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Therefore, a computational prediction method based on the known protein structural interactions will be useful to analyze large-scale protein\u2013protein interaction rules within and among complete genomes.<\/jats:p><jats:p>Results: We confirmed that all the predicted protein family interactomes (the full set of protein family interactions within a proteome) of 146 species are scale-free networks, and they share a small core network comprising 36 protein families related to indispensable cellular functions. We found two fundamental differences among prokaryotic and eukaryotic interactomes: (1) eukarya had significantly more hub families than archaea and bacteria and (2) certain special hub families determined the topology of the eukaryotic interactomes. Our comparative analysis suggests that a very small number of expansive protein families led to the evolution of interactomes and seemed tohave played a key role in species diversification.<\/jats:p><jats:p>Contact: \u00a0jong@kribb.re.kr<\/jats:p><jats:p>Supplementary information: \u00a0http:\/\/interactomics.org<\/jats:p>","DOI":"10.1093\/bioinformatics\/bti512","type":"journal-article","created":{"date-parts":[[2005,5,25]],"date-time":"2005-05-25T02:38:44Z","timestamp":1116988724000},"page":"3234-3240","source":"Crossref","is-referenced-by-count":26,"title":["Comparative interactomics analysis of protein family interaction networks using PSIMAP (protein structural interactome map)"],"prefix":"10.1093","volume":"21","author":[{"given":"Daeui","family":"Park","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Semin","family":"Lee","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dan","family":"Bolser","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael","family":"Schroeder","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael","family":"Lappe","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Donghoon","family":"Oh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jong","family":"Bhak","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2005,5,24]]},"reference":[{"key":"2023051612003945600_B1","doi-asserted-by":"crossref","unstructured":"Alexandrov, N.N. and Go, N. 1994Biological meaning, statistical significance and classification of local spatial similarities in nonhomologous proteins. 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