Pathway-driven discovery of rare mutational impact on cancer

BioMed Research International

Volumn 2014, Issue , 2014, Pages

  Ahn, Taejin ^a,b   Park, Taesung ^a  

^a Seoul National University   (South Korea)

^b Samsung Medical Center   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

MEMBRANE PROTEIN; MESSENGER RNA; PHOSPHATIDYLINOSITOL 3 KINASE; PHOSPHATIDYLINOSITOL 3 KINASE CATALYTIC ALPHA POLYPEPTIDE; PROTEIN P53; RB1 PROTEIN; UNCLASSIFIED DRUG; PIK3CA PROTEIN, HUMAN; RETINOBLASTOMA PROTEIN; TP53 PROTEIN, HUMAN;

ARTICLE; BREAST CANCER; CANCER GENETICS; GENE EXPRESSION; GENE MUTATION; HUMAN; MAJOR CLINICAL STUDY; MUTATIONAL ANALYSIS; SENSITIVITY ANALYSIS; SIGNAL TRANSDUCTION; BIOLOGY; BIOSYNTHESIS; BREAST TUMOR; FEMALE; GENE EXPRESSION REGULATION; GENETICS; MUTATION; PATHOLOGY;

BREAST NEOPLASMS; COMPUTATIONAL BIOLOGY; FEMALE; GENE EXPRESSION REGULATION, NEOPLASTIC; HUMANS; MUTATION; PHOSPHATIDYLINOSITOL 3-KINASES; RETINOBLASTOMA PROTEIN; RNA, MESSENGER; SIGNAL TRANSDUCTION; TUMOR SUPPRESSOR PROTEIN P53;

EID: 84901760166     PISSN: 23146133     EISSN: 23146141     Source Type: Journal    
DOI: 10.1155/2014/171892     Document Type: Article

References (26)

1. Lièvre A., Bachet J.-B., le Corre D., Boige V., Landi B., Emile J.-F., Côté J.-F., Tomasic G., Penna C., Ducreux M., Rougier P., Penault-Llorca F., Laurent-Puig P., KRAS mutation status is predictive of response to cetuximab therapy in colorectal cancer. Cancer Research 2006 66 8 3992 3995 2-s2.0-33646228635 10.1158/0008-5472.CAN-06-0191
2. Gazdar A. F., Activating and resistance mutations of EGFR in non-small-cell lung cancer: role in clinical response to EGFR tyrosine kinase inhibitors. Oncogene 2009 28 supplement 1 S24 S31 2-s2.0-68949201629 10.1038/onc.2009.198
3. Jones S. J. M., Laskin J., Li Y. Y., Griffith O. L., An J., Bilenky M., Butterfield Y. S., Cezard T., Chuah E., Corbett R., Fejes A., Griffith M., Yee J., Martin M., Mayo M., Melnyk N., Morin R. D., Pugh T. J., Severson T., Shah S. P., Sutcliffe M., Tam A., Terry J., Thiessen N., Thomson T., Varhol R., Zeng T., Zhao Y., Moore R. A., Huntsman D. G., Birol I., Hirst M., Holt R. A., Marra M. A., Evolution of an adenocarcinoma in response to selection by targeted kinase inhibitors. Genome Biology 2010 11, article R82 2-s2.0-77955293476 10.1186/gb-2010-11-8-r82
4. Vaske C. J., Benz S. C., Sanborn J. Z., Earl D., Szeto C., Zhu J., Haussler D., Stuart J. M., Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM. Bioinformatics 2010 26 12 237 245 2-s2.0-77954195272 10.1093/bioinformatics/btq182
5. Drier Y., Sheffer M., Domany E., Pathway-based personalized analysis of cancer. Proceedings of the National Academy of Sciences of the United States of America 2013 110 6388 6393 10.1073/pnas.1219651110
6. Tae A., Eunjin L., Nam H., Taesung P., Personalized identification of altered pathways in cancer using accumulated normal tissue data. 2013
7. Khatri P., Sirota M., Butte A. J., Ten years of pathway analysis: current approaches and outstanding challenges. PLoS Computational Biology 2012 8 e1002375
8. Yu N., Seo J., Rho K., Jang Y., Park J., Kim W. K., Lee S., hiPathDB: a human-integrated pathway database with facile visualization. Nucleic Acids Research 2011 40 797 802
9. Cheadle C., Vawter M. P., Freed W. J., Becker K. G., Analysis of microarray data using Z score transformation. Journal of Molecular Diagnostics 2003 5 2 73 81 2-s2.0-0038365368 (Pubitemid 36553428)
10. Lee E., Chuang H. Y., Kim J. W., Ideker T., Lee D., Inferring pathway activity toward precise disease classification. PLoS Computational Biology 2008 4 e1000217
11. Tu C. T., Chen B. S., New measurement methods of network robustness and response ability via microarray data'. PLoS ONE 2013 8 e55230
12. Sherman-Baust C. A., Becker K. G., Wood W. H. III, Zhang Y., Morin P. J., Gene expression and pathway analysis of ovarian cancer cells selected for resistance to cisplatin, paclitaxel, or doxorubicin. Journal of Ovarian Research 2011 4 1, article 21 2-s2.0-82655176997 10.1186/1757-2215-4-21
13. Kalita M., Tian B., Gao B., Choudhary S., Wood T. G., Carmical J. R., Systems approaches to modeling chronic mucosal inflammation. BioMed Research International 2013 2013 17 10.1155/2013/505864 505864
14. The Cancer Genome Atlas Network, Comprehensive molecular portraits of human breast tumours. Nature 2012 490 61 70
15. Mangone F. R., Bobrovnitchaia I. G., Salaorni S., Manuli E., Nagai M. A., PIK3CA exon 20 mutations are associated with poor prognosis in breast cancer patients. Clinics 2012 67 1285 1290
16. Singh B., Reddy P. G., Goberdhan A., Walsh C., Dao S., Ngai I., Chou T. C., O-charoenrat P., Levine A. J., Rao P. H., Stoffel A., p53 regulates cell survival by inhibiting PIK3CA in squamous cell carcinomas. Genes & Development 2002 16 8 984 993 2-s2.0-18344380088 10.1101/gad.973602 (Pubitemid 34408547)
17. Astanehe A., Arenillas D., Wasserman W. W., Leung P. C. K., Dunn S. E., Davies B. R., Mills G. B., Auersperg N., Mechanisms underlying p53 regulation of PIK3CA transcription in ovarian surface epithelium and in ovarian cancer. Journal of Cell Science 2008 121 5 664 674 2-s2.0-42149102636 10.1242/jcs.013029 (Pubitemid 351524165)
18. Reimand J., Arak T., Vilo J., g:Profiler-a web server for functional interpretation of gene lists (2011 update). Nucleic Acids Research 2011 39 2 W307 W315 2-s2.0-79959923522 10.1093/nar/gkr378
19. Reimand J., Kull M., Peterson H., Hansen J., Vilo J., g:Profiler-a web-based toolset for functional profiling of gene lists from large-scale experiments. Nucleic Acids Research 2007 35 W193 W200 2-s2.0-34547571030 10.1093/nar/gkm226
20. Warde-Farley D., Donaldson S. L., Comes O., Zuberi K., Badrawi R., Chao P., Franz M., Grouios C., Kazi F., Lopes C. T., Maitland A., Mostafavi S., Montojo J., Shao Q., Wright G., Bader G. D., Morris Q., The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function. Nucleic Acids Research 2010 38 2 W214 W220 2-s2.0-77954269901 10.1093/nar/gkq537
21. Wilhelm S., Carter C., Lynch M., Lowinger T., Dumas J., Smith R. A., Schwartz B., Simantov R., Kelley S., Discovery and development of sorafenib: a multikinase inhibitor for treating cancer. Nature Reviews Drug Discovery 2006 5 10 835 844 2-s2.0-33749238553 10.1038/nrd2130 (Pubitemid 44480537)
22. Wilhelm S. M., Carter C., Tang L., Wilkie D., McNabola A., Rong H., Chen C., Zhang X., Vincent P., McHugh M., Cao Y., Shujath J., Gawlak S., Eveleigh D., Rowley B., Liu L., Adnane L., Lynch M., Auclair D., Taylor I., Gedrich R., Voznesensky A., Riedl B., Post L. E., Bollag G., Trail P. A., BAY 43-9006 exhibits broad spectrum oral antitumor activity and targets the RAF/MEK/ERK pathway and receptor tyrosine kinases involved in tumor progression and angiogenesis. Cancer Research 2004 64 19 7099 7109 2-s2.0-4944249117 10.1158/0008-5472.CAN-04-1443 (Pubitemid 39331023)
23. Brose M. S., Sorafenib benefited patients with RAS, BRAF mutations. Proceedings of the European Cancer Congress September-October 2013 Amsterdam, The Netherlands. abstract no. 3155
24. Ellis M. J., Perou C. M., The genomic landscape of breast cancer as a therapeutic roadmap. Cancer Discovery 2013 3 27 34
25. Banerji S., Cibulskis K., Rangel-Escareno C., Sequence analysis of mutations and translocations across breast cancer subtypes. Nature 2012 486 405 409
26. + breast cancer. Cancer Research 2012 72 24 10.1158/0008-5472.SABCS12-PD01-04