Determining significance of pairwise co-occurrences of events in bursty sequences

BMC Bioinformatics

Volumn 9, Issue , 2008, Pages 336-

  Haiminen, Niina ^a   Mannila, Heikki ^a,b   Terzi, Evimaria ^a,c  

^a UNIVERSITY OF HELSINKI   (Finland)

^b HELSINKI INSTITUTE FOR INFORMATION TECHNOLOGY   (Finland)

^c IBM ALMADEN RESEARCH CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA SEQUENCES; REAL TIME SYSTEMS; TRANSCRIPTION; TRANSCRIPTION FACTORS;

CO-OCCURRENCE PATTERN; EVENT SEQUENCE; GENOMIC REGIONS; NUMERICAL VALUES; REGULATORY PROCESS; SEQUENCE STRUCTURE; SYNTHETIC EVENTS; TRANSCRIPTION FACTOR BINDING SITES;

BINDING SITES;

TRANSCRIPTION FACTOR;

ARTICLE; BINDING SITE; DNA SEQUENCE; DNA STRUCTURE; FALSE POSITIVE RESULT; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; STATISTICAL ANALYSIS; STATISTICAL MODEL;

EID: 52449096976     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-9-336     Document Type: Article

References (19)

1. Stormo GD DNA binding sites: Representation and discovery Bioinformatics 2000, 16:16-23 10812473
2. Makeev VJ Lifanov AP Nazina AG Papatsenko DA Distance preferences in the arrangement of binding motifs and hierarchical levels in organization of transcription regulatory information Nucleic Acids Research 2003, 31(20):6016-6026 219477 14530449
3. Levy S Hannenhalli S Workman C Enrichment of regulatory signals in conserved non-coding genomic sequence Bioinformatics 2001, 17(10):871-877 11673231
4. Hannenhalli S Levy S Predicting transcription factor synergism Nucleic Acids Research 2002, 30(19):4278-4284 140535 12364607
5. Rateitschak K Müller T Vingron M Annotating significant pairs of transcription factor binding sites in regulatory DNA In Silico Biology 2004, 4(4):479-487 15506997
6. Stepanova M Tiazhelova T Skoblov M Baranovaothers A A comparative analysis of relative occurrence of transcription factor binding sites in vertebrate genomes and gene promoter areas Bioinformatics 2005, 21(9):1789-1796 15699025
7. Blanchette M Bataille AR Chen X Poitras C Laganière J Lefèbvre C Deblois G Giguère V Ferretti V Bergeron D Coulombe B Robert F Genome-wide computational prediction of transcriptional regulatory modules reveals new insights into gene expression Genome Research 2006, 16(5):656-668 1457048 16606704
8. Klein H Vingron M Using transcription factor binding site co-occurrence to predict regulatory regions Genome Informatics 2007, 18:109-118 18546479
9. Mannila H Toivonen H Verkamo AI Discovery of frequent episodes in event sequences Data Mining and Knowledge Discovery 1997, 1(3):259-289
10. Benjamini Y Hochberg Y Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing Journal of the Royal Statistical Society. Series B 1995, 57:289-300
11. International Human Genome Sequencing Consortium Initial sequencing and analysis of the human genome Nature 2001, 409(6822):860-921 11237011
12. Sandelin A Alkema W Engström P Wasserman WW Lenhard B JASPAR: An open-access database for eukaryotic transcription factor binding profiles Nucleic Acids Res 2004:32 Database issue D91-94 308747 14681366
13. Beckstette M Homann R Giegerich R Kurtz S Fast index based algorithms and software for matching position specific scoring matrices BMC Bioinformatics 2006, 7:389 1635428 16930469
14. Chen H Sharp B Content-rich biological network constructed by mining PubMed abstracts BMC Bioinformatics 2004, 5:147 http://www.chilibot.net/ 15473905 528731
15. Matys V Kel-Margoulis OV Fricke E Liebich I Land S Barre-Dirrie A Reuter I Chekmenev D Krull M Hornischer K Voss N Stegmaier P Lewicki-Potapov B Saxel H Kel AE Wingender E TRANSFAC© and its module TRANSCompel©: Transcriptional gene regulation in eukaryotes Nucl Acids Research 2006:34 Database issue D108-D110 16381825 1347505
16. Quan Y Ji ZL Wang X Tartakoff AM Tao T Evolutionary and transcriptional analysis of karyopherin beta superfamily proteins Mol Cell Proteomics 2008, 7(7):1254-1269 18353765
17. Decoville M Giraud-Panis MJ Mosrin-Huaman C Leng M Locker D HMG boxes of DSP1 protein interact with the Rel homology domain of transcription factors Nucleic Acids Research 2000, 28(2):454-462 102508 10606643
18. Mukhopadhyay NK Ferdinand AS Mukhopadhyay L Cinar B Lutchman M Richie JP Freeman MR Liu BCS Unraveling androgen receptor interactomes by an array-based method: Discovery of proto-oncoprotein c-Rel as a negative regulator of androgen receptor Experimental Cell Research 2006, 312(19):3782-3795 17011549
19. Wood LJ Mukherjee M Dolde CE Xu Y Maher JF Bunton TE Williams JB Resar LMS HMG-I/Y, a New c-Myc Target Gene and Potential Oncogene Mol Cell Biol 2000, 20(15):5490-5502 86000 10891489