Gene Ontology Analysis of Colorectal Cancer Biomarkers Probed with Affymetrix and Illumina Microarrays

Monika Simjanoska, Ana Madevska Bogdanova, Sasho Panov

2013

Abstract

Colorectal cancer is the fourth most common cause of death worldwide. Recently, many microarray experiments have been done to investigate the expression of the genes in the colorectal tissues and thus, to find the answers for its occurrence. Previously, we used experiments obtained from both Illumina and Affymetrix microarray platforms to analyze the gene expression in healthy and carcinogenic tissues. As a result we got specific sets of biomarkers that we used to build an accurate Bayesian diagnostic system. The high degree of classifier's sensitivity and specificity intrigued us to proceed with the research of the significant genes we discovered, the biomarkers. Therefore, in this paper we aim towards biomarkers identification and the functional groups they are associated with, i.e., we performed gene ontology analysis. Investigating the genes that control the colorectal carcinogenic tissue development is of central importance to the verification of the biomarkers' revealing method's validity. Moreover, we showed the importance of their participation in the prior distributions modeling, which is the key part for achieving an accurate Bayesian classification, regardless their strict disease and disorder association.

References

  1. Ahn, W. S., Kim, K.-W., Bae, S. M., Yoon, J. H., Lee, J. M., Namkoong, S. E., Kim, J. H., Kim, C. K., Lee, Y. J., and Kim, Y.-W. (2003). Targeted cellular process profiling approach for uterine leiomyoma using cdna microarray, proteomics and gene ontology analysis. International journal of experimental pathology, 84(6):267-279.
  2. Ashburner, M., Ball, C. A., Blake, J. A., Botstein, D., Butler, H., Cherry, J. M., Davis, A. P., Dolinski, K., Dwight, S. S., Eppig, J. T., et al. (2000). Gene ontology: tool for the unification of biology. Nature genetics, 25(1):25.
  3. Baba, M., Itoh, K., and Tatsuta, M. (2004). Glycineextended gastrin induces matrix metalloproteinase-1- and-3-mediated invasion of human colon cancer cells through type i collagen gel and matrigel. International journal of cancer, 111(1):23-31.
  4. Benita, Y., Cao, Z., Giallourakis, C., Li, C., Gardet, A., and Xavier, R. J. (2010). Gene enrichment profiles reveal t-cell development, differentiation, and lineagespecific transcription factors including zbtb25 as a novel nf-at repressor. Blood, 115(26):5376-5384.
  5. Camici, M. (2008). Guanylin peptides and colorectal cancer (crc). BioMedicine & pharmacotherapy, 62(2):70-76.
  6. Chan, S. K., Griffith, O. L., Tai, I. T., and Jones, S. J. (2008). Meta-analysis of colorectal cancer gene expression profiling studies identifies consistently reported candidate biomarkers. Cancer Epidemiology Biomarkers & Prevention, 17(3):543-552.
  7. Cohen, M. B., Hawkins, J. A., and Witte, D. P. (1998). Guanylin mrna expression in human intestine and colorectal adenocarcinoma. Laboratory investigation, 78(1):101-108.
  8. Ferrero, S., Buffa, R., Pruneri, G., Siccardi, A., Pelagi, M., Lee, A., Coggi, G., and Bosari, S. (1995). The prevalence and clinical significance of chromogranin a and secretogranin ii immunoreactivity in colorectal adenocarcinomas. Virchows Archiv, 426(6):587-592.
  9. GEO ,2013. Gene Expression Omnibus.
  10. Harris, M., Clark, J., Ireland, A., Lomax, J., Ashburner, M., Foulger, R., Eilbeck, K., Lewis, S., Marshall, B., Mungall, C., et al. (2004). The gene ontology (go) database and informatics resource. Nucleic acids research, 32(Database issue):D258.
  11. Hinoue, T., Weisenberger, D. J., Lange, C. P., Shen, H., Byun, H.-M., Van Den Berg, D., Malik, S., Pan, F., Noushmehr, H., van Dijk, C. M., et al. (2012). Genome-scale analysis of aberrant dna methylation in colorectal cancer. Genome Research, 22(2):271-282.
  12. Holla, V. R., Backlund, M. G., Yang, P., Newman, R. A., and DuBois, R. N. (2008). Regulation of prostaglandin transporters in colorectal neoplasia. Cancer Prevention Research, 1(2):93-99.
  13. Holmans, P., Green, E. K., Pahwa, J. S., Ferreira, M. A., Purcell, S. M., Sklar, P., et al. (2009). Gene ontology analysis of gwa study data sets provides insights into the biology of bipolar disorder. American journal of human genetics, 85(1):13.
  14. Hong, Y., Downey, T., Eu, K., Koh, P., and Cheah, P. (2010). A metastasis-prone signature for early-stage mismatch-repair proficient sporadic colorectal cancer patients and its implications for possible therapeutics. Clinical and Experimental Metastasis, 27(2):83-90.
  15. Hui, Y., Kang, T., Xie, L., and Yuan-Yuan, L. (2010). Digout: Viewing differential expression genes as outliers. Journal of Bioinformatics and Computational Biology, 8(supp01):161-175.
  16. Imai, K., Hirata, S., Irie, A., Senju, S., Ikuta, Y., Yokomine, K., Harao, M., Inoue, M., Tsunoda, T., Nakatsuru, S., et al. (2008). Identification of a novel tumorassociated antigen, cadherin 3/p-cadherin, as a possible target for immunotherapy of pancreatic, gastric, and colorectal cancers. Clinical Cancer Research, 14(20):6487-6495.
  17. Jain, K. (2004). Applications of biochips: From diagnostics to personalized medicine. Current opinion in drug discovery & development, 7(3):285-289.
  18. Jette, C., Peterson, P. W., Sandoval, I. T., Manos, E. J., Hadley, E., Ireland, C. M., and Jones, D. A. (2004). The tumor suppressor adenomatous polyposis coli and caudal related homeodomain protein regulate expression of retinol dehydrogenase l. Journal of Biological Chemistry, 279(33):34397-34405.
  19. Jia, P., Wang, L., Meltzer, H. Y., and Zhao, Z. (2010). Common variants conferring risk of schizophrenia: a pathway analysis of gwas data. Schizophrenia research, 122(1):38-42.
  20. Jiang, W., Li, X., Rao, S., Wang, L., Du, L., Li, C., Wu, C., Wang, H., Wang, Y., and Yang, B. (2008). Constructing disease-specific gene networks using pairwise relevance metric: application to colon cancer identifies interleukin 8, desmin and enolase 1 as the central elements. BMC systems biology, 2(1):72.
  21. Jorissen, R., Lipton, L., Gibbs, P., Chapman, M., Desai, J., Jones, I., Yeatman, T., East, P., Tomlinson, I., Verspaget, H., et al. (2008). Dna copy-number alterations underlie gene expression differences between microsatellite stable and unstable colorectal cancers. Clinical Cancer Research, 14(24):8061-8069.
  22. Kinzler, K. W. and Vogelstein, B. (1996). Lessons from hereditary review colorectal cancer. Cell, 87:159-170.
  23. Kling, K., Kim, F., Cole, M., and McFadden, D. (1999). Bcell leukemia protein-2 and peptide yy chemotherapy resistance in colon cancer. The American journal of surgery, 178(5):411-414.
  24. Lascorz, J., Chen, B., Hemminki, K., and F örsti, A. (2011a). Consensus pathways implicated in prognosis of colorectal cancer identified through systematic enrichment analysis of gene expression profiling studies. PloS one, 6(4):e18867.
  25. Lascorz, J., Hemminki, K., Försti, A., et al. (2011b). Systematic enrichment analysis of gene expression profiling studies identifies consensus pathways implicated in colorectal cancer development. Journal of carcinogenesis, 10(1):7.
  26. Li, P., Lin, J., Marszlowicz, G., Valentino, M., Chang, C., Schulz, S., Pitari, G., and Waldman, S. (2009). Gcc signaling in colorectal cancer: Is colorectal cancer a paracrine deficiency syndrome? Drug news & perspectives, 22(6):313.
  27. Masaki, T., Matsuoka, H., Sugiyama, M., Abe, N., Goto, A., Sakamoto, A., and Atomi, Y. (2001). Matrilysin (mmp-7) as a significant determinant of malignant potential of early invasive colorectal carcinomas. British journal of cancer, 84(10):1317.
  28. Mori, M., Barnard, G. F., Mimori, K., Ueo, H., Akiyoshi, T., and Sugimachi, K. (1995). Overexpression of matrix metalloproteinase-7 mrna in human colon carcinomas. Cancer, 75(S6):1516-1519.
  29. Nature (2006). Nature milestones - cancer.
  30. Needham, C., Manfield, I., Bulpitt, A., Gilmartin, P., and Westhead, D. (2009). From gene expression to gene regulatory networks in arabidopsis thaliana. BMC systems biology, 3(1):85.
  31. Pagani, A., Papotti, M., Abbona, G., Bussolati, G., et al. (1995). Chromogranin gene expressions in colorectal adenocarcinomas. Modern pathology: an official journal of the United States and Canadian Academy of Pathology, Inc, 8(6):626.
  32. Roeb, E., Arndt, M., Jansen, B., Schumpelick, V., and Matern, S. (2004). Simultaneous determination of matrix metalloproteinase (mmp)-7, mmp-1,-3, and-13 gene expression by multiplex pcr in colorectal carcinomas. International journal of colorectal disease, 19(6):518-524.
  33. Sabates-Bellver, J., Van der Flier, L., de Palo, M., Cattaneo, E., Maake, C., Rehrauer, H., Laczko, E., Kurowski, M., Bujnicki, J., Menigatti, M., et al. (2007). Transcriptome profile of human colorectal adenomas. Molecular Cancer Research, 5(12):1263- 1275.
  34. Simjanoska, M., Bogdanova, A. M., and Popeska, Z. (2013a). Bayesian posterior probability classification of colorectal cancer probed with affymetrix microarray technology. In 36th International Convention on Information and Communication Technology, Electronics and Microelectronics, MIPRO, CIS Intelligent Systems.
  35. Simjanoska, M., Bogdanova, A. M., and Popeska, Z. (2013b). Recognition of colorectal carcinogenic tissue with gene expression analysis using bayesian probability. In ICT Innovations 2012, Advances in Intelligent Systems and Computing, volume 207, pages 305- 314. Springer Berlin Heidelberg.
  36. Smith, G., Carey, F. A., Beattie, J., Wilkie, M. J., Lightfoot, T. J., Coxhead, J., Garner, R. C., Steele, R. J., and Wolf, C. R. (2002). Mutations in apc, kirsten-ras, and p53alternative genetic pathways to colorectal cancer. Proceedings of the National Academy of Sciences, 99(14):9433-9438.
  37. 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., et al. (2005). Gene set enrichment analysis: a knowledge-based approach for interpreting genomewide expression profiles. Proceedings of the National Academy of Sciences of the United States of America, 102(43):15545-15550.
  38. Wang, K., Li, M., and Hakonarson, H. (2010). Analysing biological pathways in genome-wide association studies. Nature Reviews Genetics, 11(12):843-854.
  39. Watanabe, T., Kobunai, T., Toda, E., Yamamoto, Y., Kanazawa, T., Kazama, Y., Tanaka, J., Tanaka, T., Konishi, T., Okayama, Y., et al. (2006). Distal colorectal cancers with microsatellite instability (msi) display distinct gene expression profiles that are different from proximal msi cancers. Cancer research, 66(20):9804-9808.
  40. Wu, Z. and Aryee, M. (2010). Subset quantile normalization using negative control features. Journal of Computational Biology, 17(10):1385-1395.
  41. Xu, Y., Xu, Q., Yang, L., Liu, F., Ye, X., Wu, F., Ni, S., Tan, C., Cai, G., Meng, X., et al. (2013). Gene expression analysis of peripheral blood cells reveals toll-like receptor pathway deregulation in colorectal cancer. PloS one, 8(5):e62870.
  42. Zhang, Z., Xu, L., Chen, M., and Zhang, J. (1997). Expression of vasoactive intestinal peptide receptor in human colonic carcinoma cell membranes]. Hua xi yi ke da xue xue bao= Journal of West China University of Medical Sciences= Huaxi yike daxue xuebao/[bian ji zhe, Hua xi yi ke da xue xue bao bian wei hui], 28(4):380.
  43. Zheng, Q. and Wang, X.-J. (2008). Goeast: a web-based software toolkit for gene ontology enrichment analysis. Nucleic acids research, 36(suppl 2):W358-W363.
  44. Zinzindohoué, F., Lecomte, T., Ferraz, J.-M., Houllier, A.-M., Cugnenc, P.-H., Berger, A., Blons, H., and Laurent-Puig, P. (2005). Prognostic significance of mmp-1 and mmp-3 functional promoter polymorphisms in colorectal cancer. Clinical cancer research, 11(2):594-599.
Download


Paper Citation


in Harvard Style

Simjanoska M., Madevska Bogdanova A. and Panov S. (2013). Gene Ontology Analysis of Colorectal Cancer Biomarkers Probed with Affymetrix and Illumina Microarrays . In Proceedings of the 5th International Joint Conference on Computational Intelligence - Volume 1: NCTA, (IJCCI 2013) ISBN 978-989-8565-77-8, pages 396-406. DOI: 10.5220/0004554803960406


in Bibtex Style

@conference{ncta13,
author={Monika Simjanoska and Ana Madevska Bogdanova and Sasho Panov},
title={Gene Ontology Analysis of Colorectal Cancer Biomarkers Probed with Affymetrix and Illumina Microarrays},
booktitle={Proceedings of the 5th International Joint Conference on Computational Intelligence - Volume 1: NCTA, (IJCCI 2013)},
year={2013},
pages={396-406},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0004554803960406},
isbn={978-989-8565-77-8},
}


in EndNote Style

TY - CONF
JO - Proceedings of the 5th International Joint Conference on Computational Intelligence - Volume 1: NCTA, (IJCCI 2013)
TI - Gene Ontology Analysis of Colorectal Cancer Biomarkers Probed with Affymetrix and Illumina Microarrays
SN - 978-989-8565-77-8
AU - Simjanoska M.
AU - Madevska Bogdanova A.
AU - Panov S.
PY - 2013
SP - 396
EP - 406
DO - 10.5220/0004554803960406