THE PROGRESS OF PROSTATE CANCER IN PATHWAY LEVEL EXPLORED BY PROTEIN NETWORK WITH GENE EXPRESSION

Fei-Hung Hung, Hung-Wen Chiu

View Full Paper

References

  1. [1] T. Barrett, D. Troup, S. Wilhite, P. Ledoux, C. Evangelista, I.Kim, M. Tomashevsky, K. Marshall, K. Phillippy, P. Sherman, R.Muertter, M. Holko, O. Ayanbule, A. Yefanov & A. Soboleva,NCBI GEO: archive for functional genomics data sets—10 yearson, Nucleic Acids Res., 39(Database issue), 2011, D1005–D1010.
  2. [2] M. Kanehisa, S. Goto, S. Furumichi, M. Tanabe & M.Hirakawa, KEGG for representation and analysis of molecularnetworks involving diseases and drugs, Nucleic Acids Res.,38(Database issue), 2010, D355–D360.
  3. [3] G. Bebek & J. Yang, PathFinder: mining signal transductionpathway segments from protein-protein interaction networks,BMC Bioinformatics, 8, 2007, 335–350.
  4. [4] M. Steffen, A. Petti, J. Aach, P. D’haeseleer & G. Church,Automated modelling of signal transduction networks, BMCBioinformatics, 3, 2002, 34–44.
  5. [5] Y. Liu & H. Zhao, A computational approach for orderingsignal transduction pathway components from genomics andproteomics Data, BMC Bioinformatics, 5, 2007, 158.
  6. [6] J. Scott, T. Ideker, R. Karpa & R. Sharan, Efficientalgorithms for detecting signaling pathways in protein interactionnetworks, J Comput Biol., 13(2), 2006, 133–144.
  7. [7] D. Szklarczyk, A. Franceschini, M. Kuhn, M. Simonovic, A.Roth & P. Minguez, The STRING database in 2011: functionalinteraction networks of proteins, globally integrated and scored,Nucleic Acids Res., 39(Database issue), 2010, D561–D568.
  8. [8] D. Ruths, J. Tseng, L. Nakhleh & P. Ram, De NovoSignaling Pathway Predictions Based on Protein-ProteinInteraction, Targeted Therapy and Protein Microarray Analysis,LNCS, 4532, 2007, 108–118.
  9. [9] H. Chuang, E. Lee, Y. Liu, D. Lee & T. Ideker, Network-based classification of breast cancer metastasis, Mol. Syst. Biol., 3,2007, 140.
  10. [10] YP. Yu, D. Landsittel, L. Jing, J. Nelson, B. Ren, L. Liu, C.McDonald, R. Thomas, R. Dhir, S. Finkelstein, G. Michalopoulos,M. Becich & JH. Luo, Gene expression alterations in prostatecancer predicting tumor aggression and preceding development ofmalignancy, J Clin. Oncol., 22(14), 2004, 2790-2779.
  11. [11] UR. Chandran, C. Ma, R. Dhir, M. Bisceglia, M. Lyons-Weiler, W. Liang, G. Michalopoulos, M. Becich & FA. Monzon,Gene expression profiles of prostate cancer reveal involvement ofmultiple molecular pathways in the metastatic process, BMCCancer, 7(64), 2007.
  12. [12] M. Thomasson, H. Hedman, T. Junttila, K. Elenius, B.Ljungberg & R. Henriksson, ErbB4 is downregulated in renal cellcarcinoma–a quantitative RT-PCR and immunohistochemicalanalysis of the epidermal growth factor receptor family, ActaOncol., 43(5), 2004, 453–459.
  13. [13] T. Behbahani, C. Thierse, C. Baumann, D. Holl, P. Bastian,A. von Ruecker, S. M¨uller, J. Ellinger & S. Hauser, Tyrosinekinase expression profile in clear cell renal cell carcinoma, WorldJ Urol., [Epub ahead of print].
  14. [14] T. Shi, L. Liou, P. Sadhukhan, Z. Duan, A. Novick, J.Hissong, A. Almasan & J. DiDonato, Effects of resveratrol ongene expression in renal cell carcinoma, Cancer Biol. Ther., 3(9),2004, 882–888.
  15. [15] J. Copland, B. Luxon, L. Ajani, T. Maity, E. Campagnaro, H.Guo, S. LeGrand, P. Tamboli & C. Wood, Genomic profilingidentifies alterations in TGFbeta signaling through loss ofTGFbeta receptor expression in human renal cell carcinogenesisand progression, Oncogene, 22(39), 2003, 8053–8062.
  16. [16] M. Magrane & U. Consortium, UniProt Knowledgebase: ahub of integrated protein data, Database (Oxford), 2011, 2011,bar009.
  17. [17] K. Brown & I. Jurisica, Unequal evolutionary conservation ofhuman protein interactions in interologous networks, GenomeBiol., 8(5), 2007, R95.
  18. [18] F. Belinky, I. Bahir, G. Stelzer, S. Zimmerman, N.Rosen, N. Nativ, I. Dalah, T. Iny Stein, N. Rappaport, T.Mituyama, M. Safran & D. Lancet, Non-redundant compendiumof human ncRNA genes in GeneCards, Bioinformatics, 29(2),2013 255-61.19Table 2The test result of locating points at three groups of GDS2545Family Member or Alias NameGroup A Group B Group CSignificant p-value Significant p-value Significant p-valueGSTP1 DFN7, FAEES3, GST3, GSTP, GSTP1 , PI GSTP1 0.000003 GSTP1 0.000000003076NKX3-1 BAPX2; NKX3; NKX3.1; NKX3APTEN 10q23del; BZS; CWS1; DEC; GLM2;MHAM; MMAC1; PTEN1; TEP1TEP1 0.000001723GFEGF, PDGFA, PDGFB, INS, PDGFC_D,IGF1, TGFA,PDGFA 0.00493 IGF1 0.006689INS 0.00003993IGF1 0.00002488GFREGFR, ERBB1, FGFR1, PDGFRA,ERBB2, HER2, INSRR, IGF1R, PDGFRB,FGFR2FGFR20.002864FGFR1 0.001295EGFR 0.006172ERBB2 0.000000005907FGFR2 0.0000217IGF1R 0.0009311FGFR2 0.0000009558PI3KPIK3CA, PIK3CB, PIK3CD, PIK3CG,PIK3R1, PIK3R2, PIK3R3, PIK3R5,PIK3C2A, PIK3C2B, PIK3C2GPIK3CG 0.007083PIK3CA 0.00005876PIK3R1 0.000006806PIK3R2 0.0474PIK3C2A 0.002192PIK3C2B 0.0436PDK1 PDPK1; PDK1; PDPK2; PRO0461 PDPK1 0.02111 PDK1 0.003776PKB/Akt AKT1, AKT2, AKT3AKT20.0142 AKT2 0.0335AKT3 0.001146SRD5A2 SRD5A2, MGC138457Grb2GRB2, ASH; EGFRBP-GRB2; Grb3-3;MST084; MSTP084; NCKAP2GRB20.009916GRB20.01819GRB2 0.000000000001861SOS SOS1, SOS2 SOS1 0.02208 SOS2 0.02002RasHRAS; C-BAS/HAS; C-H-RAS; C-HA-RAS1; CTLO; H-RASIDX; HAMSV;HRAS1; KRAS; NRAS; RASH1HRAS0.01225KRAS0.009854 HRAS 0.00003995KRAS 0.02608RafBRAF, RAF1, ARAF, ARAF1, CRAF,PKS2; RAFA1ARAF0.0000000009557MEK1MAP2K1, MEK1, MAPKK1 , MKK1;PRKMK1,MAP2K10.02523MEK2MAP2K2, MEK2, MAPKK2, MKK2;PRKMK2MAP2K20.001385MAP2K20.005339MAP2K2 0.00005548ERKMAPK1, MAPK2, MAPK3, ERK-1;ERK1; ERT2, PRKM1; PRKM2, PRKM3MAPK10.01324AR AR, AIS; DHTR; HUMARA; HYSP1; KD;NR3C4; SBMA; SMAX1; TFMAR0.0032AR0.000000000004022HSPhtpG, HSP90A, HSP90B, HSP90B1,TRA1, ECGP; GP96; GRP94HSP90B10.00000000003789Casp9CASP9, APAF-3; APAF3; CASPASE-9c;ICE-LAP6; MCH6; PPP1R56CASP90.04144BAD BAD, BBC2, BBC6, BCL2L8 BAD 0.03744FKHR FOXO1, FKH1; FKHR; FOXO1A FOXO1 0.006002 FOXO1 0.00007959p21CDKN1A, P21, CIP1, CAP20; CDKN1;MDA-6; SDI1; WAF1; p21CIP1CDKN1A0.03011p27CDKN1B, P27, KIP1, CDKN4, MEN1B;MEN4; P27KIP1MDM2 MDM2, ACTFS; HDMX; hdm2 MDM2 0.0007657GSK3 GSK3A, GSK3B GSK3A 0.000428GSK3B0.000000000541GSK3B 0.006835IKKA IKBKA, IKKA, CHUK CHUK 0.00003134 CHUK 0.003317IKKB IKBKB, IKKB IKBKB 0.03559 IKBKB 0.03504IKKG IKBKG, IKKG, NEMO IKBKG 0.00163mTOR MTOR, FRAP, FRAP1; FRAP2; RAFT1;RAPT1MTOR0.000002106CREB1 CREB1 CREB1 0.00007958CREB2 ATF4, CREB2 ATF4 0.00002567CREB3 CREB3, LUMAN; LZIP CREB3 0.000002061CREB5 CREB5; CREBPA CREB5 0.03238CREB3L1 CREB3L1 CREB3L1 0.0002449 CREB3L1 0.002783CREB3L2 CREB3L2 CREB3L2 0.003839 CREB3L2 0.003317CREB3L3 CREB3L3CREB3L4 CREB3L4β- Catenin CTNNB1, CTNNB; MRD19; armadilloIkB NFKBIA, IKBA; MAD-3; NFKBI NFKBIA 0.01786NFkBNFKB1, RELA, NFKB2, RELB, RELRELB0.006975 NFKB1 0.00001596RELA 0.03504REL 0.02375CDK2 CDK2, p33 CDK2 0.00003416cyclin E CCNE, CCNE1, CCNE2, CYCE2 CCNE2 0.00003416Rb RB1, RB; pRb; OSRC; pp110; p105-RbE2FE2F1, E2F2, E2F3E2F20.01107 E2F2 0.03911E2F3 0.000000166CBP EP300, CREBBP, KAT3, CBP, RSTS CREBBP 0.02731p53 TP53, P53, BCC7; LFS1; TRP53 TP53 0.03197 TP53 0.001042TCF/LEF TCF7, TCF7L1, TCF7L2, LEF1, TCF7L2 0.0002974 TCF7 0.005841LEF1 0.005033 TCF7L2 0.003514LEF1 0.03955cyclin D1 CCND1, BCL1; D11S287E; PRAD1;U21B31CCND10.000001195CCND10.001473BCL2 BCL2, PPP1R50PSA KLK3, APS; KLK2A1; PSA; HK3 KLK3 0.03711 KLK3 0.04634 HK3 0.0422120Figure 2. The pathway map A for group A. This map shows the situation from normal to tumor in prostate cancer. The pinkellipses show a node in KEGG prostate cancer pathway map with significant change in gene expression at group A. Theorange ellipses show a node in KEGG prostate cancer pathway map without significant change in gene expression at group A,but a hub for pink ellipses in this map.21Figure 3. The pathway map B for group B. This map shows the situation from early prostate tumor to primary prostate tumor.The pink ellipses show a node in KEGG prostate cancer pathway map with significant change in gene expression at group B.The orange ellipses show a node in KEGG prostate cancer pathway map without significant change in gene expression atgroup B, but a hub for pink ellipses in this map.22Figure 4. The pathway map C for group C. This map shows the situation from primary prostate tumor to metastatic prostatetumor. The pink ellipses show a node in KEGG prostate cancer pathway map with significant change in gene expression atgroup C. The orange ellipses show a node in KEGG prostate cancer pathway map without significant change in geneexpression at group C, but a hub for pink ellipses in this map.

Important Links:

Go Back