Prediction-based approaches to characterize bidirectional promoters in the mammalian genome

BMC Genomics

Volumn 9, Issue SUPPL. 1, 2008, Pages

  Qu, Mary Qu ^a   Elnitski, Laura L ^a  

^a NATIONAL HUMAN GENOME RESEARCH INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA;

ARTICLE; COMPUTER PREDICTION; CPG ISLAND; EXPRESSED SEQUENCE TAG; GENBANK; GENE MAPPING; GENE SEQUENCE; GENETIC ALGORITHM; GENETIC CONSERVATION; HIDDEN MARKOV MODEL; HUMAN; NONHUMAN; NUCLEOTIDE SEQUENCE; ORTHOLOGY; PROMOTER REGION; SPECIES DIFFERENCE; ANIMAL; ARTIFICIAL INTELLIGENCE; BIOLOGICAL MODEL; BIOLOGY; COMPARATIVE STUDY; GENETICS; GENOME; GENOMICS; MAMMAL; METHODOLOGY; MOUSE; PROBABILITY;

MAMMALIA;

ANIMALS; ARTIFICIAL INTELLIGENCE; COMPUTATIONAL BIOLOGY; GENOME; GENOMICS; HUMANS; MAMMALS; MARKOV CHAINS; MICE; MODELS, GENETIC; PROMOTER REGIONS (GENETICS);

EID: 45149112416     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-9-S1-S2     Document Type: Article

References (14)

1. Adachi N Lieber MR Bidirectional gene organization: A common architectural feature of the human genome Cell 2002, 109(7):807-9. 10.1016/S0092-8674(02)00758-4 12110178
2. Trinklein ND Aldred SF Hartman SJ Schroeder DI Otillar RP Myers RM An Abundance of Bidirectional Promoters in the Human Genome Genome Res. 2004, 14:62-66. http://www.genome.org/cgi/content/abstract/14/1/62 314279 14707170 10.1101/gr.1982804
3. Yang MQ Elnitski LL A computational study of bidirectional promoters in the human genome In Lecture Notes in Bioinformatics Springer-Verlag 2007.
4. Yang MQ Koehly LM Elnitski LL Comprehensive annotation of human bidirectional promoters identifies co-regulatory relationships among somatic breast and ovarian cancer genes PLoS Computational Biology 2007, 3(4):. [(E72.eor)]
5. Hsu F Kent WJ Clawson H Kuhn RM Diekhans M Haussler D The UCSC Known Genes Bioinformatics 2006, 22(9):1036-1046. http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/9/1036 10.1093/bioinformatics/btl048 16500937
6. Benson DA Karsch-Mizrachi I Lipman DJ Ostell J Wheeler DL GenBank: update Nucleic Acids Res 2004, 32: Database issue D23-D26. 10.1093/nar/ gkh045 14681350 308779
7. Kawaji H Kasukawa T Fukuda S Katayama S Kai C Kawai J Carninci P Hayashizaki Y CAGE Basic/Analysis Databases: The CAGE resource for comprehensive promoter analysis Nucleic Acids Res 2006, 34: Database issue D632-D636. 10.1093/nar/gkj034 16381948 1347397
8. Li YY Yu H Guo ZM Guo TQ Tu K Li YX Systematic Analysis of Head-to-Head Gene Organization: Evolutionary Conservation and Potential Biological Relevance PLoS Computational Biology 2006, 2(7):. [E74]
9. Yang MQ Taylor J Elnitsk LL Rigorous Mapping of Orthologous Bidirectional Promoters in Vertebrates Defines their Evolutionary History In Proceedings of International Multi-Symposiums on Computer and Computational Sciences 2007. in press
10. Taylor J Tyekucheva S King DC Hardison RC Miller W Chiaromonte F ESPERR: learning strong and weak signals in genomic sequence alignments to identify functional elements Genome Res. 2006, 16:1596-1604. 1665643 17053093 10.1101/gr.4537706
11. Pennacchio LA Loots GG Nobrega MA Ovcharenko I Predicting tissue-specific enhancers in the human genome Genome Res. 2007, 17(2):201-211. http://www.genome.org/cgi/content/abstract/17/2/201 1781352 17210927 10.1101/gr.5972507
12. Margulies EH Blanchette M Haussler D Green ED Identification and Characterization of Multi-Species Conserved Sequences Genome Res. 2003, 13(12):2507-2518. 403793 14656959 10.1101/gr.1602203
13. Heintzman ND Stuart RK Hon G Fu Y Ching CW Hawkins RD Barrera LO Calcar SV Qu C Ching KA Wang W Weng Z Green RD Crawford GE Ren B Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome Nature Genetics 2007, 39:311-318. 10.1038/ ng1966 17277777
14. Heintzman ND Ren B The gateway to transcription: Identifying, characterizing and understanding promoters in the eukaryotic genome Cell Mol Life Sci 2007, 64(4):386-400. 10.1007/s00018-006-6295-0 17171231