Testing for treatment effects on gene ontology

BMC Bioinformatics

Volumn 9, Issue SUPPL. 9, 2008, Pages

  Lee, Taewon ^a   Desai, Varsha G ^a   Velasco, Cruz ^b   Shmookler Reis, Robert J ^c   Delongchamp, Robert R ^d  

^a NATIONAL CENTER FOR TOXICOLOGICAL RESEARCH   (United States)

^b LOUISIANA STATE UNIVERSITY HEALTH SCIENCES CENTER   (United States)

^c UNIVERSITY OF ARKANSAS FOR MEDICAL SCIENCES   (United States)

^d UNIVERSITY OF ARKANSAS FOR MEDICAL SCIENCES   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CORRELATION STRUCTURE; GENE ONTOLOGY TERMS; HYPOTHESIS TESTING; MICROARRAY EXPERIMENTS; OLIGONUCLEOTIDE MICROARRAY; SMALL SAMPLE SIZE; STATISTICAL POWER; TREATMENT EFFECTS;

COMPUTER SIMULATION; GENE EXPRESSION; MICROARRAYS; MONTE CARLO METHODS; OLIGONUCLEOTIDES;

STATISTICAL TESTS;

LAMIVUDINE; MITOCHONDRIAL DNA; NUCLEOSIDE ANALOG; USNIC ACID; ZIDOVUDINE; BIOLOGICAL MARKER; DRUG;

ANALYTIC METHOD; APOPTOSIS; COMPUTER SIMULATION; CONFERENCE PAPER; DNA MICROARRAY; DRUG MECHANISM; GENE EXPRESSION; GENETIC ANALYSIS; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; MITOCHONDRION; MONTE CARLO METHOD; NONHUMAN; OXIDATIVE PHOSPHORYLATION; STATISTICAL ANALYSIS; UNSPECIFIED SIDE EFFECT; UPREGULATION; VERTICAL TRANSMISSION; ARTICLE; DRUG EFFECT; DRUG SCREENING; DRUG THERAPY; GENE EXPRESSION PROFILING; GENETICS; METABOLISM; METHODOLOGY; OUTCOME ASSESSMENT; TREATMENT OUTCOME;

BIOLOGICAL MARKERS; DNA, MITOCHONDRIAL; DRUG EVALUATION; DRUG THERAPY; GENE EXPRESSION PROFILING; MITOCHONDRIA; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; OUTCOME ASSESSMENT (HEALTH CARE); PHARMACEUTICAL PREPARATIONS; TREATMENT OUTCOME;

EID: 49649094585     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-9-S9-S20     Document Type: Conference Paper

References (17)

1. Benjamini Y Hochberg Y Controlling the false discovery rate: A practical and power-ful approach to multiple testing Journal of the Royal Statistical Society Series B 1995, 57:289-300.
2. Storey JD Taylor JE Siegmund D Strong control, conservative point estimation, and simultaneous conservative consistency of false discovery rates: A unified approach Journal of the Royal Statistical Society, Series B 2004, 66:187-205. 10.1111/j.1467-9868.2004.00439.x
3. Allison DB Gadbury GL Heo M Fernandez JR Lee C-K Prolla TA Weindruch R A mixture model approach for the analysis of microarray gene expression data Computational Statistics and Data Analysis 2002, 39:1-20. 10.1016/ S0167-9473(01)00046-9
4. Khatri P Draghici S Ontological analysis of gene expression data: current tools, limitations, and open problems Bioinformatics 2005, 21:3587-3595. 2435250 15994189 10.1093/bioinformatics/bti565
5. Draghci S Khatri P Martins RP Ostermeier GC Krawetz SA Global functional profiling of gene expression Genomics 2003, 81:98-104. 10.1016/ S0888-7543(02)00021-6 12620386
6. Tian L Greenberg SA Kong SW Altschuler J Kohane IS Park PJ Discovering statistically significant pathways in expression profiling studies PNAS 2005, 102:13544-13549. 1200092 16174746 10.1073/pnas.0506577102
7. Pavlidis P Qin J Arango V Mann JJ Sibille E Using the gene ontology for microarray data mining: A comparison of methods and application to age effects in human prefrontal cortex Neurochemical Research 2004, 29:1213-1222. 10.1023/B:NERE.0000023608.29741.45 15176478
8. Kong SW Pu WT Park PJ A multivariate approach for integrating genome-wide expression data and biological knowledge Bioinformatics 2006, 22:2373-80. 10.1093/bioinformatics/btl401 16877751
9. Delongchamp RR Velasco C Desai VG Lee T Fuscoe JC Designing toxicogenomics studies that use DNA array technology Bioinformatics and Biology Insights 2007.
10. Delongchamp RR Lee T Velasco C A method for computing the overall statistical significance of a treatment effect among a group of genes BMC Bioinformatics 7, (Suppl 2):S11, 2006 Sep 6. 1683577 17118132 10.1186/1471-2105-7-S2-S11
11. Desai VG Lee T Delongchamp RR Moland CL Branham WS Fuscoe JC Leakey JEA Development of mitochondria-specific mouse oligonucleotide microarray and validation of data by real-time PCR Mitochondrion 2007, 7(5):322-9. 10.1016/j.mito.2007.02.004 17526437
12. Desai VG Lee T Delongchamp RR Leakey JEA Lewis SM Lee F Moland CL Branham WS Fuscoe JC NRTI-induced expression profile of mitochondrial genes in the mouse liver Mitochondrion 2008, 8(2):181-195. 10.1016/ j.mito.2008.01.002 18313992
13. Joseph A Lee T Moland CL Branham WS Fuscoe JC Leakey JEA Allaben W Lewis SM Ali AA Desai VG Effect of usnic acid on mitochondrial functions as measured by mitochondria-specific oligonucleotide microarray in liver of B6C3F1 mice Biochemical Pharmacology 2008.
14. Cherry CL Wesselingh SL Nucleoside analogues and HIV: The combined cost to mitochondria J Antimicrob Chemother 2003, 51:1091-1093. 10.1093/jac/ dkg203 12668570
15. Barret B Tardieu M Rustin P Lacroix C Chabrol B For the French perinatal cohort study group. Persistent mitochondrial dysfunction in HIV-1-exposed but uninfected infants: Clinical screening in a large prospective cohort AIDS 2003, 17:1769-1785. 10.1097/ 00002030-200308150-00006 12891063
16. Subramanian A Tamayo P Mootha VK Mukherjee S Ebert BL Gillette MA Paulovich A Pomeroy SL Golub TR Lander ES Mesirov JP A knowledge-based approach for interpreting genome-wide expression profiles PNAS 2005, 102:15545-15550. 1239896 16199517 10.1073/pnas.0506580102
17. Efron B Tibshirani R On testing the significance of sets of genes Tech report 2006 http://www-stat.stanford.edu/~tibs/GSA/