Predicting gene ontology from a global meta-analysis of 1-color microarray experiments

BMC Bioinformatics

Volumn 12, Issue SUPPL. 10, 2011, Pages

  Dozmorov, Mikhail G ^a   Giles, Cory B ^a   Wren, Jonathan D ^a  

^a OKLAHOMA MEDICAL RESEARCH FOUNDATION   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DATA SET SIZE; EXPERIMENTAL CONDITIONS; GENE ONTOLOGY; GUILT BY ASSOCIATIONS; META-ANALYSIS; MICROARRAY DATA; MICROARRAY EXPERIMENTS; PREDICTION PERFORMANCE;

EXPERIMENTS; FORECASTING; GENE EXPRESSION; MICROARRAYS;

GENE EXPRESSION REGULATION;

ARTICLE; COLOR; DNA MICROARRAY; GENE EXPRESSION PROFILING; GENETIC DATABASE; HUMAN; METHODOLOGY;

COLOR; DATABASES, GENETIC; GENE EXPRESSION PROFILING; HUMANS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS;

EID: 80054091152     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-12-S10-S14     Document Type: Article

References (34)

1. Barrett T, Suzek TO, Troup DB, Wilhite SE, Ngau WC, Ledoux P, Rudnev D, Lash AE, Fujibuchi W, Edgar R. NCBI GEO: mining millions of expression profiles--database and tools. Nucleic Acids Res 2005, 33(Database issue):D562-566. 539976, 15608262.
2. Brazma A, Parkinson H, Sarkans U, Shojatalab M, Vilo J, Abeygunawardena N, Holloway E, Kapushesky M, Kemmeren P, Lara GG, et al. ArrayExpress--a public repository for microarray gene expression data at the EBI. Nucleic Acids Res 2003, 31(1):68-71. 10.1093/nar/gkg091, 165538, 12519949.
3. Hubble J, Demeter J, Jin H, Mao M, Nitzberg M, Reddy TB, Wymore F, Zachariah ZK, Sherlock G, Ball CA. Implementation of GenePattern within the Stanford Microarray Database. Nucleic Acids Res 2009, 37(Database issue):D898-901. 2686537, 18953035.
4. Blaby-Haas CE, de Crecy-Lagard V. Mining high-throughput experimental data to link gene and function. Trends Biotechnol 2011, 29(4):174-182. 10.1016/j.tibtech.2011.01.001, 21310501.
5. Wu LF, Hughes TR, Davierwala AP, Robinson MD, Stoughton R, Altschuler SJ. Large-scale prediction of Saccharomyces cerevisiae gene function using overlapping transcriptional clusters. Nat Genet 2002, 31(3):255-265. 10.1038/ng906, 12089522.
6. Spellman PT, Sherlock G, Zhang MQ, Iyer VR, Anders K, Eisen MB, Brown PO, Botstein D, Futcher B. Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol Biol Cell 1998, 9(12):3273-3297. 25624, 9843569.
7. Stuart JM, Segal E, Koller D, Kim SK. A gene-coexpression network for global discovery of conserved genetic modules. Science 2003, 302(5643):249-255. 10.1126/science.1087447, 12934013.
8. Lee HK, Hsu AK, Sajdak J, Qin J, Pavlidis P. Coexpression analysis of human genes across many microarray data sets. Genome Res 2004, 14(6):1085-1094. 10.1101/gr.1910904, 419787, 15173114.
9. Magwene PM, Kim J. Estimating genomic coexpression networks using first-order conditional independence. Genome Biol 2004, 5(12):R100. 10.1186/gb-2004-5-12-r100, 545795, 15575966.
10. Xu J, Li CX, Li YS, Lv JY, Ma Y, Shao TT, Xu LD, Wang YY, Du L, Zhang YP, et al. MiRNA-miRNA synergistic network: construction via co-regulating functional modules and disease miRNA topological features. Nucleic Acids Res 2011, 39(3):825-836. 10.1093/nar/gkq832, 3035454, 20929877.
11. Eisen MB, Spellman PT, Brown PO, Botstein D. Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci U S A 1998, 95(25):14863-14868. 10.1073/pnas.95.25.14863, 24541, 9843981.
12. Gustin MP, Paultre CZ, Randon J, Bricca G, Cerutti C. Functional meta-analysis of double connectivity in gene co-expression networks in mammals. Physiol Genomics 2008,
13. Zhang B, Horvath S. A general framework for weighted gene co-expression network analysis. Stat Appl Genet Mol Biol 2005, 4. Article 17.
14. Han L, Zhu J. Using matrix of thresholding partial correlation coefficients to infer regulatory network. Biosystems 2008, 91(1):158-165. 10.1016/j.biosystems.2007.08.008, 17919808.
15. Wren JD. A global meta-analysis of microarray expression data to predict unknown gene functions and estimate the literature-data divide. Bioinformatics 2009, 25(13):1694-1701. 10.1093/bioinformatics/btp290, 2732319, 19447786.
16. Sahoo D, Dill DL, Gentles AJ, Tibshirani R, Plevritis SK. Boolean implication networks derived from large scale, whole genome microarray datasets. Genome Biol 2008, 9(10):R157. 10.1186/gb-2008-9-10-r157, 2760884, 18973690.
17. Morgan AA, Dudley JT, Deshpande T, Butte AJ. Dynamism in gene expression across multiple studies. Physiol Genomics 2010, 40(3):128-140. 10.1152/physiolgenomics.90403.2008, 2825768, 19920211.
18. Edwards AM, Isserlin R, Bader GD, Frye SV, Willson TM, Yu FH. Too many roads not taken. Nature 2011, 470(7333):163-165. 10.1038/470163a, 21307913.
19. Pena-Castillo L, Tasan M, Myers CL, Lee H, Joshi T, Zhang C, Guan Y, Leone M, Pagnani A, Kim WK, et al. A critical assessment of Mus musculus gene function prediction using integrated genomic evidence. Genome Biol 2008, 9 Suppl 1:S2. 2447536, 18613946.
20. Pena-Castillo L, Hughes TR. Why are there still over 1000 uncharacterized yeast genes?. Genetics 2007, 176(1):7-14. 10.1534/genetics.107.074468, 1893027, 17435240.
21. Wren JD. Extending the mutual information measure to rank inferred literature relationships. BMC Bioinformatics 2004, 5:145. 10.1186/1471-2105-5-145, 526381, 15471547.
22. Wren JD, Bekeredjian R, Stewart JA, Shohet RV, Garner HR. Knowledge discovery by automated identification and ranking of implicit relationships. Bioinformatics 2004, 20(3):389-398. 10.1093/bioinformatics/btg421, 14960466.
23. Wren JD, Garner HR. Shared relationship analysis: ranking set cohesion and commonalities within a literature-derived relationship network. Bioinformatics 2004, 20(2):191-198. 10.1093/bioinformatics/btg390, 14734310.
24. Srivastava GP, Qiu J, Xu D. Genome-wide functional annotation by integrating multiple microarray datasets using meta-analysis. Int J Data Min Bioinform 2010, 4(4):357-376. 10.1504/IJDMB.2010.034194, 20815137.
25. Daum JR, Wren JD, Daniel JJ, Sivakumar S, McAvoy JN, Potapova TA, Gorbsky GJ. Ska3 is required for spindle checkpoint silencing and the maintenance of chromosome cohesion in mitosis. Curr Biol 2009, 19(17):1467-1472. 10.1016/j.cub.2009.07.017, 2783354, 19646878.
26. Lu Y, Huggins P, Bar-Joseph Z. Cross species analysis of microarray expression data. Bioinformatics 2009, 25(12):1476-1483. 10.1093/bioinformatics/btp247, 2732912, 19357096.
27. GEO ftp data archive. , ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SOFT/GDS/
28. NCBI gene-GO mapping file. , ftp://ftp.ncbi.nih.gov/gene/DATA/gene2go.gz
29. Gene Ontolody data archive. , http://www.geneontology.org/ontology/obo_format_1_2/gene_ontology_ext.obo
30. Bolstad BM, Irizarry RA, Astrand M, Speed TP. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 2003, 19(2):185-193. 10.1093/bioinformatics/19.2.185, 12538238.
31. NCBI gene ID mapping file. , ftp://ftp.ncbi.nih.gov/gene/DATA/GENE_INFO/Mammalia/Homo_sapiensgene_info.gz
32. SBochkanov VB. AlgLib (http://www.alglib.net).
33. Oliveros JC. VENNY. An interactive tool for comparing lists with Venn Diagrams. 2007,
34. Frohlich H, Speer N, Poustka A, Beissbarth T. GOSim--an R-package for computation of information theoretic GO similarities between terms and gene products. BMC Bioinformatics 2007, 8:166. 10.1186/1471-2105-8-166, 1892785, 17519018.