Molecular signature of cancer at gene level or pathway level? Case studies of colorectal cancer and prostate cancer microarray data

Computational and Mathematical Methods in Medicine

Volumn 2013, Issue , 2013, Pages

  Chen, Jiajia ^a,b   Wang, Ying ^a,c   Shen, Bairong ^a   Zhang, Daqing ^a  

^a SOOCHOW UNIVERSITY   (China)

^b SUZHOU UNIVERSITY OF SCIENCE AND TECHNOLOGY   (China)

^c SECOND MILITARY MEDICAL UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

DATA REDUCTION; GENES; UROLOGY;

BIOLOGICAL PATHWAYS; DIFFERENTIALLY EXPRESSED GENE; EXPERIMENTAL EVIDENCE; GENETIC SIMILARITIES; MICROARRAY DATA SETS; MICROARRAY TECHNOLOGIES; MOLECULAR SIGNATURES; SIGNATURE DISCOVERY;

DISEASES;

CHEMOKINE; COMPLEMENTARY DNA; INTEGRIN; TUMOR MARKER;

ACTIN FILAMENT; ARTICLE; CELL ADHESION; COLORECTAL CANCER; DATA BASE; EXTRACELLULAR MATRIX; GENE EXPRESSION PROFILING; GENETIC ASSOCIATION; HUMAN; MICROARRAY ANALYSIS; ONCOGENE; PROSTATE CANCER; SIGNAL TRANSDUCTION; ALGORITHM; BIOLOGICAL MODEL; BIOLOGY; COHORT ANALYSIS; COLORECTAL TUMOR; DNA MICROARRAY; GENETICS; MALE; METABOLISM; METHODOLOGY; PROSTATE TUMOR; STATISTICAL ANALYSIS; STATISTICAL MODEL;

ALGORITHMS; COHORT STUDIES; COLORECTAL NEOPLASMS; COMPUTATIONAL BIOLOGY; DATA INTERPRETATION, STATISTICAL; DNA, COMPLEMENTARY; GENE EXPRESSION PROFILING; HUMANS; MALE; MODELS, BIOLOGICAL; MODELS, GENETIC; MODELS, STATISTICAL; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PROSTATIC NEOPLASMS;

EID: 84873340345     PISSN: 1748670X     EISSN: 17486718     Source Type: Journal    
DOI: 10.1155/2013/909525     Document Type: Article

References (41)

1. Dopazo J., Zanders E., Dragoni I., Amphlett G., Falciani F., Methods and approaches in the analysis of gene expression data. Journal of Immunological Methods 2001 250 1-2 93 112 2-s2.0-0035313785 10.1016/S0022-1759(01)00307-6 (Pubitemid 32209244)
2. Zhang M., Yao C., Guo Z., Zou J., Zhang L., Xiao H., Wang D., Yang D., Gong X., Zhu J., Li Y., Li X., Apparently low reproducibility of true differential expression discoveries in microarray studies. Bioinformatics 2008 24 18 2057 2063 2-s2.0-51749123784 10.1093/bioinformatics/btn365
3. Wang Y., Chen J., Li Q., Wang H., Liu G., Jing Q., Shen B., Identifying novel prostate cancer associated pathways based on integrative microarray data analysis. Computational Biology and Chemistry 2011 35 3 151 158 2-s2.0-79959713125 10.1016/j.compbiolchem.2011.04.003
4. Ein-Dor L., Kela I., Getz G., Givol D., Domany E., Outcome signature genes in breast cancer: is there a unique set? Bioinformatics 2005 21 2 171 178 2-s2.0-13444282534 10.1093/bioinformatics/bth469 (Pubitemid 40202018)
5. Rhodes D. R., Kalyana-Sundaram S., Mahavisno V., Varambally R., Yu J., Briggs B. B., Barrette T. R., Anstet M. J., Kincead-Beal C., Kulkarni P., Varambally S., Ghoshy D., Chinnaiyan A. M., Oncomine 3.0: genes, pathways, and networks in a collection of 18,000 cancer gene expression profiles. Neoplasia 2007 9 2 166 180 2-s2.0-33847246805 10.1593/neo.07112
6. MacDonald J. W., Ghosh D., COPA-cancer outlier profile analysis. Bioinformatics 2006 22 23 2950 2951 2-s2.0-33751377929 10.1093/bioinformatics/ btl433 (Pubitemid 44811570)
7. Subramanian A., Tamayo P., Mootha V. K., Mukherjee S., Ebert B. L., Gillette M. A., Paulovich A., Pomeroy S. L., Golub T. R., Lander E. S., Mesirov J. P., Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proceedings of the National Academy of Sciences of the United States of America 2005 102 43 15545 15550 2-s2.0-27344435774 10.1073/pnas.0506580102 (Pubitemid 41528093)
8. Kanehisa M., Goto S., KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Research 2000 28 1 27 30 2-s2.0-0033982936 (Pubitemid 30047706)
9. Drǎghici S., Khatri P., Martins R. P., Ostermeier G. C., Krawetz S. A., Global functional profiling of gene expression. Genomics 2003 81 2 98 104 2-s2.0-0037293075 10.1016/S0888-7543(02)00021-6 (Pubitemid 36298600)
10. Tavazoie S., Hughes J. D., Campbell M. J., Cho R. J., Church G. M., Systematic determination of genetic network architecture. Nature Genetics 1999 22 3 281 285 2-s2.0-0033028596 10.1038/10343 (Pubitemid 29297256)
11. Ekins S., Bugrim A., Brovold L., Kirillov E., Nikolsky Y., Rakhmatulin E., Sorokina S., Ryabov A., Serebryiskaya T., Melnikov A., Metz J., Nikolskaya T., Algorithms for network analysis in systems-ADME/Tox using the MetaCore and MetaDrug platforms. Xenobiotica 2006 36 10-11 877 901 2-s2.0-33751578696 10.1080/00498250600861660 (Pubitemid 44844107)
12. Tomlins S. A., Rhodes D. R., Perner S., Dhanasekaran S. M., Mehra R., Sun X. W., Varambally S., Cao X., Tchinda J., Kuefer R., Lee C., Montie J. E., Shah R. B., Pienta K. J., Rubin M. A., Chinnaiyan A. M., Recurrent fusion of TMPRSS2 and ETS transcription factor genes in prostate cancer. Science 2005 310 5748 644 648 2-s2.0-27344451557 10.1126/science.1117679 (Pubitemid 41528150)
13. Lian H., MOST: detecting cancer differential gene expression. Biostatistics 2008 9 3 411 418 2-s2.0-45849096393 10.1093/biostatistics/kxm042 (Pubitemid 351882082)
14. Tang Y., Chen J., Luo C., Kaipia A., Shen B., MicroRNA expression analysis reveals significant biological pathways in human prostate cancer. Proceedings of the 5th IEEE International Conference on Systems Biology (ISB '11) September 2011 Zhuhai, China IEEE Computer Society 203 210
15. Graudens E., Boulanger V., Mollard C., Mariage-Samson R., Barlet X., Grémy G., Couillault C., Lajémi M., Piatier-Tonneau D., Zaborski P., Eveno E., Auffray C., Imbeaud S., Deciphering cellular states of innate tumor drug responses. Genome Biology 2006 7 3, article R19 2-s2.0-33745037941 10.1186/gb-2006-7-3-r19 (Pubitemid 43871874)
16. Galamb O., Györffy B., Sipos F., Spisák S., Németh A. M., Miheller P., Tulassay Z., Dinya E., Molnár B., Inflammation, adenoma and cancer: objective classification of colon biopsy specimens with gene expression signature. Disease Markers 2008 25 1 1 16 2-s2.0-50249185512
17. Galamb O., Sipos F., Solymosi N., Spisák S., Krenács T., Tóth K., Tulassay Z., Molnár B., Diagnostic mRNA expression patterns of inflamed, benign, and malignant colorectal biopsy specimen and their correlation with peripheral blood results. Cancer Epidemiology Biomarkers and Prevention 2008 17 10 2835 2845 2-s2.0-54249151581 10.1158/1055-9965.EPI-08-0231
18. Hong Y., Ho K. S., Eu K. W., Cheah P. Y., A susceptibility gene set for early onset colorectal cancer that integrates diverse signaling pathways: implication for tumorigenesis. Clinical Cancer Research 2007 13 4 1107 1114 2-s2.0-33947202248 10.1158/1078-0432.CCR-06-1633 (Pubitemid 46424049)
19. Sabates-Bellver J., Van der Flier L. G., de Palo M., Cattaneo E., Maake C., Rehrauer H., Laczko E., Kurowski M. A., Bujnicki J. M., Menigatti M., Luz J., Ranalli T. V., Gomes V., Pastorelli A., Faggiani R., Anti M., Jiricny J., Clevers H., Marra G., Transcriptome profile of human colorectal adenomas. Molecular Cancer Research 2007 5 12 1263 1275 2-s2.0-37849013557 10.1158/1541-7786.MCR-07-0267
20. Dhanasekaran S. M., Barrette T. R., Ghosh D., Shah R., Varambally S., Kurachi K., Pienta K. J., Rubin M. A., Chinnaiyan A. M., Delineation of prognostic biomarkers in prostate cancer. Nature 2001 412 6849 822 826 2-s2.0-0035939903 10.1038/35090585 (Pubitemid 32801464)
21. Lapointe J., Li C., Higgins J. P., Van De Rijn M., Bair E., Montgomery K., Ferrari M., Egevad L., Rayford W., Bergerheim U., Ekman P., DeMarzo A. M., Tibshiran R., Botstein D., Brown P. O., Brooks J. D., Pollack J. R., Gene expression profiling identifies clinically relevant subtypes of prostate cancer. Proceedings of the National Academy of Sciences of the United States of America 2004 101 3 811 816 2-s2.0-9144251970 10.1073/pnas.0304146101 (Pubitemid 38121040)
22. Luo J., Duggan D. J., Chen Y., Sauvageot J., Ewing C. M., Bittner M. L., Trent J. M., Isaacs W. B., Human prostate cancer and benign prostatic hyperplasia: molecular dissection by gene expression profiling. Cancer Research 2001 61 12 4683 4688 2-s2.0-0035874995 (Pubitemid 32691876)
23. Magee J. A., Araki T., Patil S., Ehrig T., True L., Humphrey P. A., Catalona W. J., Watson M. A., Milbrandt J., Expression profiling reveals hepsin overexpression in prostate cancer. Cancer Research 2001 61 15 5692 5696 2-s2.0-0035423118 (Pubitemid 32769078)
24. Welsh J. B., Sapinoso L. M., Su A. I., Kern S. G., Wang-Rodriguez J., Moskaluk C. A., Frierson H. F., Hampton G. M., Analysis of gene expression identifies candidate markers and pharmacological targets in prostate cancer. Cancer Research 2001 61 16 5974 5978 2-s2.0-0035881732 (Pubitemid 32762523)
25. Tomlins S. A., Mehra R., Rhodes D. R., Cao X., Wang L., Dhanasekaran S. M., Kalyana-Sundaram S., Wei J. T., Rubin M. A., Pienta K. J., Shah R. B., Chinnaiyan A. M., Integrative molecular concept modeling of prostate cancer progression. Nature Genetics 2007 39 1 41 51 2-s2.0-33845884027 10.1038/ng1935 (Pubitemid 46026500)
26. Singh D., Febbo P. G., Ross K., Jackson D. G., Manola J., Ladd C., Tamayo P., Renshaw A. A., D'Amico A. V., Richie J. P., Lander E. S., Loda M., Kantoff P. W., Golub T. R., Sellers W. R., Gene expression correlates of clinical prostate cancer behavior. Cancer Cell 2002 1 2 203 209 2-s2.0-19044391072 10.1016/S1535-6108(02)00030-2 (Pubitemid 41039166)
27. Nanni S., Priolo C., Grasselli A., D'Eletto M., Merola R., Moretti F., Gallucci M., De Carli P., Sentinelli S., Cianciulli A. M., Mottolese M., Carlini P., Arcelli D., Helmer-Citterich M., Gaetano C., Loda M., Pontecorvi A., Bacchetti S., Sacchi A., Farsetti A., Epithelial-restricted gene profile of primary cultures from human prostate tumors: a molecular approach to predict clinical behavior of prostate cancer. Molecular Cancer Research 2006 4 2 79 92 2-s2.0-33645123129 10.1158/1541-7786.MCR-05-0098
28. Varambally S., Yu J., Laxman B., Rhodes D. R., Mehra R., Tomlins S. A., Shah R. B., Chandran U., Monzon F. A., Becich M. J., Wei J. T., Pienta K. J., Ghosh D., Rubin M. A., Chinnaiyan A. M., Integrative genomic and proteomic analysis of prostate cancer reveals signatures of metastatic progression. Cancer Cell 2005 8 5 393 406 2-s2.0-27644506613 10.1016/j.ccr.2005.10.001 (Pubitemid 41579834)
29. Lapointe J., Li C., Higgins J. P., Gene expression profiling identifies clinically relevant subtypes of prostate cancer. Proceedings of the National Academy of Sciences of the United States of America 2004 101 3 811 816 (Pubitemid 38121040)
30. Luo J., Duggan D. J., Chen Y., Sauvageot J., Ewing C. M., Bittner M. L., Trent J. M., Isaacs W. B., Human prostate cancer and benign prostatic hyperplasia: molecular dissection by gene expression profiling. Cancer Research 2001 61 12 4683 4688 2-s2.0-0035874995 (Pubitemid 32691876)
31. van't Veer L. J., Dai H., Van de Vijver M. J., He Y. D., Hart A. A. M., Mao M., Peterse H. L., Van Der Kooy K., Marton M. J., Witteveen A. T., Schreiber G. J., Kerkhoven R. M., Roberts C., Linsley P. S., Bernards R., Friend S. H., Gene expression profiling predicts clinical outcome of breast cancer. Nature 2002 415 6871 530 536 2-s2.0-18244409687 10.1038/415530a (Pubitemid 34130608)
32. Sørlie T., Perou C. M., Tibshirani R., Aas T., Geisler S., Johnsen H., Hastie T., Eisen M. B., Van De Rijn M., Jeffrey S. S., Thorsen T., Quist H., Matese J. C., Brown P. O., Botstein D., Lønning P. E., Børresen-Dale A. L., Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications. Proceedings of the National Academy of Sciences of the United States of America 2001 98 19 10869 10874 2-s2.0-0035845511 10.1073/pnas.191367098 (Pubitemid 32878711)
33. Wang Y., Klijn J. G. M., Zhang Y., Sieuwerts A. M., Look M. P., Yang F., Talantov D., Timmermans M., Meijer-Van Gelder M. E., Yu J., Jatkoe T., Berns E. M. J. J., Atkins D., Foekens J. A., Gene-expression profiles to predict distant metastasis of lymph-node-negative primary breast cancer. The Lancet 2005 365 9460 671 679 2-s2.0-13844310310 10.1016/S0140-6736(05)17947-1 (Pubitemid 40260888)
34. Hosack D. A., Dennis G. Jr., Sherman B. T., Lane H. C., Lempicki R. A., Identifying biological themes within lists of genes with EASE. Genome Biology 2003 4 10, article R70 2-s2.0-0344319833
35. Zhu J., Wang J., Guo Z., Zhang M., Yang D., Li Y., Wang D., Xiao G., GO-2D: identifying 2-dimensional cellular-localized functional modules in Gene Ontology. BMC Genomics 2007 8, article 30 2-s2.0-33846928211 10.1186/1471-2164-8-30 (Pubitemid 46232035)
36. Yang D., Li Y., Xiao H., Liu Q., Zhang M., Zhu J., Ma W., Yao C., Wang J., Wang D., Guo Z., Yang B., Gaining confidence in biological interpretation of the microarray data: the functional consistence of the significant GO categories. Bioinformatics 2008 24 2 265 271 2-s2.0-38349188469 10.1093/bioinformatics/btm558
37. Gorlov I. P., Gallick G. E., Gorlova O. Y., Amos C., Logothetis C. J., GWAS meets microarray: are the results of genome-wide association studies and gene-expression profiling consistent? Prostate cancer as an example. PLoS One 2009 4 8 2-s2.0-68349146348 10.1371/journal.pone.0006511 e6511
38. Manoli T., Gretz N., Gröne H. J., Kenzelmann M., Eils R., Brors B., Group testing for pathway analysis improves comparability of different microarray datasets. Bioinformatics 2006 22 20 2500 2506 2-s2.0-33749999763 10.1093/bioinformatics/btl424 (Pubitemid 44565992)
39. Chen J., Wang Y., Guo D., Shen B., A systems biology perspective on rational design of peptide vaccine against virus infections. Current Topics in Medicinal Chemistry 2012 12 12 1310 1319
40. Michiels S., Koscielny S., Hill C., Prediction of cancer outcome with microarrays: a multiple random validation strategy. The Lancet 2005 365 9458 488 492 2-s2.0-13444249852 10.1016/S0140-6736(05)17866-0 (Pubitemid 40215731)
41. Ein-Dor L., Zuk O., Domany E., Thousands of samples are needed to generate a robust gene list for predicting outcome in cancer. Proceedings of the National Academy of Sciences of the United States of America 2006 103 15 5923 5928 2-s2.0-33645825183 10.1073/pnas.0601231103