Brief. Bioinformatics - Identifying protein complexes and functional modules--from static PPI networks to dynamic PPI networks.

Tópicos

{ network(2748) neural(1063) input(814) }
{ sequenc(1873) structur(1644) protein(1328) }
{ framework(1458) process(801) describ(734) }
{ analysi(2126) use(1163) compon(1037) }
{ model(2656) set(1616) predict(1553) }
{ algorithm(1844) comput(1787) effici(935) }
{ import(1318) role(1303) understand(862) }
{ use(976) code(926) identifi(902) }
{ use(1733) differ(960) four(931) }
{ implement(1333) system(1263) develop(1122) }
{ system(1976) rule(880) can(841) }
{ studi(2440) review(1878) systemat(933) }
{ general(901) number(790) one(736) }
{ gene(2352) biolog(1181) express(1162) }
{ chang(1828) time(1643) increas(1301) }
{ extract(1171) text(1153) clinic(932) }
{ method(984) reconstruct(947) comput(926) }
{ case(1353) use(1143) diagnosi(1136) }
{ visual(1396) interact(850) tool(830) }
{ model(3480) simul(1196) paramet(876) }
{ signal(2180) analysi(812) frequenc(800) }
{ cost(1906) reduc(1198) effect(832) }
{ group(2977) signific(1463) compar(1072) }
{ sampl(1606) size(1419) use(1276) }
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{ drug(1928) target(777) effect(648) }
{ activ(1452) weight(1219) physic(1104) }
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{ bind(1733) structur(1185) ligand(1036) }
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{ design(1359) user(1324) use(1319) }
{ control(1307) perform(991) simul(935) }
{ model(2220) cell(1177) simul(1124) }
{ care(1570) inform(1187) nurs(1089) }
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{ risk(3053) factor(974) diseas(938) }
{ perform(999) metric(946) measur(919) }
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{ system(1050) medic(1026) inform(1018) }
{ model(2341) predict(2261) use(1141) }
{ compound(1573) activ(1297) structur(1058) }
{ perform(1367) use(1326) method(1137) }
{ studi(1119) effect(1106) posit(819) }
{ blood(1257) pressur(1144) flow(957) }
{ spatial(1525) area(1432) region(1030) }
{ record(1888) medic(1808) patient(1693) }
{ health(3367) inform(1360) care(1135) }
{ monitor(1329) mobil(1314) devic(1160) }
{ ehr(2073) health(1662) electron(1139) }
{ state(1844) use(1261) util(961) }
{ research(1218) medic(880) student(794) }
{ patient(2837) hospit(1953) medic(668) }
{ data(2317) use(1299) case(1017) }
{ age(1611) year(1155) adult(843) }
{ medic(1828) order(1363) alert(1069) }
{ data(3008) multipl(1320) sourc(1022) }
{ intervent(3218) particip(2042) group(1664) }
{ activ(1138) subject(705) human(624) }
{ time(1939) patient(1703) rate(768) }
{ patient(1821) servic(1111) care(1106) }
{ use(2086) technolog(871) perceiv(783) }
{ can(981) present(881) function(850) }
{ health(1844) social(1437) communiti(874) }
{ high(1669) rate(1365) level(1280) }
{ cancer(2502) breast(956) screen(824) }
{ result(1111) use(1088) new(759) }
{ survey(1388) particip(1329) question(1065) }
{ estim(2440) model(1874) function(577) }
{ decis(3086) make(1611) patient(1517) }
{ process(1125) use(805) approach(778) }
{ method(1969) cluster(1462) data(1082) }
{ method(2212) result(1239) propos(1039) }

Resumo

Cellular processes are typically carried out by protein complexes and functional modules. Identifying them plays an important role for our attempt to reveal principles of cellular organizations and functions. In this article, we review computational algorithms for identifying protein complexes and/or functional modules from protein-protein interaction (PPI) networks. We first describe issues and pitfalls when interpreting PPI networks. Then based on types of data used and main ideas involved, we briefly describe protein complex and/or functional module identification algorithms in four categories: (i) those based on topological structures of unweighted PPI networks; (ii) those based on characters of weighted PPI networks; (iii) those based on multiple data integrations; and (iv) those based on dynamic PPI networks. The PPI networks are modelled increasingly precise when integrating more types of data, and the study of protein complexes would benefit by shifting from static to dynamic PPI networks.

Resumo Limpo

cellular process typic carri protein complex function modul identifi play import role attempt reveal principl cellular organ function articl review comput algorithm identifi protein complex andor function modul proteinprotein interact ppi network first describ issu pitfal interpret ppi network base type data use main idea involv briefli describ protein complex andor function modul identif algorithm four categori base topolog structur unweight ppi network ii base charact weight ppi network iii base multipl data integr iv base dynam ppi network ppi network model increas precis integr type data studi protein complex benefit shift static dynam ppi network

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