Unraveling networks of co-regulated genes on the sole basis of genome sequences

Nucleic Acids Research

Volumn 39, Issue 15, 2011, Pages 6340-6358

  Brohée, Sylvain ^a   Janky, Rekins ^a   Abdel Sater, Fadi ^a   Vanderstocken, Gilles ^a   André, Bruno ^a   Van Helden, Jacques ^a  

^a UNIVERSITÉ LIBRE DE BRUXELLES   (Belgium)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTOME; TRANSCRIPTION FACTOR;

ARTICLE; CHROMATIN IMMUNOPRECIPITATION; CONTROLLED STUDY; DNA FOOTPRINTING; FUNGAL GENE; FUNGAL GENOME; GENE REGULATORY NETWORK; GENE SEQUENCE; GENETIC LINKAGE; MICROARRAY ANALYSIS; NONHUMAN; PREDICTION; PREDICTIVE VALUE; PRIORITY JOURNAL; PROMOTER REGION; REGULON; SACCHAROMYCES CEREVISIAE; SACCHAROMYCETALES; ALGORITHM; BINDING SITE; DNA MICROARRAY; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETICS; GENOMICS; METABOLISM; METHODOLOGY; PHYLOGENY; VALIDATION STUDY;

SACCHAROMYCES CEREVISIAE; SACCHAROMYCETES;

ALGORITHMS; BINDING SITES; CHROMATIN IMMUNOPRECIPITATION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, FUNGAL; GENE REGULATORY NETWORKS; GENOME, FUNGAL; GENOMICS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PHYLOGENY; PROMOTER REGIONS, GENETIC; REGULON; SACCHAROMYCES CEREVISIAE; TRANSCRIPTION FACTORS;

EID: 80055069400     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkr264     Document Type: Article

References (50)

1. Liang, S., Fuhrman, S. and Somogyi, R. (1998) Reveal, a general reverse engineering algorithm for inference of genetic network architectures. Pac. Symp. Biocomput., 18-29.
2. D'Haeseleer, P., Liang, S. and Somogyi, R. (2000) Genetic network inference: from co-expression clustering to reverse engineering. Bioinformatics, 16, 707-726.
3. Pe'er, D., Regev, A., Elidan, G. and Friedman, N. (2001) Inferring subnetworks from perturbed expression profiles. Bioinformatics, 17(Suppl. 1), S215-S224. (Pubitemid 33793513)
4. Margolin, A.A. and Califano, A. (2007) Theory and limitations of genetic network inference from microarray data. Ann. N. Y. Acad. Sci., 1115, 51-72. (Pubitemid 350134807)
5. Vadigepalli, R., Chakravarthula, P., Zak, D.E., Schwaber, J.S. and Gonye, G.E. (2003) PAINT: a promoter analysis and interaction network generation tool for gene regulatory network identification. OMICS, 7, 235-252. (Pubitemid 37267839)
6. Hertz, G.Z., Hartzell, G.W. 3rd and Stormo, G.D. (1990) Identification of consensus patterns in unaligned DNA sequences known to be functionally related. Comput. Appl. Biosci., 6, 81-92. (Pubitemid 20202464)
7. Lawrence, C.E., Altschul, S.F., Boguski, M.S., Liu, J.S., Neuwald, A.F. and Wootton, J.C. (1993) Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment. Science, 262, 208-214.
8. Bailey, T.L. and Elkan, C. (1995) The value of prior knowledge in discovering motifs with MEME. Proc. Int. Conf. Intell. Syst. Mol. Biol., 3, 21-29.
9. van Helden, J., André, B. and Collado-Vides, J. (1998) Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies J. Mol. Biol., 281, 827-842. (Pubitemid 28408432)
10. van Helden, J., Rios, A.F. and Collado-Vides, J. (2000) Discovering regulatory elements in non-coding sequences by analysis of spaced dyads. Nucleic Acids Res., 28, 1808-1818. (Pubitemid 30199315)
11. McCue, L., Thompson, W., Carmack, C., Ryan, M.P., Liu, J.S., Derbyshire, V. and Lawrence, C.E. (2001) Phylogenetic footprinting of transcription factor binding sites in proteobacterial genomes. Nucleic Acids Res., 29, 774-782. (Pubitemid 32124390)
12. Wasserman, W.W. and Fickett, J.W. (1998) Identification of regulatory regions which confer muscle-specific gene expression, J. Mol. Biol., 278, 167-181. (Pubitemid 28196158)
13. Terai, G., Takagi, T. and Nakai, K. (2001) Prediction of co-regulated genes in Bacillus subtilis on the basis of upstream elements conserved across three closely related species. Genome Biol., 2, RESEARCH0048.
14. Blanchette, M. and Tompa, M. (2002) Discovery of regulatory elements by a computational method for phylogenetic footprinting. Genome Res., 12, 739-748. (Pubitemid 34546461)
15. Sinha, S., Blanchette, M. and Tompa, M. (2004) PhyME: a probabilistic algorithm for finding motifs in sets of orthologous sequences. BMC Bioinformatics, 5, 170.
16. Alkema, W.B., Lenhard, B. and Wasserman, W.W. (2004) Regulog analysis: detection of conserved regulatory networks across bacteria: application to Staphylococcus aureus. Genome Res., 14, 1362-1373. (Pubitemid 39029234)
17. Yellaboina, S., Seshadri, J., Kumar, M.S. and Ranjan, A. (2004) PredictRegulon: a web server for the prediction of the regulatory protein binding sites and operons in prokaryote genomes. Nucleic Acids Res., 32, W318-W320. (Pubitemid 38997351)
18. Wels, M., Francke, C., Kerkhoven, R., Kleerebezem, M. and Siezen, R.J. (2006) Predicting cis-acting elements of Lactobacillus plantarum by comparative genomics with different taxonomic subgroups. Nucleic Acids Res., 34, 1947-1958. (Pubitemid 44314194)
19. Newberg, L.A., Thompson, W.A., Conlan, S., Smith, T.M., McCue, L.A. and Lawrence, C.E. (2007) A phylogenetic Gibbs sampler that yields centroid solutions for cis-regulatory site prediction. Bioinformatics, 23, 1718-1727. (Pubitemid 47250303)
20. Janky, R. and van Helden, J. (2008) Evaluation of phylogenetic footprint discovery for predicting bacterial cis-regulatory elements and revealing their evolution. BMC Bioinformatics, 9, 37.
21. van Nimwegen, E., Zavolan, M., Rajewsky, N. and Siggia, E.D. (2002) Probabilistic clustering of sequences: inferring new bacterial regulons by comparative genomics. Proc. Natl Acad. Sci. USA, 99, 7323-7328. (Pubitemid 34568691)
22. Qin, Z.S., McCue, L.A., Thompson, W., Mayerhofer, L., Lawrence, C.E. and Liu, J.S. (2003) Identification of co-regulated genes through Bayesian clustering of predicted regulatory binding sites. Nat. Biotechnol., 21, 435-439. (Pubitemid 36397665)
23. Wang, T. and Stormo, G.D. (2005) Identifying the conserved network of cis-regulatory sites of a eukaryotic genome. Proc. Natl Acad. Sci. USA, 102, 17400-17405. (Pubitemid 41740878)
24. Monsieurs, P., Thijs, G., Fadda, A.A., De Keersmaecker, S.C., Vanderleyden, J., De Moor, B. and Marchal, K. (2006) More robust detection of motifs in coexpressed genes by using phylogenetic information. BMC Bioinformatics, 7, 160.
25. Fadda, A., Fierro, A.C., Lemmens, K., Monsieurs, P., Engelen, K. and Marchal, K. (2009) Inferring the transcriptional network of Bacillus subtilis. Mol. Biosyst., 5, 1840-1852.
26. Wingender, E., Dietze, P., Karas, H. and Knuppel, R. (1996) TRANSFAC: a database on transcription factors and their DNA binding sites. Nucleic Acids Res., 24, 238-241. (Pubitemid 26085775)
27. Simonis, N., Wodak, S.J., Cohen, G.N. and van Helden, J. (2004) Combining pattern discovery and discriminant analysis to predict gene co-regulation. Bioinformatics, 20, 2370-2379. (Pubitemid 39429908)
28. Snel, B., Lehmann, G., Bork, P. and Huynen, M.A. (2000) STRING: a web-server to retrieve and display the repeatedly occurring neighbourhood of a gene. Nucleic Acids Res., 28, 3442-3444.
29. Harbison, C.T., Gordon, D.B., Lee, T.I., Rinaldi, N.J., Macisaac, K.D., Danford, T.W., Hannett, N.M., Tagne, J.B., Reynolds, D.B., Yoo, J. et al. (2004) Transcriptional regulatory code of a eukaryotic genome. Nature, 431, 99-104. (Pubitemid 39215116)
30. Thomas-Chollier, M., Sand, O., Turatsinze, J.V., Janky, R., Defrance, M., Vervisch, E., Brohée, S. and van Helden, J. (2008) RSAT: regulatory sequence analysis tools. Nucleic Acids Res., 36, W119-127.
31. Brohée, S., Faust, K., Lima-Mendez, G., Sand, O., Janky, R., Vanderstocken, G., Deville, Y. and van Helden, J. (2008) NeAT: a toolbox for the analysis of biological networks, clusters, classes and pathways. Nucleic Acids Res., 36, W444-451.
32. Jensen, L.J., Kuhn, M., Stark, M., Chaffron, S., Creevey, C., Muller, J., Doerks, T., Julien, P., Roth, A., Simonovic, M. et al. (2009) STRING 8 - a global view on proteins and their functional interactions in 630 organisms. Nucleic Acids Res., 37, D412-416.
33. Berrar, D. and Flach, P. (2011) Caveats and pitfalls of ROC analysis in clinical microarray research (and how to avoid them). Brief Bioinform.
34. Kohrer, K. and Domdey, H. (1991) Preparation of high molecular weight RNA. Methods Enzymol., 194, 398-405.
35. Wery, M., Ruidant, S., Schillewaert, S., Lepore, N. and Lafontaine, D.L. (2009) The nuclear poly(A) polymerase and Exosome cofactor Trf5 is recruited cotranscriptionally to nucleolar surveillance. RNA, 15, 406-419.
36. Schjerling, P. and Holmberg, S. (1996) Comparative amino acid sequence analysis of the C6 zinc cluster family of transcriptional regulators. Nucleic Acids Res., 24, 4599-4607. (Pubitemid 26413334)
37. Perez-Rueda, E. and Collado-Vides, J. (2000) The repertoire of DNA-binding transcriptional regulators in Escherichia coli K-12. Nucleic Acids Res., 28, 1838-1847. (Pubitemid 30199318)
38. Becker, B., Feller, A., Alami, M., Dubois, E. and Pierard, A. (1998) A nonameric core sequence is required upstream of the LYS genes of Saccharomyces cerevisiae for Lys14p-mediated activation and apparent repression by lysine. Mol. Microbiol., 29, 151-163. (Pubitemid 28318570)
39. Ashburner, M., Ball, C.A., Blake, J.A., Botstein, D., Butler, H., Cherry, J.M., Davis, A.P., Dolinski, K., Dwight, S.S., Eppig, J.T. et al. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet., 25, 25-29. (Pubitemid 30257031)
40. Vik, A. and Rine, J. (2001) Upc2p and Ecm22p, dual regulators of sterol biosynthesis in Saccharomyces cerevisiae. Mol. Cell Biol., 21, 6395-6405. (Pubitemid 32927408)
41. Xie, Y. and Varshavsky, A. (2001) RPN4 is a ligand, substrate, and transcriptional regulator of the 26 S proteasome: a negative feedback circuit. Proc. Natl Acad. Sci. USA, 98, 3056-3061. (Pubitemid 32220798)
42. Stanhill, A., Haynes, C.M., Zhang, Y., Min, G., Steele, M.C., Kalinina, J., Martinez, E., Pickart, C.M., Kong, X.P. and Ron, D. (2006) An arsenite-inducible 19 S regulatory particle-associated protein adapts proteasomes to proteotoxicity. Mol. Cell, 23, 875-885. (Pubitemid 44344518)
43. Haugen, A.C., Kelley, R., Collins, J.B., Tucker, C.J., Deng, C., Afshari, C.A., Brown, J.M., Ideker, T. and Van Houten, B. (2004) Integrating phenotypic and expression profiles to map arsenic-response networks. Genome Biol., 5, R95.
44. Cooper, T.G. (2002) Transmitting the signal of excess nitrogen in Saccharomyces cerevisiae from the Tor proteins to the GATA factors: connecting the dots. FEMS Microbiol. Rev., 26, 223-238.
45. Bar-Joseph, Z., Gerber, G.K., Lee, T.I., Rinaldi, N.J., Yoo, J.Y., Robert, F., Gordon, D.B., Fraenkel, E., Jaakkola, T.S., Young, R.A. et al. (2003) Computational discovery of gene modules and regulatory networks. Nat. Biotechnol., 21, 1337-1342. (Pubitemid 37356619)
46. Godard, P., Urrestarazu, A., Vissers, S., Kontos, K., Bontempi, G., van Helden, J. and André, B. (2007) Effect of 21 different nitrogen sources on global gene expression in the yeast Saccharomyces cerevisiae. Mol. Cell Biol., 27, 3065-3086. (Pubitemid 46581319)
47. Scherens, B., Feller, A., Vierendeels, F., Messenguy, F. and Dubois, E. (2006) Identification of direct and indirect targets of the Gln3 and Gat1 activators by transcriptional profiling in response to nitrogen availability in the short and long term. FEMS Yeast Res., 6, 777-791. (Pubitemid 44049996)
48. Bahler, J. (2005) Cell-cycle control of gene expression in budding and fission yeast. Annu. Rev. Genet., 39, 69-94. (Pubitemid 43011108)
49. Spellman, P.T., Sherlock, G., Zhang, M.Q., Iyer, V.R., Anders, K., Eisen, M.B., Brown, P.O., Botstein, D. and Futcher, B. (1998) Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol. Biol. Cell, 9, 3273-3297. (Pubitemid 28551928)
50. Lozada-Chavez, I., Angarica, V.E., Collado-Vides, J. and Contreras-Moreira, B. (2008) The role of DNA-binding specificity in the evolution of bacterial regulatory networks, J. Mol. Biol., 379, 627-643.