Word-based characterization of promoters involved in human DNA repair pathways

BMC Genomics

Volumn 10, Issue SUPPL. 1, 2009, Pages

  Lichtenberg, Jens ^a   Jacox, Edwin ^b   Welch, Joshua D ^a   Kurz, Kyle ^a   Liang, Xiaoyu ^a   Qu Yang, Mary ^b   Drews, Frank ^a   Ecker, Klaus ^a   Lee, Stephen S ^c   Elnitski, Laura ^b   Welch, Lonnie R ^a,d  

^a Ohio University   (United States)

^b NATIONAL HUMAN GENOME RESEARCH INSTITUTE   (United States)

^c UNIVERSITY OF IDAHO   (United States)

^d OHIO UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING SITE; CONFERENCE PAPER; CONTROLLED STUDY; DNA REPAIR; DNA SEQUENCE; GENETIC CONSERVATION; GENETIC DATABASE; GENETIC REGULATION; HUMAN; PROMOTER REGION; PROTEIN MOTIF; SEQUENCE ANALYSIS; SIGNAL TRANSDUCTION; ARTICLE; BIOLOGY; CLUSTER ANALYSIS; DNA BASE COMPOSITION; METHODOLOGY; STATISTICAL MODEL;

BASE COMPOSITION; CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; DNA REPAIR; HUMANS; MODELS, STATISTICAL; PROMOTER REGIONS, GENETIC;

EID: 67650556404     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-10-S1-S18     Document Type: Conference Paper

References (47)

1. Deschavanne PJ Giron A Vilain J Fagot G Fertil B Genomic signature: characterization and classification of species assessed by chaos game representation of sequences Mol Biol Evol 1999, 16(10):1391-1399. 10563018
2. Karlin S Burge C Dinucleotide relative abundance extremes: A genomic signature Trends Genet 1995, 11(7):283-290. 7482779
3. Abe T Kanaya S Kinouchi M Ichiba Y Kozuki T Ikemura T A novel bioinformatic strategy for unveiling hidden genome signatures of eukaryotes: Self-organizing map of oligonucleotide frequency Genome Inform 2002, 13:12-20. 14571370
4. Abe T Kanaya S Kinouchi M Ichiba Y Kozuki T Ikemura T Informatics for unveiling hidden genome signatures Genome Res 2003, 13(4):693-702. 430167 12671005
5. Bastien O Lespinats S Roy S Metayer K Fertil B Codani J Marechal E Analysis of the compositional biases in Plasmodium falciparum genome and proteome using Arabidopsis thaliana as a reference Gene 2004, 336(2):163-173. 15246528
6. Bentley SD Parkhill J Comparative genomic structure of prokaryotes Annu Rev Genet 2004, 38:771-792. 15568993
7. Campbell AM Mrazek J Karlin S Genome signature comparisons among prokaryote, plasmid, and mitochondrial DNA Proc Natl Acad Sci 1999, 96(16):9184-9189. 17754 10430917
8. Carbone A Kepes F Zinovyev A Codon bias signatures, organization of microorganisms in codon space, and lifestyle Mol Biol Evol 2005, 22(3):547-561. 15537809
9. Deschavanne PJ Giron A Vilain J Dufraigne C Fertil B Genomic signature is preserved in short DNA fragments IEEE International Symposium on Bioinformatics and Biomedical Engineering 2000.
10. Elhai J Determination of bias in the relative abundance of oligonucleotides in DNA sequences J Comput Biol 2001, 8(2):151-175. 11454303
11. Fertil B Massin M Lespinats S Devic C Dumee P Giron A GENSTYLE: exploration and analysis of DNA sequences with genomic signature Nucleic Acids Res 2005, 33:512-515.
12. Gentles AJ Karlin S Genome-scale compositional comparisons in eukaryotes Genome Res 2001, 11(4):540-546. 311039 11282969
13. Jeffrey H Chaos game representation of gene structure Nucleic Acids Res 1990, 18(8):2163-2170. 330698 2336393
14. Karlin S Global dinucleotide signatures and analysis of genomic heterogeneity Curr Opin Microbiol 1998, 1(5):598-610. 10066522
15. Karlin S Campbell AM Mrazek J Comparative DNA analysis across diverse genomes Annu Rev Genet 1998, 32:185-225. 9928479
16. Karlin S Mrazek J Campbell AM Compositional biases of bacterial genomes and evolutionary implications J Bacteriol 1997, 179(12):3899-3913. 179198 9190805
17. Karlin S Mrazek J Gentles AJ Genome comparisons and analysis Curr Opin Struct Biol 2003, 13(3):344-352. 12831886
18. Li J Sayood K A Genome Signature Based on Markov Modeling Proceedings of the 27th Annual International Conference of the IEEE - Engineering in Medicine and Biology Society: 2005; Shanghai 2005.
19. Wong K Finan TM Golding GB Dinucleotide compositional analysis of Sinorhizobium meliloti using the genome signature: Distinguishing chromosomes and plasmids Funct Integr Genomics 2002, 2(6):274-281. 12444420
20. Zhang C Zhang R Ou H The Z curve database: A graphic representation of genome sequences Bioinformatics 2003, 19(5):593-599. 12651717
21. Fickett JW Wasserman WW Discovery and modeling of transcriptional regulatory regions Curr Opin Biotechnol 2000, 11(1):19-24. 10679343
22. Schones DE Sumazin P Zhang MQ Similarity of position frequency matrices for transcription factor binding sites Bioinformatics 2005, 21(3):307-313. 15319260
23. Wasserman WW Fickett JW Identification of regulatory regions which confer muscle-specific gene expression J Mol Biol 1998, 278(1):167-181. 9571041
24. Wasserman WW Palumbo M Thompson W Fickett JW Lawrence CE Human-mouse genome comparisons to locate regulatory sites Nat Genet 2000, 26(2):225-228. 11017083
25. Joshi-Tope G Gillespie M Vastrik I D'Eustachio P Schmidt E Reactome: A knowledgebase of biological pathways Nucleic Acids Res 2005, 33:D428-432. 540026 15608231
26. Yang MQ Elnitski L A computational study of bidirectional promoters in the human genome Springer Verlag Lecture Notes in Bioinformatics Zhang Y Heidelberg 2007:361-371.
27. Adachi N Lieber MR Bidirectional gene organization: A common architectural feature of the human genome Cell 2002, 109:807-809. 12110178
28. Yang MQ Koehly LM Elnitski LL Comprehensive annotation of bidirectional promoters identifies co-regulation among breast and ovarian cancer genes PLoS Comput Biol 2007, 3(4):e72. 1853124 17447839
29. Seila AC Calabrese JM Levine SS Yeo GW Rahl PB Flynn RA Young RA Sharp PA Divergent Transcription from Active Promoters Science 2008. 1162253
30. Wingender E Chen X Hehl R Karas H Liebich I TRANSFAC: An integrated system for gene expression regulation Nucleic Acids Res 2000, 28:316-319. 102445 10592259
31. Bryne JC Valen E Tang MH Marstrand T Winther O JASPAR, the open access database of transcription factor-binding profiles: New content and tools in the 2008 update Nucleic Acids Res 2008, 36:D102-106. 2238834 18006571
32. Herold J Kurtz S Giegerich R Efficient computation of absent words in genomic sequences BMC Bioinformatics 2008, 9(1):167. 2375138 18366790
33. Hampikian G Andersen T Absent sequences: Nullomers and primes Pac Symp Biocomput 2007:355-366. 17990505
34. Stein LD Mungall C Shu S Caudy M Mangone M Day A Nickerson E Stajich JE Harris TW Arva A The generic genome browser: A building block for a model organism system database Genome Res 2002, 12(10):1599-1610. 187535 12368253
35. Jacox E Elnitski L Finding Occurrences of Relevant Functional Elements in Genomic Signatures International Journal of Computational Science 2008.
36. Xie X Lu J Kulbokas EJ Golub TR Mootha V Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals Nature 2005, 434:338-345. 15735639
37. Chekmenev DS Haid C Kel AE P-Match: Transcription factor binding site search by combining patterns and weight matrices Nucleic Acids Res 2005, 33:W432-437. 1160202 15980505
38. Siepel A Bejerano G Pedersen JS Hinrichs AS Hou M Rosenbloom K Clawson H Spieth J Hillier LW Richards S et al. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes Genome Res 2005, 15(8):1034-1050. 1182216 16024819
39. Kent WJ Sugnet CW Furey TS Roskin KM Pringle TH Zahler AM Haussler AD The Human Genome Browser at UCSC Genome Res 2002, 12(6):996-1006. 186604 12045153
40. Bailey TL Williams N Misleh C Li WW MEME: Discovering and analyzing DNA and protein sequence motifs Nucleic Acids Res 2006, 34:W369-373. 1538909 16845028
41. Roth FP Hughes JD Estep PW Church GM Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation Nat Biotech 1998, 16(10):939-945.
42. Lichtenberg J Jacox E Yang MQ Elnitski L Welch L Word-based characterization of the bidirectional promoters from the human DNA-repair pathways The 2008 International Conference on Bioinformatics and Computational Biology Las Vegas 2008.
43. Lichtenberg J Morris P Ecker K Welch L Discovery of regulatory elements in oomycete orthologs The 2008 International Conference on Bioinformatics and Computational Biology Las Vegas 2008.
44. Lenhard B Wasserman WW TFBS: Computational framework for transcription factor binding site analysis Bioinformatics 2002, 18:1135-1136. 12176838
45. Larkin MA Blackshields G Brown NP Chenna R McGettigan PA McWilliam H Valentin F Wallace IM Wilm A Lopez R et al. ClustalW and ClustalX version 2.0 Bioinformatics 2007, 23(21):2947-2948. 17846036
46. Birney E Stamatoyannopoulos JA Dutta A Guigo R Gingeras TR Margulies EH Weng Z: Snyder M Dermitzakis ET Thurman RE Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project Nature 2007, 447(7146):799-816. 2212820 17571346
47. Wasserman WW Sandelin A Applied bioinformatics for the identification of regulatory elements Nat Rev Genet 2004, 5(4):276-287. 15131651