Gepoclu: A software tool for identifying and analyzing gene positional clusters in large-scale gene expression analysis

BMC Bioinformatics

Volumn 12, Issue , 2011, Pages

  Dottorini, Tania ^a   Senin, Nicola ^a   Mazzoleni, Giorgio ^a,b   Magnusson, Kalle ^b   Crisanti, Andrea ^b  

^a UNIVERSITY OF PERUGIA   (Italy)

^b IMPERIAL COLLEGE LONDON   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

CLUSTER VISUALIZATION; CO-LOCALIZED GENES; EUKARYOTIC ORGANISMS; FULLY PROGRAMMABLES; GENE EXPRESSION ANALYSIS; INTERACTIVE ENVIRONMENTS; TEMPORAL AND SPATIAL; TRANSCRIPTIONAL PROGRAM;

COMPUTER SOFTWARE;

GENE EXPRESSION;

EUKARYOTA;

ANIMAL; ANOPHELES GAMBIAE; ARTICLE; BIOLOGY; CLUSTER ANALYSIS; COMPUTER PROGRAM; DNA MICROARRAY; DROSOPHILA MELANOGASTER; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENETICS; METHODOLOGY; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION;

ANIMALS; ANOPHELES GAMBIAE; CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; DROSOPHILA MELANOGASTER; GENE EXPRESSION; GENE EXPRESSION PROFILING; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; SOFTWARE;

EID: 78951483250     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-12-34     Document Type: Article

References (42)

1. Osbourn AE, Field B. Operons. Cell Mol Life Sci 2009, 66(23):3755-3775. 10.1007/s00018-009-0114-3, 2776167, 19662496.
2. Hurst LD, Pal C, Lercher MJ. The evolutionary dynamics of eukaryotic gene order. Nat Rev Genet 2004, 5(4):299-310. 10.1038/nrg1319, 15131653.
3. Koonin EV. Evolution of genome architecture. Int J Biochem Cell Biol 2009, 41(2):298-306. 10.1016/j.biocel.2008.09.015, 18929678.
4. Lawrence JG. Shared strategies in gene organization among prokaryotes and eukaryotes. Cell 2002, 110(4):407-413. 10.1016/S0092-8674(02)00900-5, 12202031.
5. Michalak P. Coexpression, coregulation, and cofunctionality of neighboring genes in eukaryotic genomes. Genomics 2008, 91(3):243-248. 10.1016/j.ygeno.2007.11.002, 18082363.
6. Sproul D, Gilbert N, Bickmore WA. The role of chromatin structure in regulating the expression of clustered genes. Nat Rev Genet 2005, 6(10):775-781. 10.1038/nrg1688, 16160692.
7. Caron H, van Schaik B, van der Mee M, Baas F, Riggins G, van Sluis P, Hermus MC, van Asperen R, Boon K, Voute PA, Heisterkamp S, van Kampen A, Versteeg R. The human transcriptome map: clustering of highly expressed genes in chromosomal domains. Science 2001, 291(5507):1289-1292. 10.1126/science.1056794, 11181992.
8. Janga SC, Collado-Vides J, Babu MM. Transcriptional regulation constrains the organization of genes on eukaryotic chromosomes. Proc Natl Acad Sci USA 2008, 105(41):15761-15766. 10.1073/pnas.0806317105, 2562535, 18840678.
9. Kalmykova AI, Nurminsky DI, Ryzhov DV, Shevelyov YY. Regulated chromatin domain comprising cluster of co-expressed genes in Drosophila melanogaster. Nucleic Acids Res 2005, 33(5):1435-1444. 10.1093/nar/gki281, 1062873, 15755746.
10. Lercher MJ, Blumenthal T, Hurst LD. Coexpression of neighboring genes in Caenorhabditis elegans is mostly due to operons and duplicate genes. Genome Res 2003, 13(2):238-243. 10.1101/gr.553803, 420373, 12566401.
11. Nelander S, Larsson E, Kristiansson E, Mansson R, Nerman O, Sigvardsson M, Mostad P, Lindahl P. Predictive screening for regulators of conserved functional gene modules (gene batteries) in mammals. BMC Genomics 2005, 6(1):68. 10.1186/1471-2164-6-68, 1134656, 15882449.
12. Purmann A, Toedling J, Schueler M, Carninci P, Lehrach H, Hayashizaki Y, Huber W, Sperling S. Genomic organization of transcriptomes in mammals: Coregulation and cofunctionality. Genomics 2007, 89(5):580-587. 10.1016/j.ygeno.2007.01.010, 17369017.
13. Ren XY, Fiers MW, Stiekema WJ, Nap JP. Local coexpression domains of two to four genes in the genome of Arabidopsis. Plant Physiol 2005, 138(2):923-934. 10.1104/pp.104.055673, 1150408, 15923337.
14. Roy PJ, Stuart JM, Lund J, Kim SK. Chromosomal clustering of muscle-expressed genes in Caenorhabditis elegans. Nature 2002, 418(6901):975-979.
15. Schmid M, Davison TS, Henz SR, Pape UJ, Demar M, Vingron M, Scholkopf B, Weigel D, Lohmann JU. A gene expression map of Arabidopsis thaliana development. Nat Genet 2005, 37(5):501-506. 10.1038/ng1543, 15806101.
16. Semon M, Duret L. Evolutionary origin and maintenance of coexpressed gene clusters in mammals. Mol Biol Evol 2006, 23(9):1715-1723. 10.1093/molbev/msl034, 16757654.
17. Singer GA, Lloyd AT, Huminiecki LB, Wolfe KH. Clusters of co-expressed genes in mammalian genomes are conserved by natural selection. Mol Biol Evol 2005, 22(3):767-775. 10.1093/molbev/msi062, 15574806.
18. Spellman PT, Rubin GM. Evidence for large domains of similarly expressed genes in the Drosophila genome. J Biol 2002, 1(1):5. 10.1186/1475-4924-1-5, 117248, 12144710.
19. Vogel JH, von Heydebreck A, Purmann A, Sperling S. Chromosomal clustering of a human transcriptome reveals regulatory background. BMC Bioinformatics 2005, 6:230. 10.1186/1471-2105-6-230, 1261156, 16171528.
20. Williams EJ, Bowles DJ. Coexpression of neighboring genes in the genome of Arabidopsis thaliana. Genome Res 2004, 14(6):1060-1067. 10.1101/gr.2131104, 419784, 15173112.
21. Williams EJ, Hurst LD. Clustering of tissue-specific genes underlies much of the similarity in rates of protein evolution of linked genes. J Mol Evol 2002, 54(4):511-518. 10.1007/s00239-001-0043-8, 11956689.
22. Zhan S, Horrocks J, Lukens LN. Islands of co-expressed neighbouring genes in Arabidopsis thaliana suggest higher-order chromosome domains. Plant J 2006, 45(3):347-357. 10.1111/j.1365-313X.2005.02619.x, 16412082.
23. Bergeron A, Corteel S, Raffinot M. The algorithmic of gene teams. LectNotes in Comput Sci 2002, 2452:464-476.
24. Calabrese PP, Chakravarty S, Vision TJ. Fast identification and statistical evaluation of segmental homologies in comparative maps. Bioinformatics 2003, 19(Suppl 1):i74-80. 10.1093/bioinformatics/btg1008, 12855440.
25. He X, Goldwasser MH. Identifying conserved gene clusters in the presence of homology families. JComputBiol 2005, 12:638-656.
26. Lercher MJ, Urrutia AO, Hurst LD. Clustering of housekeeping genes provides a unified model of gene order in the human genome. Nat Genet 2002, 31(2):180-183. 10.1038/ng887, 11992122.
27. Marinotti O, Calvo E, Nguyen QK, Dissanayake S, Ribeiro JM, James AA. Genome-wide analysis of gene expression in adult Anopheles gambiae. Insect Mol Biol 2006, 15(1):1-12. 10.1111/j.1365-2583.2006.00610.x, 16469063.
28. Dottorini T, Nicolaides L, Ranson H, Rogers DW, Crisanti A, Catteruccia F. A genome-wide analysis in Anopheles gambiae mosquitoes reveals 46 male accessory gland genes, possible modulators of female behavior. Proc Natl Acad Sci USA 2007, 104(41):16215-16220. 10.1073/pnas.0703904104, 2042187, 17901209.
29. Adams MD, Celniker SE, Holt RA, Evans CA, Gocayne JD, Amanatides PG, Scherer SE, Li PW, Hoskins RA, Galle RF, George RA, Lewis SE, Richards S, Ashburner M, Henderson SN, Sutton GG, Wortman JR, Yandell MD, Zhang Q, Chen LX, Brandon RC, Rogers YH, Blazej RG, Champe M, Pfeiffer BD, Wan KH, Doyle C, Baxter EG, Helt G, Nelson CR, et al. The genome sequence of Drosophila melanogaster. Science 2000, 287(5461):2185-2195. 10.1126/science.287.5461.2185, 10731132.
30. Holt RA, Subramanian GM, Halpern A, Sutton GG, Charlab R, Nusskern DR, Wincker P, Clark AG, Ribeiro JM, Wides R, Salzberg SL, Loftus B, Yandell M, Majoros WH, Rusch DB, Lai Z, Kraft CL, Abril JF, Anthouard V, Arensburger P, Atkinson PW, Baden H, de Berardinis V, Baldwin D, Benes V, Biedler J, Blass C, Bolanos R, Boscus D, Barnstead M, et al. The genome sequence of the malaria mosquito Anopheles gambiae. Science 2002, 298(5591):129-149. 10.1126/science.1076181, 12364791.
31. Sharakhova MV, Hammond MP, Lobo NF, Krzywinski J, Unger MF, Hillenmeyer ME, Bruggner RV, Birney E, Collins FH. Update of the Anopheles gambiae PEST genome assembly. Genome Biol 2007, 8(1):R5.. 10.1186/gb-2007-8-1-r5, 1839121, 17210077.
32. Matlab. The MathWorks, Inc. Natick, MA (US)., http://www.mathworks.com
33. Cohen BA, Mitra RD, Hughes JD, Church GM. A computational analysis of whole-genome expression data reveals chromosomal domains of gene expression. Nat Genet 2000, 26(2):183-186. 10.1038/79896, 11017073.
34. Li Q, Lee BT, Zhang L. Genome-scale analysis of positional clustering of mouse testis-specific genes. BMC Genomics 2005, 6(1):7. 10.1186/1471-2164-6-7, 548148, 15656914.
35. Seno S, Takenaka Y, Kai C, Kawai J, Carninci P, Hayashizaki Y, Matsuda H. A method for similarity search of genomic positional expression using CAGE. PLoS Genet 2006, 2(4):e44. 10.1371/journal.pgen.0020044, 1449887, 16683027.
36. Boutanaev AM, Kalmykova AI, Shevelyov YY, Nurminsky DI. Large clusters of co-expressed genes in the Drosophila genome. Nature 2002, 420(6916):666-669. 10.1038/nature01216, 12478293.
37. SPSS. IBM Corporation. Somers, NY (US)., http://www.spss.com
38. Mueller JL, Ravi Ram K, McGraw LA, Bloch Qazi MC, Siggia ED, Clark AG, Aquadro CF, Wolfner MF. Cross-species comparison of Drosophila male accessory gland protein genes. Genetics 2005, 171(1):131-143. 10.1534/genetics.105.043844, 1456506, 15944345.
39. Simmerl E, Schafer M, Schafer U. Structure and regulation of a gene cluster for male accessory gland transcripts in Drosophila melanogaster. Insect Biochem Mol Biol 1995, 25(1):127-137. 10.1016/0965-1748(94)00034-F, 7711745.
40. Swanson WJ, Clark AG, Waldrip-Dail HM, Wolfner MF, Aquadro CF. Evolutionary EST analysis identifies rapidly evolving male reproductive proteins in Drosophila. Proc Natl Acad Sci USA 2001, 98(13):7375-7379. 10.1073/pnas.131568198, 34676, 11404480.
41. Walker MJ, Rylett CM, Keen JN, Audsley N, Sajid M, Shirras AD, Isaac RE. Proteomic identification of Drosophila melanogaster male accessory gland proteins, including a pro-cathepsin and a soluble gamma-glutamyl transpeptidase. Proteome Sci 2006, 4:9. 10.1186/1477-5956-4-9, 1462989, 16670001.
42. Wolfner MF, Harada HA, Bertram MJ, Stelick TJ, Kraus KW, Kalb JM, Lung YO, Neubaum DM, Park M, Tram U. New genes for male accessory gland proteins in Drosophila melanogaster. Insect Biochem Mol Biol 1997, 27(10):825-834. 10.1016/S0965-1748(97)00056-8, 9474779.