From 'omes to biology

Animal Genetics

Volumn 37, Issue SUPPL. 1, 2006, Pages 48-56

  Quackenbush, J ^a  

^a HARVARD SCHOOL OF PUBLIC HEALTH   (United States)

Author keywords

Genomics; Integration; Microarray data; Review; Systems biology

Indexed keywords

ANIMAL; ARTICLE; CHROMOSOME MAP; CLUSTER ANALYSIS; DNA MICROARRAY; GENE EXPRESSION PROFILING; GENOME; GENOMICS; HUMAN; METHODOLOGY; MOUSE; SYSTEMS BIOLOGY;

ANIMALS; CHROMOSOME MAPPING; CLUSTER ANALYSIS; GENE EXPRESSION PROFILING; GENOME; GENOMICS; HUMANS; MICE; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; SYSTEMS BIOLOGY;

EID: 33746217025     PISSN: 02689146     EISSN: 13652052     Source Type: Journal    
DOI: 10.1111/j.1365-2052.2006.01476.x     Document Type: Article

References (32)

1. Algotsson A. & Winblad B. (2004) Patients with Alzheimer's Disease may be particularly susceptible to adverse effects of statins. Dementia and Geriatric Cognitive Disorders 17, 109-16.
2. Artz G. & Wynne J. (2000) Restrictive Cardiomyopathy. Current Treatment Options in Cardiovascular Medicine 2, 431-8.
3. Ashburner M., Ball C.A., Blake J.A. et al. (2000) Gene ontology: tool for the unification of biology. Nature Genetics 25, 25-9.
4. Ball C.A., Sherlock G., Parkinson H. et al. (2002) Submission of Microarray Data to Public Repositories. Science 298, 539.
5. Ball C.A., Brazma A., Causton H. et al. (2004) Standards for microarray data. PLoS Biol 2, E317.
6. Brazma A., Hingamp P., Quackenbush J. et al. (2001) Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nature Genetics 29, 365-71.
7. Cook D.N., Wang S., Wang Y. et al. (2004) Genetic regulation of endotoxin-induced airway disease. Genomics 83, 961-9.
8. Dahlquist K.D., Salomonis N., Vranizan K., Lawlor S.C. & Conklin B.R. (2002) GenMAPP, a new tool for viewing and analyzing microarray data on biological pathways. Nature Genetics 31, 19-20.
9. Djebbari A., Karamycheva S., Howe E. & Quackenbush J. (2005) MeSHer: identifying biological concepts in microarray assays based on PubMed references and MeSH terms. Bioinformatics 21, 3324-6.
10. Eschrich S., Yang I., Bloom G. et al. (2005) Molecular staging for survival prediction of colorectal cancer patients. Journal of Clinical Oncology 23, 3526-35.
11. Hosack D.A., Dennis G. Jr, Sherman B.T., Lane H.C. & Lempicki R.A. (2003) Identifying biological themes within lists of genes with EASE. Genome Biology 4, R70.
12. Hubbard T., Barker D., Birney E. et al. (2002) The Ensembl genome database project. Nucleic Acids Research 30, 38-41.
13. Huber W., von Heydebreck A., Sultmann H., Poustka A. & Vingron M. (2002) Variance stabilization applied to microarray data calibration and to the quantification of differential expression. Bioinformatics 18(Suppl. 1), S96-104.
14. Irizarry R.A., Warren D., Spencer F. et al. (2005) Multiple-laboratory comparison of microarray platforms. Nature Methods 2, 345-50.
15. Kwong K.Y., Bloom G.C., Yang I. et al. (2005) Synchronous global assessment of gene and protein expression in colorectal cancer progression. Genomics 86, 142-58.
16. Larkin J.E., Frank B.C., Gaspard R.M., Duka I., Gavras H. & Quackenbush J. (2004) Cardiac transcriptional response to acute and chronic angiotensin II treatments. Physiol Genomics 18, 152-66.
17. Larkin J.E., Frank B.C., Gavras H., Sultana R. & Quackenbush J. (2005) Independence and reproducibility across microarray platforms. Nature Methods 2, 337-44.
18. Lee Y., Sultana R., Pertea G. et al. (2002) Cross-referencing eukaryotic genomes: TIGR Orthologous Gene Alignments (TOGA). Genome Research 12, 493-502.
19. Lee Y., Tsai J., Sunkara S., Karamycheva S., Pertea G., Sultana R., Antonescu V., Chan A., Cheung F. & Quackenbush J. (2005) The TIGR Gene Indices: clustering and assembling EST and known genes and integration with eukaryotic genomes. Nucleic Acids Research 33(Database Issue), D71-4.
20. Liang F., Holt I., Pertea G., Karamycheva S., Salzberg S.L. & Quackenbush J. (2000) Gene index analysis of the human genome estimates approximately 120,000 genes. Nature Genetics 25, 239-40.
21. Ogata H., Goto S., Sato K., Fujibuchi W., Bono H. & Kanehisa M. (1999) KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Research 27, 29-34.
22. Pertea G., Huang X., Liang F. et al. (2003) TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets. Bioinformatics 19, 651-2.
23. Saeed A.I., Sharov V., White J. et al. (2003) TM4: a free, open-source system for microarray data management and analysis. Biotechniques 34, 374-8.
24. Schadt E.E., Lamb J., Yang X. et al. (2005) An integrative genomics approach to infer causal associations between gene expression and disease. Nature Genetics 37, 710-7.
25. Sparks D.L., Martin T.A., Gross D.R. & Hunsaker J.C. III. (2000) Link between heart disease, cholesterol, and Alzheimer's disease: a review. Microscopy Research and Technique 50, 287-90.
26. Spellman P.T., Miller M., Stewart J. et al. (2002) Design and implementation of microarray gene expression markup language (MAGE-ML). Genome Biology 3, RESEARCH0046.
27. Stuart J.M., Segal E., Koller D. & Kim S.K. (2003) A gene-coexpression network for global discovery of conserved genetic modules. Science 302, 249-55.
28. Tsai J., Sultana R., Lee Y., Pertea G., Karamycheva K., Antonescu V., Cho J., Parvizi B., Cheung F. & Quackenbush J. (2001) RESOURCERER: a database for annotating and linking microarray resources within and across species. Genome Biology 2, software 0002.1-2.4.
29. Tusher V.G., Tibshirani R. & Chu G. (2001) Significance analysis of microarrays applied to the ionizing radiation response. Proceedings of the National Academy of Sciences of the United States of America 98, 5116-21.
30. Weis B.K. (2005) Standardizing global gene expression analysis between laboratories and across platforms. Nature Methods 2, 351-6.
31. Yang I.V., Chen E., Hasseman J.P. et al. (2002a) Within the fold: assessing differential expression measures and reproducibility in microarray assays. Genome Biology 3, research 0062.
32. Yang Y.H., Dudoit S., Luu P., Lin D.M., Peng V., Ngai J. & Speed T.P. (2002b) Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Research 30, e15.