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Secreted Phosphoprotein 1 Upstream Invasive Network Construction and Analysis of Lung Adenocarcinoma Compared with Human Normal Adjacent Tissues by Integrative Biocomputation

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Abstract

The aim of this study is to set up single molecular secreted phosphoprotein 1 (SPP1) upstream invasive network of lung adenocarcinoma. This paper proposed an integrated method based on linear programming and a decomposition procedure with integrated analysis of the significant function cluster using Kappa statistics and fuzzy heuristic clustering. Our study proved that only modules appearing in lung adenocarcinoma include cytokine module (CXCL13, GREM1_2 inhibition), cell adhesion module (COL11A1_2 activation; CDH3 inhibition), and receptor binding module (NMU activation; CXCL13, GREM1_2 inhibition), which increase the invasion of cancer cell. We compared skeletal development, signal, biological regulation, sequence variant modules between human normal adjacent tissues and lung adenocarcinoma. SPP1 skeletal development module appears in human normal adjacent tissues (COL11A1_1 activation; COL10A1 inhibition), whereas in lung adenocarcinoma (COL11A1_2, COL1A2 activation); signal module appears in human normal adjacent tissues (COL11A1_1, CXCL13, MMP11, SPINK1 activation; COL10A1, COL3A1 inhibition), whereas in lung adenocarcinoma (COL11A1_2, COL1A2, MMP12 activation; CDH3, CXCL13, GREM1_2, MMP11, SPINK1 inhibition); biological regulation module appears in human normal adjacent tissues (CXCL13, MKI67, PYCR1 activation; NEK2, SPDEF, TOP2A_2, TOX3_1 inhibition), whereas in lung adenocarcinoma (HMGB3, MKI67, NMU, PYCR1, TOX3_2 activation; CXCL13, SPDEF, TOP2A_2 inhibition); sequence variant module appears in human normal adjacent tissues (COL11A1_1, MKI67, MMP11 activation; ASPM, COL10A1, COL3A1, NEK2, TMPRSS4, TOP2A_2 inhibition), whereas in lung adenocarcinoma (COL11A1_2, COL1A2, HMMR, MKI67, MMP12 activation; ABCC3, ASPM, CDH3, MMP11, TOP2A_2 inhibition). It can be deduced that modules above in human normal adjacent tissues reflect the invasive inhibition of normal cells, whereas in lung adenocarcinoma increase the invasion of cancer cell. Our study of SPP1 upstream invasive network may be useful to identify novel and potentially targets for prognosis and therapy of lung adenocarcinoma.

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Abbreviations

GENE_SYMBOL :

Gene name

COL3A1:

Collagen, type iii, alpha 1 (ehlers-danlos syndrome type iv, autosomal)

COL10A1:

Collagen, type x, alpha 1 (schmid metaphyseal chondrodysplasia)

TOP2A:

Topoisomerase (dna) ii alpha 170 kDa

ABCC3:

ATP-binding cassette, sub-family c (cftr/mrp), member 3

COL11A1:

Collagen, type xi, alpha 1

TMPRSS4:

Type ii membrane serine protease

GREM1:

Gremlin 1, cysteine knot superfamily, homolog (Xenopus laevis)

PYCR1:

Pyrroline-5-carboxylate reductase 1

ASPM:

Pypothetical protein flj10517

HMMR:

Hyaluronan-mediated motility receptor (rhamm)

COL1A2:

Collagen, type i, alpha 2

SPPI:

Secreted phosphoprotein 1 (osteopontin, bone sialoprotein i, early tlymphocyte activation 1)

SPINK1:

Serine peptidase inhibitor, kazal type 1

NMU:

Neuromedin u

CDH3:

Cadherin 3, type 1, p-cadherin (placental)

HMGB3:

High-mobility group box 3

NEK2:

Nima (never in mitosis gene a)-related kinase 2

TOX3:

Trinucleotide repeat containing 9

MKI67:

Antigen identified by monoclonal antibody ki-67

SPDEF:

Sam pointed domain containing ets transcription factor

MMP12:

Matrix metallopeptidase 12 (macrophage elastase)

CXCL13:

Chemokine (c-x-c motif) ligand 13 (b-cell chemoattractant)

MMP11:

Matrix metallopeptidase 11 (stromelysin 3)

References

  1. Ahmad, S., Kolli, S., et al. (2008). A putative role for RHAMM/HMMR as a negative marker of stem cell-containing population of human limbal epithelial cells. Stem Cells, 26(6), 1609–1619.

    Article  CAS  PubMed  Google Scholar 

  2. Al-Kuraya, K., Novotny, H., et al. (2007). HER2, TOP2A, CCND1, EGFR and C-MYC oncogene amplification in colorectal cancer. Journal of Clinical Pathology, 60(7), 768–772.

    Article  CAS  PubMed  Google Scholar 

  3. Arriola, E., Marchio, C., et al. (2008). Genomic analysis of the HER2/TOP2A amplicon in breast cancer and breast cancer cell lines. Laboratory Investigation, 88(5), 491–503.

    Article  CAS  PubMed  Google Scholar 

  4. Bahmanyar, S., Kaplan, D. D., et al. (2008). beta-Catenin is a Nek2 substrate involved in centrosome separation. Genes and Development, 22(1), 91–105.

    Article  CAS  PubMed  Google Scholar 

  5. Baptista, C., Santos, M. A., et al. (2008). Phage SPP1 reversible adsorption to Bacillus subtilis cell wall teichoic acids accelerates virus recognition of membrane receptor YueB. Journal of Bacteriology, 190(14), 4989–4996.

    Article  CAS  PubMed  Google Scholar 

  6. Behera, M. A., Feng, L., et al. (2007). Thrombospondin-1 and thrombospondin-2 mRNA and TSP-1 and TSP-2 protein expression in uterine fibroids and correlation to the genes COL1A1 and COL3A1 and to the collagen cross-link hydroxyproline. Reproductive Sciences, 14(8 Suppl), 63–76.

    Article  CAS  PubMed  Google Scholar 

  7. Beser, A. R., Tuzlali, S., et al. (2007). HER-2, TOP2A and chromosome 17 alterations in breast cancer. Pathology Oncology Research, 13(3), 180–185.

    Article  PubMed  Google Scholar 

  8. Campa, D., Vodicka, P., et al. (2008). Could polymorphisms in ATP-binding cassette C3/multidrug resistance associated protein 3 (ABCC3/MRP3) modify colorectal cancer risk? European Journal of Cancer, 44(6), 854–857.

    Article  CAS  PubMed  Google Scholar 

  9. Carleton, S. M., McBride, D. J., et al. (2008). Role of genetic background in determining phenotypic severity throughout postnatal development and at peak bone mass in Col1a2 deficient mice (oim). Bone, 42(4), 681–694.

    Article  CAS  PubMed  Google Scholar 

  10. Chamberlain, J. R., Deyle, D. R., et al. (2008). Gene targeting of mutant COL1A2 alleles in mesenchymal stem cells from individuals with osteogenesis imperfecta. Molecular Therapy, 16(1), 187–193.

    Article  CAS  PubMed  Google Scholar 

  11. Chan, M. M., Lu, X., et al. (2007). Serial transplantation of NMU-induced rat mammary tumors: A model of human breast cancer progression. International Journal of Cancer, 121(3), 474–485.

    Article  CAS  Google Scholar 

  12. Chang, Y. S., Kim, H. J., et al. (2007). Elevated circulating level of osteopontin is associated with advanced disease state of non-small cell lung cancer. Lung Cancer, 57(3), 373–380.

    Article  PubMed  Google Scholar 

  13. Chong, I. W., Chang, M. Y., et al. (2006). Great potential of a panel of multiple hMTH1, SPD, ITGA11 and COL11A1 markers for diagnosis of patients with non-small cell lung cancer. Oncology Reports, 16(5), 981–988.

    CAS  PubMed  Google Scholar 

  14. Desir, J., Cassart, M., et al. (2008). Primary microcephaly with ASPM mutation shows simplified cortical gyration with antero-posterior gradient pre- and post-natally. American Journal of Medical Genetics. Part A, 146A(11), 1439–1443.

    Article  CAS  PubMed  Google Scholar 

  15. Dunlap, K. A., Erikson, D. W., et al. (2008). Progesterone and placentation increase secreted phosphoprotein one (SPP1 or osteopontin) in uterine glands and stroma for histotrophic and hematotrophic support of ovine pregnancy. Biology of Reproduction, 79(5), 983–990.

    Article  CAS  PubMed  Google Scholar 

  16. Fedarko, N. S., Jain, A., et al. (2001). Elevated serum bone sialoprotein and osteopontin in colon, breast, prostate, and lung cancer. Clinical Cancer Research, 7(12), 4060–4066.

    CAS  PubMed  Google Scholar 

  17. Fong, Y. C., Liu, S. C., et al. (2009). Osteopontin increases lung cancer cells migration via activation of the alphavbeta3 integrin/FAK/Akt and NF-kappaB-dependent pathway. Lung Cancer, 64(3), 263–270.

    Article  PubMed  Google Scholar 

  18. Frost, P. (2008). The spread of alphabetical writing may have favored the latest variant of the ASPM gene. Medical Hypotheses, 70(1), 17–20.

    Article  CAS  PubMed  Google Scholar 

  19. Fujimori, A., Yaoi, T., et al. (2008). Ionizing radiation downregulates ASPM, a gene responsible for microcephaly in humans. Biochemical and Biophysical Research Communications, 369(3), 953–957.

    Article  CAS  PubMed  Google Scholar 

  20. Gault, V. A., Hunter, K., et al. (2007). Characterisation and glucoregulatory actions of a novel acylated form of the (Pro3)GIP receptor antagonist in type 2 diabetes. Biological Chemistry, 388(2), 173–179.

    Article  CAS  PubMed  Google Scholar 

  21. Gault, V. A., Irwin, N., et al. (2005). Chemical ablation of gastric inhibitory polypeptide receptor action by daily (Pro3)GIP administration improves glucose tolerance and ameliorates insulin resistance and abnormalities of islet structure in obesity-related diabetes. Diabetes, 54(8), 2436–2446.

    Article  CAS  PubMed  Google Scholar 

  22. Gebhard, S., Hattori, T., et al. (2007). BAC constructs in transgenic reporter mouse lines control efficient and specific LacZ expression in hypertrophic chondrocytes under the complete Col10a1 promoter. Histochemistry and Cell Biology, 127(2), 183–194.

    Article  CAS  PubMed  Google Scholar 

  23. Hagemann, C., Anacker, J., et al. (2008). Expression analysis of the autosomal recessive primary microcephaly genes MCPH1 (microcephalin) and MCPH5 (ASPM, abnormal spindle-like, microcephaly associated) in human malignant gliomas. Oncology Reports, 20(2), 301–308.

    CAS  PubMed  Google Scholar 

  24. Hagen, A. I., Bofin, A. M., et al. (2007). Amplification of TOP2A and HER-2 genes in breast cancers occurring in patients harbouring BRCA1 germline mutations. Acta Oncologica, 46(2), 199–203.

    Article  CAS  PubMed  Google Scholar 

  25. Ho, M. S., Tsang, K. Y., et al. (2007). COL10A1 nonsense and frame-shift mutations have a gain-of-function effect on the growth plate in human and mouse metaphyseal chondrodysplasia type Schmid. Human Molecular Genetics, 16(10), 1201–1215.

    Article  CAS  PubMed  Google Scholar 

  26. Hua, T., Zhang, D., et al. (2008). Correlation of COL3A1 gene with type III collagen stability in intracranial aneurysm. Zhonghua Yi Xue Za Zhi, 88(7), 445–448.

    CAS  PubMed  Google Scholar 

  27. Huang da, W., Sherman, B. T., et al. (2007). The DAVID Gene Functional Classification Tool: A novel biological module-centric algorithm to functionally analyze large gene lists. Genome Biology, 8(9), R183.

    Article  PubMed  CAS  Google Scholar 

  28. Huijts, P. E., Vreeswijk, M. P., et al. (2007). Clinical correlates of low-risk variants in FGFR2, TNRC9, MAP3K1, LSP1 and 8q24 in a Dutch cohort of incident breast cancer cases. Breast Cancer Research, 9(6), R78.

    Article  PubMed  CAS  Google Scholar 

  29. Indelman, M., Bergman, R., et al. (2002). A missense mutation in CDH3, encoding P-cadherin, causes hypotrichosis with juvenile macular dystrophy. Journal of Investigative Dermatology, 119(5), 1210–1213.

    Article  CAS  PubMed  Google Scholar 

  30. Indelman, M., Eason, J., et al. (2007). Novel CDH3 mutations in hypotrichosis with juvenile macular dystrophy. Clinical and Experimental Dermatology, 32(2), 191–196.

    Article  CAS  PubMed  Google Scholar 

  31. Irwin, N., Green, B. D., et al. (2006). Biological activity and antidiabetic potential of synthetic fragment peptides of glucose-dependent insulinotropic polypeptide, GIP(1–16) and (Pro3)GIP(1–16). Regulatory Peptides, 135(1–2), 45–53.

    Article  CAS  PubMed  Google Scholar 

  32. Irwin, N., McClean, P. L., et al. (2007). Early administration of the glucose-dependent insulinotropic polypeptide receptor antagonist (Pro3)GIP prevents the development of diabetes and related metabolic abnormalities associated with genetically inherited obesity in ob/ob mice. Diabetologia, 50(7), 1532–1540.

    Article  CAS  PubMed  Google Scholar 

  33. Ito, S., Kimura, K., et al. (2007). Induction of matrix metalloproteinases (MMP3, MMP12 and MMP13) expression in the microglia by amyloid-beta stimulation via the PI3K/Akt pathway. Experimental Gerontology, 42(6), 532–537.

    Article  CAS  PubMed  Google Scholar 

  34. Jung, H., Lee, K. P., et al. (2008). TMPRSS4 promotes invasion, migration and metastasis of human tumor cells by facilitating an epithelial-mesenchymal transition. Oncogene, 27(18), 2635–2647.

    Article  CAS  PubMed  Google Scholar 

  35. Kebebew, E., Peng, M., et al. (2005). ECM1 and TMPRSS4 are diagnostic markers of malignant thyroid neoplasms and improve the accuracy of fine needle aspiration biopsy. Annals of Surgery, 242(3), 353–361. (discussion 361–363).

    PubMed  Google Scholar 

  36. Kitamura, Y., Hirouchi, M., et al. (2008). Increasing systemic exposure of methotrexate by active efflux mediated by multidrug resistance-associated protein 3 (mrp3/abcc3). Journal of Pharmacology and Experimental Therapeutics, 327(2), 465–473.

    Article  CAS  PubMed  Google Scholar 

  37. Kjaer, K. W., Hansen, L., et al. (2005). Distinct CDH3 mutations cause ectodermal dysplasia, ectrodactyly, macular dystrophy (EEM syndrome). Journal of Medical Genetics, 42(4), 292–298.

    Article  CAS  PubMed  Google Scholar 

  38. Kobayashi, H., Parton, A., et al. (2007). Multidrug resistance-associated protein 3 (Mrp3/Abcc3/Moat-D) is expressed in the SAE Squalus acanthias shark embryo-derived cell line. Zebrafish, 4(4), 261–275.

    Article  CAS  PubMed  Google Scholar 

  39. Kokuryo, T., Senga, T., et al. (2007). Nek2 as an effective target for inhibition of tumorigenic growth and peritoneal dissemination of cholangiocarcinoma. Cancer Research, 67(20), 9637–9642.

    Article  CAS  PubMed  Google Scholar 

  40. Korytina, G. F., Akhmadishina, L. Z., et al. (2008). Polymorphism in promoter regions of matrix metalloproteinases (MMP1, MMP9, and MMP12) in chronic obstructive pulmonary disease patients. Genetika, 44(2), 242–249.

    CAS  PubMed  Google Scholar 

  41. Lee, S. T., Kim, J. A., et al. (2008). A novel COL3A1 gene mutation in patient with aortic dissected aneurysm and cervical artery dissections. Heart and Vessels, 23(2), 144–148.

    Article  PubMed  Google Scholar 

  42. Levy, A., Zucman, J., et al. (1992). Assignment of the human stromelysin 3 (STMY3) gene to the q11.2 region of chromosome 22. Genomics, 13(3), 881–883.

    Article  CAS  PubMed  Google Scholar 

  43. Li, Q., Jiang, Q., et al. (2007). Targeted ablation of Abcc1 or Abcc3 in Abcc6(−/−) mice does not modify the ectopic mineralization process. Experimental Dermatology, 16(10), 853–859.

    CAS  PubMed  Google Scholar 

  44. Lin, S. Y., Pan, H. W., et al. (2008). ASPM is a novel marker for vascular invasion, early recurrence, and poor prognosis of hepatocellular carcinoma. Clinical Cancer Research, 14(15), 4814–4820.

    Article  CAS  PubMed  Google Scholar 

  45. Lintell, N. A., Maguire, D. J., et al. (2007). Analysis of SDHD and MMP12 in an affected solar keratosis and control cohort. Advances in Experimental Medicine and Biology, 599, 79–85.

    Article  CAS  PubMed  Google Scholar 

  46. Maciel, T. T., Melo, R. S., et al. (2008). Gremlin promotes vascular smooth muscle cell proliferation and migration. Journal of Molecular and Cellular Cardiology, 44(2), 370–379.

    Article  CAS  PubMed  Google Scholar 

  47. Majava, M., Hoornaert, K. P., et al. (2007). A report on 10 new patients with heterozygous mutations in the COL11A1 gene and a review of genotype-phenotype correlations in type XI collagenopathies. American Journal of Medical Genetics. Part A, 143(3), 258–264.

    Article  PubMed  CAS  Google Scholar 

  48. Maruyama, K., Konno, N., et al. (2008). Isolation and characterisation of four cDNAs encoding neuromedin U (NMU) from the brain and gut of goldfish, and the inhibitory effect of a deduced NMU on food intake and locomotor activity. Journal of Neuroendocrinology, 20(1), 71–78.

    CAS  PubMed  Google Scholar 

  49. Matsuoka, Y., Kobayashi, T., et al. (2008). Molecular cloning of Plk1 and Nek2 and their expression in mature gonads of the teleost fish Nile tilapia (Oreochromis niloticus). Molecular Reproduction and Development, 75(6), 989–1001.

    Article  CAS  PubMed  Google Scholar 

  50. McClean, P. L., Gault, V. A., et al. (2008). Daily administration of the GIP-R antagonist (Pro3)GIP in streptozotocin-induced diabetes suggests that insulin-dependent mechanisms are critical to anti-obesity-diabetes actions of (Pro3)GIP. Diabetes Obesity and Metabolism, 10(4), 336–342.

    Article  CAS  Google Scholar 

  51. Megarbane, A., Chouery, E., et al. (2008). A multiplex family with possible metaphyseal Spahr-type dysplasia and exclusion of RMRP and COL10A1 as candidate genes. American Journal of Medical Genetics. Part A, 146A(14), 1865–1870.

    Article  CAS  PubMed  Google Scholar 

  52. Mi, J., Guo, C., et al. (2007). Protein phosphatase-1alpha regulates centrosome splitting through Nek2. Cancer Research, 67(3), 1082–1089.

    Article  CAS  PubMed  Google Scholar 

  53. Mio, F., Chiba, K., et al. (2007). A functional polymorphism in COL11A1, which encodes the alpha 1 chain of type XI collagen, is associated with susceptibility to lumbar disc herniation. American Journal of Human Genetics, 81(6), 1271–1277.

    Article  CAS  PubMed  Google Scholar 

  54. Murphy, A. J., Hughes, C. A., et al. (2007). Low-level TOP2A amplification in prostate cancer is associated with HER2 duplication, androgen resistance, and decreased survival. Cancer Research, 67(6), 2893–2898.

    Article  CAS  PubMed  Google Scholar 

  55. Myllarniemi, M., Lindholm, P., et al. (2008). Gremlin-mediated decrease in bone morphogenetic protein signaling promotes pulmonary fibrosis. American Journal of Respiratory and Critical Care Medicine, 177(3), 321–329.

    Article  CAS  PubMed  Google Scholar 

  56. Myllarniemi, M., Vuorinen, K., et al. (2008). Gremlin localization and expression levels partially differentiate idiopathic interstitial pneumonia severity and subtype. Journal of Pathology, 214(4), 456–463.

    Article  CAS  PubMed  Google Scholar 

  57. Nemeth, M. J., Cline, A. P., et al. (2005). Hmgb3 deficiency deregulates proliferation and differentiation of common lymphoid and myeloid progenitors. Blood, 105(2), 627–634.

    Article  CAS  PubMed  Google Scholar 

  58. Nemeth, M. J., Curtis, D. J., et al. (2003). Hmgb3: An HMG-box family member expressed in primitive hematopoietic cells that inhibits myeloid and B-cell differentiation. Blood, 102(4), 1298–1306.

    Article  CAS  PubMed  Google Scholar 

  59. Nemeth, M. J., Kirby, M. R., et al. (2006). Hmgb3 regulates the balance between hematopoietic stem cell self-renewal and differentiation. Proceedings of National Academy of Sciences of the United States of America, 103(37), 13783–13788.

    Article  CAS  Google Scholar 

  60. Nielsen, K. V., Ejlertsen, B., et al. (2008). The value of TOP2A gene copy number variation as a biomarker in breast cancer: Update of DBCG trial 89D. Acta Oncologica, 47(4), 725–734.

    Article  CAS  PubMed  Google Scholar 

  61. O’Brien, C., Cavet, G., et al. (2008). Functional genomics identifies ABCC3 as a mediator of taxane resistance in HER2-amplified breast cancer. Cancer Research, 68(13), 5380–5389.

    Article  PubMed  CAS  Google Scholar 

  62. O’Reilly, D. A., Witt, H., et al. (2008). The SPINK1 N34S variant is associated with acute pancreatitis. European Journal of Gastroenterology and Hepatology, 20(8), 726–731.

    Article  PubMed  CAS  Google Scholar 

  63. Paredes, J., Albergaria, A., et al. (2005). P-cadherin overexpression is an indicator of clinical outcome in invasive breast carcinomas and is associated with CDH3 promoter hypomethylation. Clinical Cancer Research, 11(16), 5869–5877.

    Article  CAS  PubMed  Google Scholar 

  64. Park, K. S., Korfhagen, T. R., et al. (2007). SPDEF regulates goblet cell hyperplasia in the airway epithelium. Journal of Clinical Investigation, 117(4), 978–988.

    Article  CAS  PubMed  Google Scholar 

  65. Parker, J. C., Irwin, N., et al. (2007). Metabolic effects of sub-chronic ablation of the incretin receptors by daily administration of (Pro3)GIP and exendin(9–39)amide in obese diabetic (ob/ob) mice. Biological Chemistry, 388(2), 221–226.

    Article  CAS  PubMed  Google Scholar 

  66. Picchio, M. C., Scala, E., et al. (2008). CXCL13 is highly produced by Sezary cells and enhances their migratory ability via a synergistic mechanism involving CCL19 and CCL21 chemokines. Cancer Research, 68(17), 7137–7146.

    Article  CAS  PubMed  Google Scholar 

  67. Poh, S. L., el Khadali, F., et al. (2008). Oligomerization of the SPP1 scaffolding protein. Journal of Molecular Biology, 378(3), 551–564.

    Article  CAS  PubMed  Google Scholar 

  68. Rellos, P., Ivins, F. J., et al. (2007). Structure and regulation of the human Nek2 centrosomal kinase. The Journal of Biological Chemistry, 282(9), 6833–6842.

    Article  CAS  PubMed  Google Scholar 

  69. Rerknimitr, R., Shotelersuk, V., et al. (2008). A novel SPINK1 gene mutation, c.206C>T, in a Thai patient with chronic alcoholic pancreatitis. JOP, 9(1), 33–36.

    PubMed  Google Scholar 

  70. Rioja, I., Hughes, F. J., et al. (2008). Potential novel biomarkers of disease activity in rheumatoid arthritis patients: CXCL13, CCL23, transforming growth factor alpha, tumor necrosis factor receptor superfamily member 9, and macrophage colony-stimulating factor. Arthritis and Rheumatism, 58(8), 2257–2267.

    Article  CAS  PubMed  Google Scholar 

  71. Rucinski, M., Ziolkowska, A., et al. (2008). Neuromedin U directly stimulates growth of cultured rat calvarial osteoblast-like cells acting via the NMU receptor 2 isoform. International Journal of Molecular Medicine, 22(3), 363–368.

    CAS  PubMed  Google Scholar 

  72. Sansonno, D., Tucci, F. A., et al. (2008). Increased serum levels of the chemokine CXCL13 and up-regulation of its gene expression are distinctive features of HCV-related cryoglobulinemia and correlate with active cutaneous vasculitis. Blood, 112(5), 1620–1627.

    Article  CAS  PubMed  Google Scholar 

  73. Schultz, I. J., Kiemeney, L. A., et al. (2006). Survivin and MKI67 mRNA expression in bladder washings of patients with superficial urothelial cell carcinoma correlate with tumor stage and grade but do not predict tumor recurrence. Clinical Chemistry, 52(7), 1440–1442.

    Article  CAS  PubMed  Google Scholar 

  74. Shimizu, F., Matsuzaki, T., et al. (2008). Estradiol suppresses NMU mRNA expression during sexual maturation in the female rat pituitary. International Journal of Developmental Neuroscience, 26(3–4), 381–384.

    Article  CAS  PubMed  Google Scholar 

  75. Shimosegawa, T., Kume, K., et al. (2008). SPINK1, ADH2, and ALDH2 gene variants and alcoholic chronic pancreatitis in Japan. Journal of Gastroenterology and Hepatology, 23 Suppl 1, S82–S86.

    Article  PubMed  CAS  Google Scholar 

  76. Shin, A., Cai, Q., et al. (2005). Genetic polymorphisms in the matrix metalloproteinase 12 gene (MMP12) and breast cancer risk and survival: The Shanghai Breast Cancer Study. Breast Cancer Research, 7(4), R506–R512.

    Article  CAS  PubMed  Google Scholar 

  77. Shpargel, K. B., Makishima, T., et al. (2004). Col11a1 and Col11a2 mRNA expression in the developing mouse cochlea: Implications for the correlation of hearing loss phenotype with mutant type XI collagen genotype. Acta Oto-Laryngologica, 124(3), 242–248.

    Article  CAS  PubMed  Google Scholar 

  78. Shukla, A., Barrett, T. F., et al. (2006). Transcriptional up-regulation of MMP12 and MMP13 by asbestos occurs via a PKCdelta-dependent pathway in murine lung. FASEB Journal, 20(7), 997–999.

    Article  CAS  PubMed  Google Scholar 

  79. Spicer, A. P., Roller, M. L., et al. (1995). The human and mouse receptors for hyaluronan-mediated motility, RHAMM, genes (HMMR) map to human chromosome 5q33.2-qter and mouse chromosome 11. Genomics, 30(1), 115–117.

    Article  CAS  PubMed  Google Scholar 

  80. Sprecher, E., Bergman, R., et al. (2001). Hypotrichosis with juvenile macular dystrophy is caused by a mutation in CDH3, encoding P-cadherin. Nature Genetics, 29(2), 134–136.

    Article  CAS  PubMed  Google Scholar 

  81. Stich, S., Loch, A., et al. (2008). Human periosteum-derived progenitor cells express distinct chemokine receptors and migrate upon stimulation with CCL2, CCL25, CXCL8, CXCL12, and CXCL13. European Journal of Cell Biology, 87(6), 365–376.

    Article  CAS  PubMed  Google Scholar 

  82. Su, Y., Eason, R. R., et al. (2007). In utero exposure to maternal diets containing soy protein isolate, but not genistein alone, protects young adult rat offspring from NMU-induced mammary tumorigenesis. Carcinogenesis, 28(5), 1046–1051.

    Article  CAS  PubMed  Google Scholar 

  83. Sun, Y., Wang, L., et al. (2008). Integrative decomposition procedure and Kappa statistics set up ATF2 ion binding module in Malignant Pleural Mesothelioma (MPM). Frontiers of Electrical and Electronic Engineering in China, 3(4), 381–387.

    Article  Google Scholar 

  84. Szymko-Bennett, Y. M., Kurima, K., et al. (2003). Auditory function associated with Col11a1 haploinsufficiency in chondrodysplasia (cho) mice. Hearing Research, 175(1–2), 178–182.

    Article  CAS  PubMed  Google Scholar 

  85. Takagi, R., Higashi, T., et al. (2008). B cell chemoattractant CXCL13 is preferentially expressed by human Th17 cell clones. Journal of Immunology, 181(1), 186–189.

    CAS  Google Scholar 

  86. Tanaka, S., & Ramirez, F. (2007). The first intron of the human alpha2(I) collagen gene (COL1A2) contains a novel interferon-gamma responsive element. Matrix Biology, 26(3), 185–189.

    Article  CAS  PubMed  Google Scholar 

  87. Taniuchi, K., Nakagawa, H., et al. (2005). Overexpressed P-cadherin/CDH3 promotes motility of pancreatic cancer cells by interacting with p120ctn and activating rho-family GTPases. Cancer Research, 65(8), 3092–3099.

    CAS  PubMed  Google Scholar 

  88. Tchetina, E. V., Di Battista, J. A., et al. (2007). Prostaglandin PGE2 at very low concentrations suppresses collagen cleavage in cultured human osteoarthritic articular cartilage: This involves a decrease in expression of proinflammatory genes, collagenases and COL10A1, a gene linked to chondrocyte hypertrophy. Arthritis Research and Therapy, 9(4), R75.

    Article  PubMed  CAS  Google Scholar 

  89. Tomlins, S. A., Rhodes, D. R., et al. (2008). The role of SPINK1 in ETS rearrangement-negative prostate cancers. Cancer Cell, 13(6), 519–528.

    Article  CAS  PubMed  Google Scholar 

  90. Traut, W., Scholzen, T., et al. (1998). Assignment1 of the murine Ki-67 gene (Mki67) to chromosome band 7F3–F5 by in situ hybridization. Cytogenetics and Cell Genetics, 83(1–2), 12–13.

    CAS  PubMed  Google Scholar 

  91. Vermi, W., Lonardi, S., et al. (2008). Identification of CXCL13 as a new marker for follicular dendritic cell sarcoma. Journal of Pathology, 216(3), 356–364.

    Article  CAS  PubMed  Google Scholar 

  92. Walsh, D. W., Roxburgh, S. A., et al. (2008). Co-regulation of Gremlin and Notch signalling in diabetic nephropathy. Biochimica et Biophysica Acta, 1782(1), 10–21.

    CAS  PubMed  Google Scholar 

  93. Wang, E. B., Zhao, Q., et al. (2008). Expression of COL1a1 and COL3a1 in the capsule of children with developmental dislocation of the hip. Zhongguo Dang Dai Er Ke Za Zhi, 10(4), 493–496.

    CAS  PubMed  Google Scholar 

  94. Wang, L., Sun, Y., et al. (2009). FOS proliferating network construction in early colorectal cancer (CRC) based on integrative significant function cluster and inferring analysis. Cancer Investigation, 27(8), 816–824.

    Article  CAS  PubMed  Google Scholar 

  95. Wang, L., Sun, Y., et al. (2009). Integrative decomposition procedure and Kappa statistics for the distinguished single molecular network construction and analysis. Journal of Biomedicine and Biotechnology, 2009, 726728.

    PubMed  Google Scholar 

  96. Wang, Q., Peng, Z. H., et al. (2008). Inhibition of COL1A1 and COL3A1 expression by RNA interference in human skin fibroblasts. Nan Fang Yi Ke Da Xue Xue Bao, 28(1), 1–6.

    PubMed  Google Scholar 

  97. Wang, Y., Joshi, T., et al. (2006). Inferring gene regulatory networks from multiple microarray datasets. Bioinformatics, 22(19), 2413–2420.

    Article  CAS  PubMed  Google Scholar 

  98. Wordinger, R. J., Zode, G., et al. (2008). Focus on molecules: Gremlin. Experimental Eye Research, 87(2), 78–79.

    Article  CAS  PubMed  Google Scholar 

  99. Wu, G., Qiu, X. L., et al. (2008). Small molecule targeting the Hec1/Nek2 mitotic pathway suppresses tumor cell growth in culture and in animal. Cancer Research, 68(20), 8393–8399.

    Article  CAS  PubMed  Google Scholar 

  100. Wu, W., Baxter, J. E., et al. (2007). Alternative splicing controls nuclear translocation of the cell cycle-regulated Nek2 kinase. Journal of Biological Chemistry, 282(36), 26431–26440.

    Article  CAS  PubMed  Google Scholar 

  101. Yamada, H., Shinmura, K., et al. (2005). Effect of splice-site polymorphisms of the TMPRSS4, NPHP4 and ORCTL4 genes on their mRNA expression. Journal of Genetics, 84(2), 131–136.

    Article  CAS  PubMed  Google Scholar 

  102. Zimmermann, P., Boeuf, S., et al. (2008). Correlation of COL10A1 induction during chondrogenesis of mesenchymal stem cells with demethylation of two CpG sites in the COL10A1 promoter. Arthritis and Rheumatism, 58(9), 2743–2753.

    Article  PubMed  Google Scholar 

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Acknowledgments

This work was supported by the National Natural Science Foundation in China (No. 60673109 and No.60871100) and the Teaching and Scientific Research Foundation for the Returned Overseas Chinese Scholars, State Education Ministry. State Key Lab of Pattern Recognition Open Foundation. Major science and technology projects of new transgene biological breeds (2009ZX08012-001B). Key project of philosophical and social science of MOE (07JZD0005).

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Authors and Affiliations

  1. Biomedical Center, School of Electronics Engineering, Beijing University of Posts and Telecommunications, Beijing, 100876, China

    Ying Sun, Lin Wang & Juxiang Huang

  2. Lab of Computational Linguistics, School of Humanities and Social Sciences, Tsinghua University, Beijing, 100084, China

    Minghu Jiang

  3. Department of Epidemiology and Preventive Medicine, University of Maryland Medicine, Baltimore, USA

    Zhenqiu Liu

  4. Department of Biology-Bioanalytic, Institute of Pharmacia & Molecular Biotechnology, University of Heidelberg, 69120, Heidelberg, Germany

    Stefan Wolfl

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  1. Ying Sun
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  2. Lin Wang
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  3. Minghu Jiang
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  5. Zhenqiu Liu
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  6. Stefan Wolfl
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Correspondence to Lin Wang.

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Ying Sun, Lin Wang, Minghu Jiang—Equal contribution.

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Sun, Y., Wang, L., Jiang, M. et al. Secreted Phosphoprotein 1 Upstream Invasive Network Construction and Analysis of Lung Adenocarcinoma Compared with Human Normal Adjacent Tissues by Integrative Biocomputation. Cell Biochem Biophys 56, 59–71 (2010). https://doi.org/10.1007/s12013-009-9071-6

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