Yeast gene CMR1/YDL156W is consistently co-expressed with genes participating in DNA-metabolic processes in a variety of stringent clustering experiments

Journal of the Royal Society Interface

Volumn 10, Issue 81, 2013, Pages

  Abu Jamous, Basel ^a   Fa, Rui ^a   Roberts, David J ^b,c   Nandi, Asoke K ^a,d  

^a UNIVERSITY OF LIVERPOOL   (United Kingdom)

^b NHS BLOOD AND TRANSPLANT   (United Kingdom)

^c UNIVERSITY OF OXFORD   (United Kingdom)

^d UNIVERSITY OF JYVÄSKYLÄ   (Finland)

Author keywords

Binarization of consensus partition matrix; CMR1 YDL156W; DNA repair; DNA replication; G1 S transition

Indexed keywords

DATA REDUCTION; DNA; EXPERIMENTS; GENES; METABOLISM; PROTEINS; REPAIR; YEAST;

CMR1/YDL156W; DNA REPAIR; DNA REPLICATIONS; G1/S TRANSITION; PARTITION MATRIXES;

TRANSCRIPTION;

CMR1 PROTEIN; DNA POLYMERASE; FUNGAL PROTEIN; REPLICATION FACTOR A; UNCLASSIFIED DRUG; CMR1 PROTEIN, S CEREVISIAE; DNA; DNA BINDING PROTEIN; DNA DIRECTED DNA POLYMERASE; SACCHAROMYCES CEREVISIAE PROTEIN;

ARTICLE; CELL CYCLE REGULATION; COMPUTER MODEL; DNA METABOLISM; DNA REPAIR; DNA REPLICATION; DNA TRANSCRIPTION; FUNGAL GENE; G1 PHASE CELL CYCLE CHECKPOINT; GENE EXPRESSION; MICROARRAY ANALYSIS; NONHUMAN; PROTEIN FUNCTION; PROTEOMICS; BIOLOGICAL MODEL; CLUSTER ANALYSIS; GENE; GENE EXPRESSION PROFILING; GENETICS; METABOLISM; SACCHAROMYCES CEREVISIAE; STATISTICS;

CLUSTER ANALYSIS; DNA; DNA-BINDING PROTEINS; DNA-DIRECTED DNA POLYMERASE; GENE EXPRESSION PROFILING; GENES, CDC; MICROARRAY ANALYSIS; MODELS, GENETIC; REPLICATION PROTEIN A; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS;

MLCS; MLOWN;

EID: 84875737191     PISSN: 17425689     EISSN: 17425662     Source Type: Journal    
DOI: 10.1098/rsif.2012.0990     Document Type: Article

References (38)

1. Palsson B, Zengler K. 2010 The challenges of integrating multi-omic data sets. Nat. Chem. Biol. 6, 787-789. (doi:10.1038/nchembio.462)
2. Pena JM, Lozano JA, Larranaga P. 1999 An empirical comparison of four initialization methods for the KMeans algorithm. Pattern Recognit. Lett. 20, 1027-1040. (doi:10.1016/S0167-8655(99)00069-0)
3. Eisen MB, Spellman PT, Brown PO, Botstein D. 1998 Cluster analysis and display of genome-wide expression patterns. Proc. Natl Acad. Sci. USA 95, 14 863-14 868. (doi:10.1073/pnas.95.25.14863)
4. Kohonen TE. 1997 Self-organizing maps. New York, NY: Springer.
5. Salem SA, Jack LB, Nandi AK. 2008 Investigation of self-organizing oscillator networks for use in clustering microarray data. IEEE Trans. Nanobiosci. 7, 65-79. (doi:10.1109/TNB.2008.2000151)
6. Ayad HG, Kamel MS. 2010 On voting-based consensus of cluster ensembles. Pattern Recogn. 43, 1943-1953. (doi:10.1016/j.patcog.2009.11.012)
7. Fred A, Jain AK. 2002 Data clustering using evidence accumulation. Proc. 16th Int. Conf. Pattern Recognit. 4, 276-280.
8. Strehl A, Ghosh J. 2002 Cluster ensembles: a knowledge reuse framework for combining multiple partitions. J. Mach. Learn. Res. 3, 583-617.
9. Abu-Jamous B, Fa R, Nandi AK, Roberts DJ. 2012 Binarization of consensus partition matrix for ensemble clustering. In Proc. 20th European Signal Processing Conf. (EUSIPCO-2012), Bucharest, Romania, 27-31 August 2012, pp. 2193-2197.
10. Abu-Jamous B, Fa R, Roberts RJ, Nandi AK. 2012 Comprehensive analysis of multiple microarray datasets by binarization of consensus partition matrix. In 2012 IEEE Int. Workshop on Machine Learning for Signal Processing (MLSP 2012), Santander, Spain, 23-26 September 2012. (doi:10.1109/MLSP.2012.6349787)
11. Choi DH, Kwon SH, Kim JH. 2012 Saccharomyces cerevisiae Cmr1 protein preferentially binds to UVdamaged DNA in vitro. J. Microbiol. 50, 112-118. (doi:10.1007/s12275-012-1597-4)
12. Gilmore JM, Sardiu ME, Venkatesh S, Stutzman B, Peak A, Seidel CW, Workman JL, Florens L, Washburn MP. 2012 Characterization of a highly conserved histone related protein, Ydl156w, and its functional associations using quantitative proteomic analyses. Mol. Cellular Proteomics 11, M111.011544. (doi:10.1074/mcp.M111.011544)
13. Tkach JM et al. 2012 Dissecting DNA damage response pathways by analysing protein localization and abundance changes during DNA replication stress. Nat. Cell Biol. 14, 966-976. (doi:10.1038/ncb2549)
14. Pramila T, Wu W, Miles S, Noble WS, Breeden LL. 2006 The Forkhead transcription factor Hcm1 regulates chromosome segregation genes and fills the S-phase gap in the transcriptional circuitry of the cell cycle. Genes Dev. 20, 2266-2278. (doi:10. 1101/gad.1450606)
15. Spellman PT, Sherlock G, Zhang MQ, Iyer VR, Anders K, Eisen MB, Brown PO, Botstein D, Futcher B. 1998 Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol. Biol. Cell 9, 3273-3297.
16. Cho RJ et al. 1998 A genome-wide transcriptional analysis of the mitotic cell cycle. Mol. Cell 2, 65-73. (doi:10.1016/S1097-2765(00)80114-8)
17. Vega-Pons S, Ruiz-Shulcloper J. 2011 A survey of clustering ensemble algorithms. Int. J. Pattern Recognit. Artif. Intell. 25, 337-372. (doi:10.1142/S0218001411008683)
18. Dimitriadou E, Weingessel A, Hornik K. 2002 A combination scheme for fuzzy clustering. Int. J. Pattern Recognit. Artif. Intell. 16, 901-912. (doi:10.1142/S0218001402002052)
19. Xiao X, Dow ER, Eberhart R, Miled ZB, Oppelt RJ. 2003 Gene clustering using self-organizing maps and particle swarm optimization. In IEEE Parallel and Distributed Processing Symp. Proc., Indianapolis, USA, 22-26 April 2003, pp. 154-163. (doi:10. 1109/IPDPS.2003.1213290).
20. Rhouma MBH, Frigui H. 2001 Self-organization of pulse-coupled oscillators with application to clustering. IEEE Trans. Pattern Anal. Mach. Intell. 23, 1-16. (doi:10.1109/34.908968)
21. SGD. 2012 GO Slim Mapper. (accessed 2012 November) See http://www.yeastgenome.org/cgibin/GO/goSlim-Mapper.pl.
22. Brohee S, Janky R, Abdel-Sater F, Vanderstocken G, Andre B, Helden JV. 2011 Unraveling networks of co-regulated genes on the sole basis of genome sequences. Nucleic Acids Res. 39, 6340-6358. (doi:10.1093/nar/gkr264)
23. Fernandez MA, Rueda C, Peddada SD. 2012 Identification of a core set of signature cell cycle genes whose relative order of time to peak expression is conserved across species. Nucleic Acids Res. 40, 2823-2832. (doi:10.1093/nar/ gkr1077)
24. Longhese MP, Plevani P, Lucchini G. 1994 Replication factor A is required in vivo for DNA replication, repair, and recombination. Mol. Cell. Biol. 14, 7884-7890.
25. Huttner D, Ulrich HD. 2008 Cooperation of replication protein A with the ubiquitin ligase Rad18 in DNA damage bypass. Cell Cycle 7, 3629-3633. (doi:10.4161/cc.7.23.7166)
26. Lou H, Komata M, Katou Y, Guan Z, Reis CC, Budd M, Shirahige K, Campbell JL. 2008 Mrc1 and DNA polymerase epsilon function together in linking DNA replication and the S phase checkpoint. Mol. Cell 32, 106-117. (doi:10.1016/j.molcel.2008.08.020)
27. Collins SR et al. 2007 Functional dissection of protein complexes involved in yeast chromosome biology using a genetic interaction map. Nature 446, 806-810. (doi:10.1038/nature05649)
28. Kawasaki Y, Kim HD, Kojima A, Seki T, Sugino A. 2006 Reconstitution of Saccharomyces cerevisiae prereplicative complex assembly in vitro. Genes Cells 11, 745-756. (doi:10.1111/j.1365-2443.2006. 00975.x)
29. Zhu W, Ukomadu C, Jha S, Senga T, Dhar SK, Wohlschlegel JA, Nutt LK, Kornbluth S, Dutta A. 2007 Mcm10 and And-1/CTF4 recruit DNA polymerase a to chromatin for initiation of DNA replication. Genes Dev. 21, 2288-2299. (doi:10. 1101/gad.1585607)
30. Strunnikov AV, Jessberger R. 1999 Structural maintenance of chromosomes (SMC) proteins: conserved molecular properties for multiple biological functions. Eur. J. Biochem. 263, 6-13. (doi:10.1046/j.1432-1327.1999.00509.x)
31. Jones S, Sgouros J. 2001 The cohesin complex: sequence homologies, interaction networks and shared motifs. Genome Biol. 2, 0009-00012. (doi:10.1186/gb-2001-2-3-research0009)
32. Koch C, Moll T, Neuberg M, Ahorn H, Nasmyth K. 1993 A role for the transcription factors Mbpl and Swi4 in progression from G1 to S phase. Science 261, 1551-1557. (doi:10.1126/science.8372350)
33. Bahler J. 2005 Cell-cycle control of gene expression in budding and fission yeast. Annu. Rev. Genet. 39, 69-94. (doi:10.1146/annurev.genet.39. 110304.095808)
34. McIntosh EM. 1993 MCB elements and the regulation of DNA replication genes in yeast. Curr. Genet. 24, 185-192. (doi:10.1007/BF00351790)
35. Liu Y, Kao HI, Bambara RA. 2004 Flap endonuclease 1: a central component of DNA metabolism. Annu. Rev. Biochem. 73, 589-615. (doi:10.1146/annurev. biochem.73.012803.092453)
36. Reagan MS, Pittenger C, Siede W, Friedberg EC. 1995 Characterization of a mutant strain of Saccharomyces cerevisiae with a deletion of the RAD27 gene, a structural homolog of the RAD2 nucleotide excision repair gene. J. Bacteriol. 177, 364-371.
37. Karanja KK, Livingston DM. 2009 C-terminal flap endonuclease (rad27) mutations: lethal interactions with a DNA ligase I mutation (cdc9-p) and suppression by proliferating cell nuclear antigen (POL30) in Saccharomyces cerevisiae. Genetics 183, 63-78. (doi:10.1534/genetics.109.103937)
38. Bowers J, Sokolsky T, Quach T, Alani E. 1999 A mutation in the MSH6 subunit of the Saccharomyces cerevisiae MSH2-MSH6 complex disrupts mismatch recognition. J. Biol. Chem. 274, 16 115-16 125. (doi:10.1074/jbc.274.23.16115).