Biol 2009, 10:R54.
76. Martinez N.J., Ow M.C., Reece-Hoyes J.S., Barrasa M.I., Ambros V.R., Walhout A.J. Genome-scale spatiotemporal analysis of Caenorhabditis elegans microRNA promoter activity. Genome Res 2008, 18:2005-2015.
77. Stoeckius M., Maaskola J., Colombo T., Rahn H.P., Friedlander M.R., Li N., Chen W., Piano F., Rajewsky N. Large-scale sorting of C. elegans embryos reveals the dynamics of small RNA expression. Nat Methods 2009, 6:745-751.
78. Lewis B.P., Burge C.B., Bartel D.P. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 2005, 120:15-20.
79. Lall S., Grun D., Krek A., Chen K., Wang Y.L., Dewey C.N., Sood P., Colombo T., Bray N., Macmenamin P., et al. A genome-wide map of conserved microRNA targets in C. elegans. Curr Biol 2006, 16:460-471.
80. Ambros V. MicroRNAs and developmental timing. Curr Opin Genet Dev 2011, 21:511-517.
81. Kaufman E.J., Miska E.A. The microRNAs of Caenorhabditis elegans. Semin Cell Dev Biol 2010, 21:728-737.
82. Didiano D., Hobert O. Molecular architecture of a miRNA-regulated 3' UTR. RNA 2008, 14:1297-1317.
83. Hammell C.M., Karp X., Ambros V. A feedback circuit involving let-7-family miRNAs and DAF-12 integrates environmental signals and developmental timing in Caenorhabditis elegans. Proc Natl Acad Sci U S A 2009, 106:18668-18673.
84. Nelson K.M., Weiss G.J. MicroRNAs and cancer: past, present, and potential future. Mol Cancer Ther 2008, 7:3655-3660.
85. Roush S., Slack F.J. The let-7 family of microRNAs. Trends Cell Biol 2008, 18:505-516.
86. Yang X., Lin X., Zhong X., Kaur S., Li N., Liang S., Lassus H., Wang L., Katsaros D., Montone K., et al. Double-negative feedback loop between reprogramming factor LIN28 and microRNA let-7 regulates aldehyde dehydrogenase 1-positive cancer stem cells. Cancer Res 2010, 70:9463-9472.
87. Boehm M., Slack F.J. MicroRNA control of lifespan and metabolism. Cell Cycle 2006, 5:837-840.
88. Kato M., Chen X., Inukai S., Zhao H., Slack F.J. Age-associated changes in expression of small, noncoding RNAs, including microRNAs, in C. elegans. RNA 2011, 10:1804-1820.
89. Abbott A.L., Alvarez-Saavedra E., Miska E.A., Lau N.C., Bartel D.P., Horvitz H.R., Ambros V. The let-7 MicroRNA family members mir-48, mir-84, and mir-241 function together to regulate developmental timing in Caenorhabditis elegans. Dev Cell 2005, 9:403-414.
90. Nimmo R.A., Slack F.J. An elegant miRror: microRNAs in stem cells, developmental timing and cancer. Chromosoma 2009, 118:405-418.
91. Tewari M., Hu P.J., Ahn J.S., Ayivi-Guedehoussou N., Vidalain P.O., Li S., Milstein S., Armstrong C.M., Boxem M., Butler M.D., et al. Systematic interactome mapping and genetic perturbation analysis of a C. elegans TGF-beta signaling network. Mol Cell 2004, 13:469-482.
92. Pujana M.A., Han J.D., Starita L.M., Stevens K.N., Tewari M., Ahn J.S., Rennert G., Moreno V., Kirchhoff T., Gold B., et al. Network modeling links breast cancer susceptibility and centrosome dysfunction. Nat Genet 2007, 39:1338-1349.
93. Grove C.A., De Masi F., Barrasa M.I., Newburger D.E., Alkema M.J., Bulyk M.L., Walhout A.J. A multiparameter network reveals extensive divergence between C. elegans bHLH transcription factors. Cell 2009, 138:314-327.
94. Tarca A.L., Carey V.J., Chen X.W., Romero R., Draghici S. Machine learning and its applications to biology. PLoS Comput Biol 2007, 3:e116.
95. Zhong W., Sternberg P.W. Genome-wide prediction of C. elegans genetic interactions. Science 2006, 311:1481-1484.
96. Lee I., Lehner B., Crombie C., Wong W., Fraser A.G., Marcotte E.M. A single gene network accurately predicts phenotypic effects of gene perturbation in Caenorhabditis elegans. Nat Genet 2008, 40:181-188.
97. Lee I., Lehner B., Vavouri T., Shin J., Fraser A.G., Marcotte E.M. Predicting genetic modifier loci using functional gene networks. Genome Res 2010, 20:1143-1153.
98. Myers C.L., Chiriac C., Troyanskaya O.G. Discovering biological networks from diverse functional genomic data. Methods Mol Biol 2009, 563:157-175.
99. Shannon P., Markiel A., Ozier O., Baliga N.S., Wang J.T., Ramage D., Amin N., Schwikowski B., Ideker T. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 2003, 13:2498-2504.
100. Breitkreutz B.J., Stark C., Tyers M. Osprey: a network visualization system. Genome Biol 2003, 4:R22.
101. Hu Z., Hung J.H., Wang Y., Chang Y.C., Huang C.L., Huyck M., DeLisi C. VisANT 3.5: multi-scale network visualization, analysis and inference based on the gene ontology. Nucleic Acids Res 2009, 37:W115-W121.
102. Theocharidis A., van Dongen S., Enright A.J., Freeman T.C. Network visualization and analysis of gene expression data using BioLayout Express(3D). Nat Protoc 2009, 4:1535-1550.
103. Kao H.L., Gunsalus K.C. Browsing multidimensional molecular networks with the generic network browser (N-Browse). Curr Protoc Bioinform 2008, (Chapter 9: Unit 9 11).
104. Brauchle M., Kiontke K., MacMenamin P., Fitch D.H., Piano F. Evolution of early embryogenesis in rhabditid nematodes. Dev Biol 2009, 335:253-262.
105. Bader G.D., Hogue C.W. An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinform 2003, 4:2.
106. Rhrissorrakrai K., Gunsalus K.C. MINE: Module identification in networks. BMC Bioinform 2011, 12:192.
107. Enright A.J., Van Dongen S., Ouzounis C.A. An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res 2002, 30:1575-1584.
108. Adamcsek B., Palla G., Farkas I.J., Derenyi I., Vicsek T. CFinder: locating cliques and overlapping modules in biological networks. Bioinformatics 2006, 22:1021-1023.
109. Brohee S., Faust K., Lima-Mendez G., Sand O., Janky R., Vanderstocken G., Deville Y., van Helden J. NeAT: a toolbox for the analysis of biological networks, clusters, classes and pathways. Nucleic Acids Res 2008, 36:W444-W451.
110. Hafner M., Landthaler M., Burger L., Khorshid M., Hausser J., Berninger P., Rothballer A., Ascano M., Jungkamp A.C., Munschauer M., et al. Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP. Cell 2010, 141:129-141.
111. Lebedeva S., Jens M., Theil K., Schwanhausser B., Selbach M., Landthaler M., Rajewsky N. Transcriptome-wide analysis of regulatory interactions of the RNA-binding protein HuR. Mol Cell 2011, 43:340-352.
112. Li Z., Vizeacoumar F.J., Bahr S., Li J., Warringer J., Vizeacoumar F.S., Min R., Vandersluis B., Bellay J., Devit M., et al. Systematic exploration of essential yeast gene function with temperature-sensitive mutants. Nat Biotechnol 2011, 29:361-367.
113. Kim S.K., Lund J., Kiraly M., Duke K., Jiang M., Stuart J.M., Eizinger A., Wylie B.N., Davidson G.S. A gene expression map for Caenorhabditis elegans. Science 2001, 293:2087-2092.
114. Watts D.J., Strogatz S.H. Collective dynamics of 'small-world' networks. Nature 1998, 393:440-442.
115. Jeong H., Mason S.P., Barabasi A.L., Oltvai Z.N. Lethality and centrality in protein networks. Nature 2001, 411:41-42.
116. Girvan M., Newman M.E. Community structure in social and biological networks. Proc Natl Acad Sci U S A 2002, 99:7821-7826.
117. Ravasz E., Somera A.L., Mongru D.A., Oltvai Z.N., Barabasi A.L. Hierarchical organization of modularity in metabolic networks. Science 2002, 297:1551-1555.
118. Berriz G.F., Beaver J.E., Cenik C., Tasan M., Roth F.P. Next generation software for functional trend analysis. Bioinformatics 2009, 25:3043-3044.