MOTIVATION: Many genomes have been completely sequenced. However, detecting and analyzing their protein-protein interactions by experimental methods such as co-immunoprecipitation, tandem affinity purification and Y2H is not as fast as genome sequencing. Therefore, a computational prediction method based on the known protein structural interactions will be useful to analyze large-scale protein-protein interaction rules within and among complete genomes. 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 to have played a key role in species diversification. SUPPLEMENTARY INFORMATION: http://interactomics.org.
MOTIVATION: Many genomes have been completely sequenced. However, detecting and analyzing their protein-protein interactions by experimental methods such as co-immunoprecipitation, tandem affinity purification and Y2H is not as fast as genome sequencing. Therefore, a computational prediction method based on the known protein structural interactions will be useful to analyze large-scale protein-protein interaction rules within and among complete genomes. 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 to have played a key role in species diversification. SUPPLEMENTARY INFORMATION: http://interactomics.org.
Authors: Jaroslav Kubrycht; Karel Sigler; Michal Růzicka; Pavel Soucek; Jirí Borecký; Petr Jezek Journal: J Mol Evol Date: 2006-10-06 Impact factor: 2.395
Authors: Andrés F Flórez; Daeui Park; Jong Bhak; Byoung-Chul Kim; Allan Kuchinsky; John H Morris; Jairo Espinosa; Carlos Muskus Journal: BMC Bioinformatics Date: 2010-09-27 Impact factor: 3.169
Authors: Timothy Ravasi; Harukazu Suzuki; Carlo Vittorio Cannistraci; Shintaro Katayama; Vladimir B Bajic; Kai Tan; Altuna Akalin; Sebastian Schmeier; Mutsumi Kanamori-Katayama; Nicolas Bertin; Piero Carninci; Carsten O Daub; Alistair R R Forrest; Julian Gough; Sean Grimmond; Jung-Hoon Han; Takehiro Hashimoto; Winston Hide; Oliver Hofmann; Atanas Kamburov; Mandeep Kaur; Hideya Kawaji; Atsutaka Kubosaki; Timo Lassmann; Erik van Nimwegen; Cameron Ross MacPherson; Chihiro Ogawa; Aleksandar Radovanovic; Ariel Schwartz; Rohan D Teasdale; Jesper Tegnér; Boris Lenhard; Sarah A Teichmann; Takahiro Arakawa; Noriko Ninomiya; Kayoko Murakami; Michihira Tagami; Shiro Fukuda; Kengo Imamura; Chikatoshi Kai; Ryoko Ishihara; Yayoi Kitazume; Jun Kawai; David A Hume; Trey Ideker; Yoshihide Hayashizaki Journal: Cell Date: 2010-03-05 Impact factor: 41.582