dorsal/arxiv
View SchemaGraph theoretic analysis of protein interaction networks of eukaryotes
| Authors | K. -I. Goh, B. Kahng, D. Kim |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0502018 |
| URL | https://arxiv.org/abs/q-bio/0502018 |
| DOI | 10.1016/j.physa.2005.03.044 |
| Journal | Physica A 357, 512 (2005). |
Abstract
Thanks to recent progress in high-throughput experimental techniques, the datasets of large-scale protein interactions of prototypical multicellular species, the nematode worm Caenorhabditis elegans and the fruit fly Drosophila melanogaster, have been assayed. The datasets are obtained mainly by using the yeast hybrid method, which contains false-positive and false-negative simultaneously. Accordingly, while it is desirable to test such datasets through further wet experiments, here we invoke recent developed network theory to test such high throughput datasets in a simple way. Based on the fact that the key biological processes indispensable to maintaining life are universal across eukaryotic species, and the comparison of structural properties of the protein interaction networks (PINs) of the two species with those of the yeast PIN, we find that while the worm and the yeast PIN datasets exhibit similar structural properties, the current fly dataset, though most comprehensively screened ever, does not reflect generic structural properties correctly as it is. The modularity is suppressed and the connectivity correlation is lacking. Addition of interlogs to the current fly dataset increases the modularity and enhances the occurrence of triangular motifs as well. The connectivity correlation function of the fly, however, remains distinct under such interlogs addition, for which we present a possible scenario through an in silico modeling.
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"abstract": "Thanks to recent progress in high-throughput experimental techniques, the\ndatasets of large-scale protein interactions of prototypical multicellular\nspecies, the nematode worm Caenorhabditis elegans and the fruit fly Drosophila\nmelanogaster, have been assayed. The datasets are obtained mainly by using the\nyeast hybrid method, which contains false-positive and false-negative\nsimultaneously. Accordingly, while it is desirable to test such datasets\nthrough further wet experiments, here we invoke recent developed network theory\nto test such high throughput datasets in a simple way. Based on the fact that\nthe key biological processes indispensable to maintaining life are universal\nacross eukaryotic species, and the comparison of structural properties of the\nprotein interaction networks (PINs) of the two species with those of the yeast\nPIN, we find that while the worm and the yeast PIN datasets exhibit similar\nstructural properties, the current fly dataset, though most comprehensively\nscreened ever, does not reflect generic structural properties correctly as it\nis. The modularity is suppressed and the connectivity correlation is lacking.\nAddition of interlogs to the current fly dataset increases the modularity and\nenhances the occurrence of triangular motifs as well. The connectivity\ncorrelation function of the fly, however, remains distinct under such interlogs\naddition, for which we present a possible scenario through an in silico\nmodeling.",
"arxiv_id": "q-bio/0502018",
"authors": [
"K. -I. Goh",
"B. Kahng",
"D. Kim"
],
"categories": [
"q-bio.MN"
],
"doi": "10.1016/j.physa.2005.03.044",
"journal_ref": "Physica A 357, 512 (2005).",
"title": "Graph theoretic analysis of protein interaction networks of eukaryotes",
"url": "https://arxiv.org/abs/q-bio/0502018"
},
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