Proteomic identification network analysis of haptoglobin as a key regulator associated with liver fibrosis

Applied Biochemistry and Biotechnology

Volumn 169, Issue 3, 2013, Pages 832-846

  Zhang, Aihua ^a   Sun, Hui ^a   Sun, Wejun ^a   Ye, Yuan ^a   Wang, Xijun ^a  

^a HEILONGJIANG UNIVERSITY OF CHINESE MEDICINE   (China)

Author keywords

Liver fibrosis; Mass spectrometry; Protein protein interaction network; Proteomics; Two dimensional gel electrophoresis

Indexed keywords

EXPERIMENTAL INVESTIGATIONS; LIVER FIBROSIS; MATRIX ASSISTED LASER DESORPTION/IONIZATION; PROTEIN INTERACTION NETWORKS; PROTEIN-PROTEIN INTERACTION NETWORKS; PROTEOMICS; TIME OF FLIGHT MASS SPECTROMETRY; TWO-DIMENSIONAL GEL ELECTROPHORESIS;

ACTIVE NETWORKS; BIOINFORMATICS; CELL DEATH; ELECTROPHORESIS; MASS SPECTROMETRY; MOLECULAR BIOLOGY; SIGNAL TRANSDUCTION;

PROTEINS;

CARBON TETRACHLORIDE; DNA; HAPTOGLOBIN;

ANIMAL EXPERIMENT; ANIMAL MODEL; APOPTOSIS; ARTICLE; BIOINFORMATICS; CELL COMMUNICATION; CONTROLLED STUDY; DISEASE COURSE; DNA REPAIR; ENERGY YIELD; LIVER FIBROSIS; MALE; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; NONHUMAN; OXIDATION REDUCTION REACTION; PROTEIN EXPRESSION; PROTEIN PROTEIN INTERACTION; RAT; SIGNAL TRANSDUCTION; TWO DIMENSIONAL GEL ELECTROPHORESIS; UPREGULATION; ANIMAL; BIOLOGY; CHEMICALLY INDUCED DISORDER; LIVER CIRRHOSIS; METABOLISM; METHODOLOGY; MOUSE; PROTEIN BINDING; PROTEOMICS;

ANIMALS; CARBON TETRACHLORIDE; COMPUTATIONAL BIOLOGY; HAPTOGLOBINS; LIVER CIRRHOSIS; MICE; PROTEIN BINDING; PROTEOMICS;

EID: 84883038394     PISSN: 02732289     EISSN: 15590291     Source Type: Journal    
DOI: 10.1007/s12010-012-0001-5     Document Type: Article

References (29)

1. Behrends, C., Sowa, M. E., Gygi, S. P., & Harper, J. W. (2010). Network organization of the human autophagy system. Nature, 466(7302), 68-76.
2. Stuart, L. M., Boulais, J., Charriere, G. M., Hennessy, E. J., Brunet, S., Jutras, I., Goyette, G., Rondeau, C., Letarte, S., Huang, H., Ye, P., Morales, F., Kocks, C., Bader, J. S., Desjardins, M., & Ezekowitz, R. A. (2007). A systems biology analysis of the Drosophila phagosome. Nature, 445(7123), 95-101.
3. Jørgensen, C., Sherman, A., Chen, G. I., Pasculescu, A., Poliakov, A., Hsiung, M., Larsen, B., Wilkinson, D. G., Linding, R., & Pawson, T. (2009). Cell-specific information processing in segregating populations of Eph receptor ephrin-expressing cells. Science, 326(5959), 1502-1509.
4. Zhang, K., Yuan, K., Wu, H., Li, Q., Wang, Y., Chen, S., Zhang, L., Gu, H., & Fu, R. (2012). Identification of potential markers related to neoadjuvant chemotherapy sensitivity of breast cancer by SELDI-TOF MS. Applied Biochemistry and Biotechnology, 166(3), 753-763.
5. Tang, C., Iwahara, J., & Clore, G. M. (2006). Visualization of transient encounter complexes in protein-protein association. Nature, 444(7117), 383-386.
6. Jielile, J., Jialili, A., Sabirhazi, G., Shawutali, N., Redati, D., Chen, J., Tang, B., Bai, J., & Aldyarhan, K. (2011). Proteomic analysis of differential protein expression of Achilles tendon in a rabbit model by twodimensional polyacrylamide gel electrophoresis at 21 days postoperation. Applied Biochemistry and Biotechnology, 165(3-4), 1092-1106.
7. Yu, H., Braun, P., Yildirim, M. A., Lemmens, I., Venkatesan, K., Sahalie, J., Hirozane-Kishikawa, T., Gebreab, F., Li, N., Simonis, N., Hao, T., Rual, J. F., Dricot, A., Vazquez, A., Murray, R. R., Simon, C., Tardivo, L., Tam, S., Svrzikapa, N., Fan, C., de Smet, A. S., Motyl, A., Hudson, M. E., Park, J., Xin, X., Cusick, M. E., Moore, T., Boone, C., Snyder, M., Roth, F. P., Barabási, A. L., Tavernier, J., Hill, D. E., & Vidal, M. (2008). High-quality binary protein interaction map of the yeast interactome network. Science, 322(5898), 104-110.
8. Hew, C. S., & Gam, L. H. (2011). Proteome analysis of abundant proteins extracted from the leaf of Gynura procumbens (Lour.) Merr. Applied Biochemistry and Biotechnology, 165(7-8), 1577-1586.
9. Wang, X., Zhang, A., Sun, H., Wu, G., Sun, W., & Yan, G. (2012). Network generation enhances interpretation of proteomics data sets by a combination of two-dimensional polyacrylamide gel electrophoresis and matrix-Assisted laser desorption/ionization-time of flight mass spectrometry. Analyst, 137 (20), 4703-4711.
10. Li, F., Glinskii, O. V., Zhou, J., Wilson, L. S., Barnes, S., Anthony, D. C., & Glinsky, V. V. (2011). Identification and analysis of signaling networks potentially involved in breast carcinoma metastasis to the brain. PLoS One, 6(7), e21977.
11. Bonetta, L. (2010). Protein-protein interactions: interactome under construction. Nature, 468(7325), 851-854.
12. Franzosa, E. A., & Xia, Y. (2011). Structural principles within the human-virus protein-protein interaction network. Proceedings of the National Academy of Sciences of the United States of America, 108(26), 10538-41053.
13. Shannon, P., Markiel, A., Ozier, O., Baliga, N. S., Wang, J. T., Ramage, D., Amin, N., Schwikowski, B., & Ideker, T. (2003). Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Research, 13, 2498-2504.
14. Deighton, R. F., Kerr, L. E., Short, D. M., Allerhand, M., Whittle, I. R., & McCulloch, J. (2010). Network generation enhances interpretation of proteomic data from induced apoptosis. Proteomics, 10(6), 1307-1315.
15. Koh, G. C., Porras, P., Aranda, B., Hermjakob, H., & Orchard, S. E. (2012). Analyzing protein-protein interaction networks. Journal of Proteome Research, 11(4), 2014-2031.
16. White, I. R., Patel, K., Symonds, W. T., Dev, A., Griffin, P., Tsokanas, N., Skehel, M., Liu, C., Zekry, A., Cutler, P., Gattu,M., Rockey, D. C., Berrey,M. M., &McHutchison, J. G. (2007). Serum proteomic analysis focused on fibrosis in patients with hepatitis C virus infection. Journal of Translational Medicine, 5, 33.
17. Ngai, H. H., Sit,W. H., Jiang, P. P., Thongboonkerd, V., &Wan, J. M. (2007). Markedly increased urinary preprohaptoglobin and haptoglobin in passive Heymann nephritis: a differential proteomics approach. Journal of Proteome Research, 6(8), 3313-3320.
18. Ang, I. L., Poon, T. C., Lai, P. B., Chan, A. T., Ngai, S. M., Hui, A. Y., Johnson, P. J., & Sung, J. J. (2006). Study of serum haptoglobin and its glycoforms in the diagnosis of hepatocellular carcinoma: a glycoproteomic approach. Journal of Proteome Research, 5(10), 2691-2700.
19. Ahmed, N., Barker, G., Oliva, K. T., Hoffmann, P., Riley, C., Reeve, S., Smith, A. I., Kemp, B. E., Quinn, M. A., & Rice, G. E. (2004). Proteomic-based identification of haptoglobin-1 precursor as a novel circulating biomarker of ovarian cancer. British Journal of Cancer, 91(1), 129-140.
20. Zhang, A., Sun, H., Yuan, Y., Sun,W., Jiao, G., &Wang, X. (2011). An in vivo analysis of the therapeutic and synergistic properties of Chinese medicinal formula Yin-Chen-Hao-Tang based on its active constituents. Fitoterapia, 82(8), 1160-1168.
21. Heo, M., Maslov, S., & Shakhnovich, E. (2011). Topology of protein interaction network shapes protein abundances and strengths of their functional and nonspecific interactions. Proceedings of the National Academy of Sciences of the United States of America, 108(10), 4258-4263.
22. Lim, S. R., Gooi, B. H., Singh, M., & Gam, L. H. (2011). Analysis of differentially expressed proteins in colorectal cancer using hydroxyapatite column and SDS-PAGE. Applied Biochemistry and Biotechnology, 165(5-6), 1211-1224.
23. Jensen, L. J., Kuhn, M., Stark, M., Chaffron, S., Creevey, C., Muller, J., Doerks, T., Julien, P., Roth, A., Simonovic, M., Bork, P., & von Mering, C. (2009). STRING 8 -A global view on proteins and their functional interactions in 630 organisms. Nucleic Acids Research, 37, D412-D416.
24. Bakal, C., Linding, R., Llense, F., Heffern, E., Martin-Blanco, E., Pawson, T., & Perrimon, N. (2008). Phosphorylation networks regulating JNK activity in diverse genetic backgrounds. Science, 322(5900), 453-456.
25. Gutiérrez-Sánchez, G., Atwood, J., Kolli, V. S., Roussos, S., & Augur, C. (2012). Initial proteome analysis of caffeine-induced proteins in Aspergillus tamarii using two-dimensional fluorescence difference gel electrophoresis. Applied Biochemistry and Biotechnology, 166(8), 2064-2077.
26. Karthik, D., Ilavenil, S., Kaleeswaran, B., Sunil, S., & Ravikumar, S. (2012). Proteomic analysis of plasma proteins in diabetic rats by 2D electrophoresis and MALDI-TOF-MS. Applied Biochemistry and Biotechnology, 166(6), 1507-1519.
27. Wang, X., Zhang, A., Han, Y.,Wang, P., Sun, H., Song, G., Dong, T., Yuan, Y., Yuan, X., Zhang,M., Xie, N., Zhang,H., Dong,H.,&Dong,W. (2012).Urinemetabolomics analysis for biomarker discovery and detection of jaundice syndrome in patients with liver disease. Molecular & Cellular Proteomics, 11(8), 370-380.
28. McDermott, J. E., Diamond, D. L., Corley, C., Rasmussen, A. L., Katze, M. G., & Waters, K. M. (2012). Topological analysis of protein co-Abundance networks identifies novel host targets important for HCV infection and pathogenesis. BMC Systems Biology, 6, 28.
29. Chakraborty, C., Pal, S., Doss, C. G., Wen, Z. H., & Lin, C. S. (2012). In silico analyses of COMT, an important signaling cascade of dopaminergic neurotransmission pathway, for drug development of Parkinson's disease. Applied Biochemistry and Biotechnology, 167(4), 845-860.