Bioinformatics exploration of PAK1 (P21-activated kinase-1) revealed potential network gene elements in breast invasive carcinoma

References

• Adam, L., Vadlamudi, R., Kondapaka, S. B., Chernoff, J., Mendelsohn, J., & Kumar, R. (1998). Heregulin regulates cytoskeletal reorganization and cell migration through the p21-activated kinase-1 via phosphatidylinositol-3 kinase. Journal of Biological Chemistry, 273, 28238–28246.10.1074/jbc.273.43.28238
   PubMed Web of Science ®Google Scholar
• Arias-Romero, L. E., Villamar-Cruz, O., Pacheco, A., Kosoff, R., Huang, M., & Muthuswamy, S. K. (2010). A Rac-Pak signaling pathway is essential for ErbB2-mediated transformation of human breast epithelial cancer cells. Oncogene, 29, 5839–5849.10.1038/onc.2010.318
   PubMed Web of Science ®Google Scholar
• Banerji, S., Cibulskis, K., Rangel-Escareno, C., Brown, K. K., Carter, S. L., Frederick, A. M., & Cortes, M. L. (2012). Sequence analysis of mutations and translocations across breast cancer subtypes. Nature, 486, 405–409.10.1038/nature11154
   PubMed Web of Science ®Google Scholar
• Barker, W. C., Garavelli, J. S., Huang, H., McGarvey, P. B., Orcutt, B. C., Srinivasarao, G. Y., Pfeiffer, F. (2000). The protein information resource (PIR). Nucleic Acids Research, 28, 41–44.10.1093/nar/28.1.41
   PubMed Web of Science ®Google Scholar
• Beeser, A., Jaffer, Z. M., Hofmann, C., & Chernoff, J. (2005). Role of group A p21-activated kinases in activation of extracellular-regulated kinase by growth factors. Journal of Biological Chemistry, 280, 36609–36615.10.1074/jbc.M502306200
   PubMed Web of Science ®Google Scholar
• Bokoch, G. M. (2003). Biology of the p21-activated kinases. Annual Review of Biochemistry, 72, 743–781.10.1146/annurev.biochem.72.121801.161742
   PubMed Web of Science ®Google Scholar
• Bostner, J., Waltersson, M. A., Fornander, T., Skoog, L., Nordenskjöld, B., & Stål, O. (2007). Amplification of CCND1 and PAK1 as predictors of recurrence and tamoxifen resistance in postmenopausal breast cancer. Oncogene, 26, 6997–7005.10.1038/sj.onc.1210506
   PubMed Web of Science ®Google Scholar
• Cancer Genome Atlas Network. (2012). Comprehensive molecular characterization of human colon and rectal cancer. Nature, 487, 330–337.
   PubMed Web of Science ®Google Scholar
• Cerami, E., Gao, J., Dogrusoz, U., Gross, B. E., Sumer, S. O., Aksoy, B. A., & Antipin, Y. (2012). The cBio cancer genomics portal: An open platform for exploring multidimensional cancer genomics data. Cancer Discovery, 2, 401–404.10.1158/2159-8290.CD-12-0095
   PubMed Web of Science ®Google Scholar
• Chan, C. H., Lee, S. W., Li, C. F., Wang, J., Yang, W. L., Wu, C. Y., & Hung, M. C. (2010). Deciphering the transcriptional complex critical for RhoA gene expression and cancer metastasis. Nature Cell Biology, 12, 457–467.10.1038/ncb2047
   PubMed Web of Science ®Google Scholar
• Chen, R., Li, L., & Weng, Z. (2003). ZDOCK: An initial-stage protein-docking algorithm. Proteins: Structure, Function, and Bioinformatics, 52, 80–87.10.1002/(ISSN)1097-0134
   PubMed Web of Science ®Google Scholar
• Ciriello, G., Gatza, M. L., Beck, A. H., Wilkerson, M. D., Rhie, S. K., Pastore, A., & Bowlby, R. (2015). Comprehensive molecular portraits of invasive lobular breast cancer. Cell, 163, 506–519.10.1016/j.cell.2015.09.033
   PubMed Web of Science ®Google Scholar
• Eirew, P., Steif, A., Khattra, J., Ha, G., Yap, D., Farahani, H., & Laks, E. (2015). Dynamics of genomic clones in breast cancer patient xenografts at single-cell resolution. Nature, 518, 422–426.
   PubMed Web of Science ®Google Scholar
• Elsheikh, S., Green, A. R., Aleskandarany, M. A., Grainge, M., Paish, C. E., Lambros, M. B., & Ellis, I. O. (2008). CCND1 amplification and cyclin D1 expression in breast cancer and their relation with proteomic subgroups and patient outcome. Breast Cancer Research and Treatment, 109, 325–335.10.1007/s10549-007-9659-8
   PubMed Web of Science ®Google Scholar
• Eswaran, J., Li, D. Q., Shah, A., & Kumar, R. (2012). Molecular pathways: targeting p21-activated kinase 1 signaling in cancer–opportunities, challenges, and limitations. Clinical Cancer Research 15, 18, 3743–9.
   PubMed Web of Science ®Google Scholar
• Furukawa, T., Kanai, N., Shiwaku, H. O., Soga, N., Uehara, A., & Horii, A. (2006). AURKA is one of the downstream targets of MAPK1/ERK2 in pancreatic cancer. Oncogene, 25, 4831–4839.10.1038/sj.onc.1209494
   PubMed Web of Science ®Google Scholar
• Gao, J., Aksoy, B. A., Dogrusoz, U., Dresdner, G., Gross, B., Sumer, S. O., & Cerami, E. (2013). Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal. Science Signaling, 6, 1–34.
   Web of Science ®Google Scholar
• Gene Ontology Consortium. (2004). The gene ontology (GO) database and informatics resource. Nucleic Acids Research, 32, D258–D261.
   PubMed Web of Science ®Google Scholar
• Huang, D. W., Sherman, B. T., & Lempicki, R. A. (2009). Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nature Protocols, 4, 44–57.
   PubMed Web of Science ®Google Scholar
• Kamran, M. Z., Patil, P., & Gude, R. P. (2013). Role of STAT3 in cancer metastasis and translational advances. BioMed Research International, 2013, 1–15.10.1155/2013/421821
   Web of Science ®Google Scholar
• Kanehisa, M., & Goto, S. (2000). KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Research, 28, 27–30.10.1093/nar/28.1.27
   PubMed Web of Science ®Google Scholar
• King, T. D., Suto, M. J., & Li, Y. (2012). The wnt/β-catenin signaling pathway: A potential therapeutic target in the treatment of triple negative breast cancer. Journal of Cellular Biochemistry, 113, 13–18.10.1002/jcb.v113.1
   PubMed Web of Science ®Google Scholar
• Kisseleva, T., Bhattacharya, S., Braunstein, J., & Schindler, C. W. (2002). Signaling through the JAK/STAT pathway, recent advances and future challenges. Gene, 285, 1–24.10.1016/S0378-1119(02)00398-0
   PubMed Web of Science ®Google Scholar
• Kumar, R., Gururaj, A. E., & Barnes, C. J. (2006). p21-activated kinases in cancer. Nature Reviews Cancer, 6, 459–471.10.1038/nrc1892
   PubMed Web of Science ®Google Scholar
• Laskowski, R. A. (2001). PDBsum: Summaries and analyses of PDB structures. Nucleic Acids Research, 29, 221–222.10.1093/nar/29.1.221
   PubMed Web of Science ®Google Scholar
• Levy, D. E., & Darnell, J. E. (2002). Signalling: STATs: Transcriptional control and biological impact. Nature Reviews Molecular Cell Biology, 3, 651–662.10.1038/nrm909
   PubMed Web of Science ®Google Scholar
• Li, L., Chen, R., & Weng, Z. (2003). RDOCK: Refinement of rigid-body protein docking predictions. Proteins: Structure, Function, and Genetics, 53, 693–707.10.1002/(ISSN)1097-0134
   PubMed Web of Science ®Google Scholar
• Marlin, J. W., Eaton, A., Montano, G. T., Chang, Y. W. E., & Jakobi, R. (2009). Elevated p21-activated kinase 2 activity results in anchorage-independent growth and resistance to anticancer drug–induced cell death. Neoplasia, 11, 286–297.10.1593/neo.81446
   PubMed Web of Science ®Google Scholar
• Maroto, B., Ye, M. B., von Lohneysen, K., Schnelzer, A., & Knaus, U. G. (2008). P21-activated kinase is required for mitotic progression and regulates Plk1. Oncogene, 27, 4900–4908.10.1038/onc.2008.131
   PubMed Web of Science ®Google Scholar
• Mertins, P., Mani, D. R., Ruggles, K. V., Gillette, M. A., Clauser, K. R., Wang, P., … Kawaler, E. (2016). Proteogenomics connects somatic mutations to signalling in breast cancer. Nature, 534, 55–62.10.1038/nature18003
   PubMed Web of Science ®Google Scholar
• Oliveros, J. C. (2007–2015). Venny. An interactive tool for comparing lists with Venn’s diagrams. Retrieved from http://bioinfogp.cnb.csic.es/tools/venny/index.html
   Google Scholar
• Pakala, S. B., Rayala, S. K., Wang, R. A., Ohshiro, K., Mudvari, P., Reddy, S. D., … Kumar, R. (2013). MTA1 promotes STAT3 transcription and pulmonary metastasis in breast cancer. Cancer Research, 73, 3761–3770.10.1158/0008-5472.CAN-12-3998
   PubMed Web of Science ®Google Scholar
• Pierce, B., & Weng, Z. (2007). ZRANK: Reranking protein docking predictions with an optimized energy function. Proteins: Structure, Function, and Bioinformatics, 67, 1078–1086.10.1002/prot.21373
   PubMed Web of Science ®Google Scholar
• Rebhan, M., Chalifa-Caspi, V., Prilusky, J., & Lancet, D. (1997). GeneCards: Integrating information about genes, proteins and diseases. Trends in Genetics, 13, 163.10.1016/S0168-9525(97)01103-7
   PubMed Web of Science ®Google Scholar
• Shannon, P., Markiel, A., Ozier, O., Baliga, N. S., Wang, J. T., Ramage, D., & Ideker, T. (2003). Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genome Research, 13, 2498–2504.10.1101/gr.1239303
   PubMed Web of Science ®Google Scholar
• Shrestha, Y., Schafer, E. J., Boehm, J. S., Thomas, S. R., He, F., Du, J., & Polyak, K. (2012). PAK1 is a breast cancer oncogene that coordinately activates MAPK and MET signaling. Oncogene, 31, 3397–3408.10.1038/onc.2011.515
   PubMed Web of Science ®Google Scholar
• Somanath, P. R., Vijai, J., Kichina, J. V., Byzova, T., & Kandel, E. S. (2009). The role of PAK-1 in activation of MAP kinase cascade and oncogenic transformation by Akt. Oncogene, 28, 2365–2369.10.1038/onc.2009.114
   PubMed Web of Science ®Google Scholar
• Stephens, P. J., Tarpey, P. S., Davies, H., Van Loo, P., Greenman, C., Wedge, D. C., & Yates, L. R. (2012). The landscape of cancer genes and mutational processes in breast cancer. Nature, 486, 400–404.
   PubMed Web of Science ®Google Scholar
• Von Mering, C., Huynen, M., Jaeggi, D., Schmidt, S., Bork, P., & Snel, B. (2003). STRING: A database of predicted functional associations between proteins. Nucleic Acids Research, 31, 258–261.10.1093/nar/gkg034
   PubMed Web of Science ®Google Scholar
• Yu, H., Pardoll, D., & Jove, R. (2009). STATs in cancer inflammation and immunity: A leading role for STAT3. Nature Reviews Cancer, 9, 798–809.10.1038/nrc2734
   PubMed Web of Science ®Google Scholar
• Zhou, H., & Kramer, R. H. (2005). Integrin engagement differentially modulates epithelial cell motility by RhoA/ROCK and PAK1. Journal of Biological Chemistry, 280, 10624–10635.10.1074/jbc.M411900200
   PubMed Web of Science ®Google Scholar