Revisiting the centrality–lethality hypothesis

On 27 August, 2013

Mtb_700_centrality_lethalityProtein networks, describing physical interactions as well as functional associations between proteins, have been unravelled for many organisms in the recent past. Databases such as the STRING provide excellent resources for the analysis of such networks. In this contribution, we revisit the organisation of protein networks, particularly the centrality–lethality hypothesis, which hypothesises that nodes with higher centrality in a network are more likely to produce lethal phenotypes on removal, compared to nodes with lower centrality. We consider the protein networks of a diverse set of 20 organisms, with essentiality information available in the Database of Essential Genes and assess the relationship between centrality measures and lethality. For each of these organisms, we obtained networks of high confidence interactions from the STRING database, and computed network parameters such as degree, betweenness centrality, closeness centrality and pairwise disconnectivity indices.

We observe that the networks considered here are predominantly disassortative. Further, we observe that essential nodes in a network have a significantly higher average degree and betweenness centrality, compared to the network average. Most previous studies have evaluated the centrality–lethality hypothesis for Saccharomyces cerevisiae and Escherichia coli; we here observe that the centrality–lethality hypothesis hold goods for a large number of organisms, with certain limitations. Betweenness centrality may also be a useful measure to identify essential nodes, but measures like closeness centrality and pairwise disconnectivity are not significantly higher for essential nodes.

Original Paper: 

  • [DOI] K. Raman, N. Damaraju, and G. K. Joshi, “The organisational structure of protein networks: revisiting the centrality–lethality hypothesis,” Systems and Synthetic Biology, vol. 8, iss. 1, pp. 73-81, 2014.
    [bibtex]
    @article{Raman2014Organisational,
      abstract = {Protein networks, describing physical interactions as well as functional associations between proteins, have been unravelled for many organisms in the recent past. Databases such as the {STRING} provide excellent resources for the analysis of such networks. In this contribution, we revisit the organisation of protein networks, particularly the centrality–lethality hypothesis, which hypothesises that nodes with higher centrality in a network are more likely to produce lethal phenotypes on removal, compared to nodes with lower centrality. We consider the protein networks of a diverse set of 20 organisms, with essentiality information available in the Database of Essential Genes and assess the relationship between centrality measures and lethality. For each of these organisms, we obtained networks of high-confidence interactions from the {STRING} database, and computed network parameters such as degree, betweenness centrality, closeness centrality and pairwise disconnectivity indices. We observe that the networks considered here are predominantly disassortative. Further, we observe that essential nodes in a network have a significantly higher average degree and betweenness centrality, compared to the network average. Most previous studies have evaluated the centrality–lethality hypothesis for Saccharomyces cerevisiae and Escherichia coli; we here observe that the centrality–lethality hypothesis hold goods for a large number of organisms, with certain limitations. Betweenness centrality may also be a useful measure to identify essential nodes, but measures like closeness centrality and pairwise disconnectivity are not significantly higher for essential nodes.},
      added-at = {2018-12-02T16:09:07.000+0100},
      author = {Raman, Karthik and Damaraju, Nandita and Joshi, Govind K.},
      biburl = {https://www.bibsonomy.org/bibtex/20691cb0a4fc6369cd4a1a26431f4ec25/karthikraman},
      booktitle = {Systems and Synthetic Biology},
      doi = {10.1007/s11693-013-9123-5},
      interhash = {f6d38f674f700948f52f300f89824891},
      intrahash = {0691cb0a4fc6369cd4a1a26431f4ec25},
      issn = {1872-5333},
      journal = {Systems and Synthetic Biology},
      keywords = {centrality gene-essentiality lethality myown networks protein-protein-interactions},
      month = mar,
      number = 1,
      pages = {73--81},
      posted-at = {2013-08-27 04:40:08},
      priority = {2},
      timestamp = {2019-04-17T12:59:21.000+0200},
      title = {The organisational structure of protein networks: revisiting the centrality--lethality hypothesis},
      url = {http://dx.doi.org/10.1007/s11693-013-9123-5},
      volume = 8,
      year = 2014
    }

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