Warehousing re-annotated cancer genes for biomarker meta-analysis

Computer Methods and Programs in Biomedicine

Volumn 111, Issue 1, 2013, Pages 166-180

  Orsini, M ^a   Travaglione, A ^a   Capobianco, E ^b,c  

^a CRS4 Bioinformatics ^*  (Italy)

^b UNIVERSITY OF MIAMI   (United States)

^c CNR   (Italy)

Author keywords

Cancer transcriptomics; Data warehousing; Re annotation

Indexed keywords

BIO-MARKER DISCOVERY; COMPARATIVE EVALUATIONS; GENE EXPRESSION DATA; GENOTYPE-PHENOTYPE ASSOCIATIONS; RE-ANNOTATION; TARGET IDENTIFICATION; TRANSCRIPTOMICS; TRANSLATIONAL RESEARCH;

BIOINFORMATICS; CELL CULTURE; DATA WAREHOUSES; DISEASES; EXPERIMENTS; GENE EXPRESSION; TISSUE;

DATA INTEGRATION;

BIOLOGICAL MARKER; TUMOR MARKER;

ADENOCARCINOMA; ARTICLE; BIOINFORMATICS; CANCER STAGING; CLINICAL DATA REPOSITORY; COLON CANCER; GENE EXPRESSION; GENOTYPE PHENOTYPE CORRELATION; INFORMATION PROCESSING; INFORMATION SYSTEM; TRANSCRIPTOMICS; TUMOR GENE;

COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; DATA MINING; DATABASES, GENETIC; GENETIC ASSOCIATION STUDIES; GENOMICS; HUMANS; META-ANALYSIS AS TOPIC; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; ONCOGENES; TRANSLATIONAL MEDICAL RESEARCH; TUMOR MARKERS, BIOLOGICAL;

EID: 84878491393     PISSN: 01692607     EISSN: 18727565     Source Type: Journal    
DOI: 10.1016/j.cmpb.2013.03.010     Document Type: Article

References (19)

1. Barrett T., Edgar R. Reannotation of array probes at NCBI's GEO database. Nature Methods 2008, 5(2):117.
2. Brazma A., Hingamp P., Quackenbush J., Sherlock G., Spellman P., Stoeckert C., Aach J., Ansorge W., Ball C.A., Causton H.C., Gaasterland T., Glenisson P., Holstege F.C., Kim I.F., Markowitz V., Matese J.C., Parkinson H., Robinson A., Sarkans U., Schulze-Kremer S., Stewart J., Taylor R., Vilo J.M. Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nature Genetics 2001, 29(4):365-371.
3. Brazma A., Parkinson H., Sarkans U., Shojatalab M., Vilo J., Abeygunawardena N., Holloway E., Kapushesky M., Kemmeren P., Lara G.G., Oezcimen A., Rocca-Serra P., Sansone S.A.S.A. ArrayExpress-a public repository for microarray gene expression data at the EBI. NAR 1 2003, 31(1):68-71.
4. Chan S.K., Griffith O.L., Tai I.T., Jones S.J.M. Meta-analysis of colorectal cancer gene expression profiling studies identifies consistently reported candidate biomarkers. Cancer Epidemiology, Biomarkers and Prevention 2008, 17(3):543-550.
5. Cui X., Loraine A.E. Consistency analysis of redundant probe sets on affymetrix three-prime expression arrays and applications to differential mRNA processing. PLoS ONE 2009, 4(1):e4229.
6. Deutsch E.W., Ball C.A., Berman J.J., Bova G.S., Brazma A., Bumgarner R.E., Campbell D., Causton H.C., Christiansen J.H., Daian F., Dauga D., Davidson D.R., Gimenez G., Goo Y.A., Grimmond S., Henrich T., Herrmann B.G., Johnson M.H., Korb M., Mills J.C., Oudes A.J., Parkinson H.E., Pascal L.E., Pollet N., Quackenbush J., Ramialison M., Ringwald M., Salgado D., Sansone S.A., Sherlock G., Stoeckert C.J, Swedlow J., Taylor R.C., Walashek L., Warford A., Wilkinson D.G., Zhou Y., Zon L.I., Liu A.Y. Minimum information specification for in situ hybridization and immunohistochemistry experiments (MISFISHIE). Nature Biotechnology 2008, 26(3):305-312.
7. Gong X., Wu R., Zhang Y., Zhao W., Cheng L., Gu Y., Zhang L., Wang J., Zhu J., Guo Z. Extracting consistent knowledge from highly inconsistent cancer gene data sources. BMC Bioinformatics 2010, 11:76.
8. Griffith O.L., Melck A., Jones S.J.M., Wiseman S.M. Meta-analysis and meta-review of thyroid cancer gene expression profiling studies identifies important diagnostic biomarkers. Journal of Clinical Oncology 2006, 24:5043-5051.
9. http://www.ebi.ac.uk/microarray-as/ae/.
10. http://www.ncbi.nlm.nih.gov/geo/.
11. Ikeo K., Ishi-i J., Tamura T., Gojobori T., Tateno Y. CIBEX: center for information biology gene expression database. Comptes Rendus Biologies 2003, 326(10-11):1079-1082.
12. Lacson R., Pitzer E., Hinske C., Galante P., Ohno-Machado L. Evaluation of a large-scale biomedical data annotation initiative. BMC Bioinformatics 2009, 10(Suppl 9):S10.
13. Lacson R., Pitzer E., Kim J., Galante P., Hinske C., Ohno-Machado L. DSGeo: software tools for cross-platform analysis of gene expression data in GEO. Journal of Biomedical Informatics 2010, 43(5):709-715.
14. Neerincx P.B., Casel P., Prickett D., Nie H., Watson M., Leunissen J.A., Groenen M.A., Klopp C. Comparison of three microarray probe annotation pipelines: differences in strategies and their effect on downstream analysis. BMC Proceedings 2009, 16:3.
15. Pitzer E., Lacson R., Hinske C., Kim J., Galante P.A.F., Ohno-Machado L. Towards large-scale sample annotation in gene expression repositories. BMC Bioinformatics 2009, 10(Suppl. 9):S9.
16. Shah N.H., Rubin D.L., Supekar K.S., Musen M.A. Ontology-based annotation and query of tissue microarray data. AMIA Annual Symposium Proceedings 2006, 709-713.
17. Steinhoff C., Vingron M. Normalization and quantification of differential expression in gene expression microarrays. Briefings in Bioinformatics 2006, 7(2):166-177.
18. Whetzel P.L., Parkinson H., Causton H.C., Fan L., Fostel J., Fragoso G., Game L., Heiskanen M., Morrison N., Rocca-Serra P., Sansone S.A., Taylor C., White J., Stoeckert C.J. The MGED ontology: a resource for semantics-based description of microarray experiments. Bioinformatics 2006, 22(7):866-873.
19. Zhang M., Zhang L., Zou J., Yao C., Xiao H., Liu Q., Wang J., Wang D., Wang C., Guo Z. Evaluating reproducibility of differential expression discoveries in microarray studies by considering correlated molecular changes. Bioinformatics 2009, 25(13):1662-1668.