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Analysing protein–protein interaction networks of human liver cancer cell lines with diverse metastasis potential

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Abstract

Purpose

Human hepatocellular carcinoma (HCC) is one of the most mortal tumor. In a previous study, we had constructed glycoprotein expression profiles and glycoprotein databases of three human liver cancer cell lines with diverse metastasis potential. In order to discover vital glycoproteins related to pathogenesis and metastasis of HCC, in this study we analyzed previous data with bioinformatic approach.

Methods

We took previous data to draw the protein–protein interaction (PPI) networks of liver cell lines by searching IntACT database and then using Pajeck software. Further more, we compared the differences between the three PPI networks by drawing the PPI networks of differential glycoproteins and by naming differential display PPI networks.

Results

Large numbers of proliferation and apoptosis-relative proteins interact with the differential glycoproteins, and among the differential glycoproteins there are many interactions.

Conclusions

We conclude that neither single nor several proteins cause malignant proliferation of liver cells. “Molecule groups” concept should be introduced into diagnosis and metastasis prediction of the HCC.

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Abbreviations

HCC:

Human hepatocellular carcinoma

PPI:

Protein–protein interaction network

References

  • Armano G, Mancosu G, Milanesi L (2005) A hybrid genetic-neural system for predicting protein secondary structure. BMC Bioinformatics 6(Suppl 4):S3

    Article  PubMed  Google Scholar 

  • Batagelj V, Mrvar A (1998) Pajek–program for large network analysis. Connections 21:47–57

    Google Scholar 

  • Chagoyen M, Carmona-Saez P, Shatkay H (2006) Discovering semantic features in the literature: a foundation for building functional associations. BMC Bioinformatics 7:41

    Article  PubMed  Google Scholar 

  • Deeds EJ, Ashenberg O, Shakhnovich E (2006) A simple physical model for scaling in protein–protein interaction networks. PNAS 103:311–316

    Article  PubMed  CAS  Google Scholar 

  • Englbrecht CC, Facius A (2005) Bioinformatics challenges in proteomics. Comb Chem High Throughput Screen 8:705–715

    Article  PubMed  CAS  Google Scholar 

  • Fung ET, Weinberger SR, Gavin E (2005) Bioinformatics approaches in clinical proteomics. Expert Rev Proteomics 2:847–862

    Article  PubMed  CAS  Google Scholar 

  • Hermjakob H, Montecchi-Palazzi L, Bader G, Wojcik J, Salwinski L, Ceol A, Moore S, Orchard S, Sarkans U, Mering CV, Roechert B, Poux S, Jung E, Mersch H, Kersey P, Lappe M, Lix Y, Zeng R, Rana D, Nikolski M, Husi H, Brun C, Shanker K, Grant SGN, Sander C, Bork P, Zhu WM, Pandey A, Brazma A, Jacq B, Vidal M, Sherman D, Legrain P, Cesareni G, Xenarios I, Eisenberg D, Steipe B, Hogue C, Apweiler R (2004a) The HUPO PSI molecular interaction format–a community standard for the representation of protein interaction data. Nat Biotechnol 22:177–183

    Article  PubMed  CAS  Google Scholar 

  • Hermjakob H, Montecchi-Palazzi L, Lewington C, Mudali S, Kerrien S, Orchard S, Vingron M, Roechert B, Roepstorff P, Valencia A, Margalit H, Armstrong J, Bairoch A, Cesareni G, Sherman D, Apweiler R (2004b) IntAct–an open source molecular interaction database. Nucl Acids Res 32:452–455

    Article  Google Scholar 

  • Iragne F, Nikolski M, Mathieu B, Auber D, Sherman D (2005) ProViz is a tool for the visualization of protein–protein interaction networks, developed by the IntAct European project. Bioinformatics 21:272–274

    Article  PubMed  CAS  Google Scholar 

  • Kremer A, Schneider R, Terstappen GC (2005) A bioinformatics perspective on proteomics: data storage, analysis, and integration. Biosci Rep 25:95–106

    Article  PubMed  CAS  Google Scholar 

  • Ludemann A, Weicht D, Selbig J, Kopka J (2004) PaVESy: Pathway visualization and editing system. Bioinformatics 20:2841–2844

    Article  PubMed  Google Scholar 

  • Thorgeirsson SS, Lee JS, Grisham JW (2006) Functional genomics of hepatocellular carcinoma. Hepatology 43:S145–S150

    Article  PubMed  CAS  Google Scholar 

  • Uetz P, Dong YA, Zeretzke C, Atzler C, Baiker A, Berger B, Rajagopala SV, Roupelieva M, Rose D, Fossum E, Haas J (2006) Herpesviral protein networks and their Interaction with the human Proteome. Science 311:239–242

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgments

This research was supported by National Basic 425 Research Priorities Programme (001CB510205), National Nature 426 Science Foundation (30170416) and National Tenth Five-Year Plan Key Scientific Programme (2004BA703B02).

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Authors and Affiliations

  1. Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, 200032, China

    Hai-jun Zhou, Yin-kun Liu, Qiang-ling Shun & Kun Guo

  2. Department of Pulmonology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China

    Zhuozhe Li

  3. Department of Chemistry, Fudan University, Shanghai, 200433, China

    Dong Yun

Authors
  1. Hai-jun Zhou
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  2. Yin-kun Liu
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  3. Zhuozhe Li
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  4. Dong Yun
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  5. Qiang-ling Shun
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  6. Kun Guo
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Corresponding author

Correspondence to Yin-kun Liu.

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Zhou, Hj., Liu, Yk., Li, Z. et al. Analysing protein–protein interaction networks of human liver cancer cell lines with diverse metastasis potential. J Cancer Res Clin Oncol 133, 663–672 (2007). https://doi.org/10.1007/s00432-007-0218-9

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  • DOI: https://doi.org/10.1007/s00432-007-0218-9

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