HKC: An Algorithm to Predict Protein Complexes in Protein-Protein Interaction Networks

Table 2

All novel predictions by HKC on MIPS data set. Each column gives the original ID of clusters (ID), cluster score (S), number of nodes (N), number of edges (E), and the protein names in each cluster.

ID	𝑆	𝑁	𝐸	Protein names
1	21.5	38	406	YLR200w,YNL153c,YDR318w,YOR349w,YHR191c,YEL003w,YJL013c,YLR085c,YPL269w,YHR129c,YOR026w,YMR055c,YPL155c,YCL029c,YMR048w, YML094w,YJL030w,YGR188c,YCL016c,YPR135w,YML124c,YPR141c,YER016w,YOR058c,YER007w,YDR150w,YGR078c,YJR053w,YEL061c, YMR294w,YMR299c,YPL008w,YMR078c,YGL086w,YPL174c,YFL037w,YOL012c,YPL241c
2	20.1	33	328	YPL008w,YMR078c,YGR188c,YGL086w,YCL016c,YPL241c,YMR294w,YER007w,YOR058c,YER016w,YPR141c,YPR135w,YJL030w,YPL155c,YOR026w, YHR129c,YPL269w,YJL013c,YDR254w,YDR318w,YFL037w,YPL174c,YEL061c,YGR078c,YLR200w,YML124c,YML094w,YCL029c,YEL003w,YOR349w, YNL153c,YMR138w,YOR265w
3	19.7	27	260	YGL086w,YMR078c,YCL016c,YGR188c,YMR048w,YOR026w,YJL013c,YHR191c,YOR349w,YDR318w,YPL008w,YEL061c,YGR078c,YLR200w,YER016w, YPR141c,YPR135w,YJL030w,YML094w,YEL003w,YNL153c,YDL003w,YDR254w,YJR135c,YPR046w,YPL018w,YLR381w
4	18. 9	28	260	YGR188c,YLR381w,YPL018w,YDR254w,YDR318w,YOL012c,YGL086w,YPL008w,YGR078c,YDL003w,YLR200w,YML094w,YMR048w,YLR085c, YEL003w,YOR349w,YNL153c,YNL298w,YMR078c,YEL061c,YER016w,YPR141c,YPR135w,YCL016c,YJL030w,YHR191c, YOR195w,YGL216w
5	15.2	24	179	YNL271c,YNL322c,YBL061c,YBR023c,YGR229c,YBL007c,YER155c,YLR330w,YHR030c,YNL298w,YDL029w,YJR075w,YGR078c,YLR200w,YLR337c, YML094w,YDR388w,YCR009c,YBR234c,YEL003w,YJL095w,YNL153c,YJL020c,YMR109w
6	15.2	25	185	YER155c,YEL003w,YGR078c,YML094w,YNL271c,YGR229c,YNL298w,YLR337c,YNL153c,YLR200w,YHR030c,YBL007c,YCR009c,YJL095w,YDR245w, YBL061c,YHR142w,YLR330w, YDL029w,YDR388w,YBR023c,YBR234c,YJR075w,YNL322c,YDR129c
7	14.8	27	196	YBL007c,YEL003w,YGR078c,YLR200w,YML094w,YNL153c,YNL298w,YJL095w,YHR111w,YGR229c,YBR234c,YCR009c,YER111c,YBR023c,YDR388w, YHR030c,YDL029w,YLR330w,YHR142w,YDR424c,YNL271c,YFR019w,YBL061c,YPL031c,YBR200w,YER155c,YOR326w
8	14.6	25	178	YLR337c,YNL322c,YNL271c,YBL007c,YLR200w,YBL061c,YHR142w,YLR330w,YML094w,YBR023c,YNL233w,YCR009c,YJR075w,YNL153c,YNL298w, YDL029w,YHR030c,YJL183w,YDR388w,YBR234c,YGR229c,YLR342w,YJL095w,YJL099w,YJR118c
9	14.3	21	146	YNL250w,YER016w,YPR141c,YHR191c,YGL163c,YMR078c,YMR190c,YKL113c,YOR144c,YCL061c,YER173w,YPR135w,YCL016c,YMR048w,YLR234w, YJL092w,YLR103c,YML032c,YPL194w,YNL273w,YJR043c
10	14.3	21	147	YML032c,YER016w,YJR043c,YMR078c,YNL273w,YLR103c,YPR135w,YCL016c,YMR048w,YHR191c,YGL163c,YMR190c,YDR004w,YOR144c,YER095w, YCL061c,YDR076w,YER173w,YNL250w,YJL092w,YKL113c
11	14.2	21	146	YNL298w,YHR030c,YJL095w,YMR109w,YBR023c,YDL029w,YBR234c,YGR078c,YLR200w,YBL061c,YML094w,YDR388w,YJL020c,YCR009c,YGR229c, YEL003w,YNL153c,YLR337c,YEL031w,YBL007c,YJR075w
13	13.9	23	155	YLR200w,YNL271c,YNL153c,YBR234c,YNL322c,YHR142w,YER111c,YBL007c,YCR009c,YGR229c,YJL095w,YNL298w,YLR330w,YBR023c,YJR075w, YBL061c,YDL029w,YHR030c,YJR118c,YDR388w,YBL047c,YNL233w,YLR342w
14	13.7	23	153	YHR191c,YML032c,YHR031c,YMR078c,YCL061c,YCL016c,YMR048w,YNL273w,YNL250w,YPR135w,YMR190c,YKL113c,YLR234w,YJR043c,YOR144c, YLR103c,YJL092w,YOL006c,YPL024w, YBR098w,YDR386w,YLR235c,YDR363w
15	13.6	23	154	YER173w,YKL113c,YML032c,YNL273w,YOR144c,YMR048w,YJR043c,YMR078c,YCL061c,YLR103c,YPR135w,YCL016c,YHR191c,YMR190c,YPL024w, YDR052c,YNL250w,YHR031c,YLR235c,YLR234w,YJL092w,YDL017w,YHR154w
16	13.3	21	136	YPL194w,YML032c,YNL250w,YJL092w,YLR103c,YMR078c,YCL016c,YHR191c,YGL163c,YJR043c,YMR190c,YKL113c,YNL273w,YCL061c,YER016w, YER173w,YPR135w,YMR048w,YOR144c,YDL013w,YER116c
17	12.9	22	138	YER016w,YGL163c,YHR191c,YNL273w,YML032c,YLR103c,YMR078c,YKL113c,YOR144c,YCL061c,YPR135w,YNL250w,YCL016c,YHR031c,YMR048w, YLR234w,YJL092w,YJR043c,YMR190c,YDR363w,YBR228w,YLR135w
20	10.8	13	66	YER146w,YDR378c,YNL147w,YLR438c-a,YER112w,YJL124c,YCR077c,YBL026w,YJR022w,YOL149w,YGL173c,YNL118c,YEL015w
21	10.8	11	54	YBL026w,YER146w,YDR378c,YJR022w,YNL147w,YLR438c-a,YER112w,YOL149w,YJL124c,YCR077c,YGL173c
24	10	17	82	YBL061c,YDR388w,YBR023c,YJL095w,YNL298w,YNL271c,YLR330w,YHR030c,YER111c,YGR229c,YER155c,YPL031c,YMR307w,YOR008c,YLR342w, YLR371w,YLR332w
25	9.9	17	81	YJL095w,YDL029w,YCR009c,YNL298w,YBL061c,YDR388w,YER111c,YGR229c,YNL322c,YLR330w,YHR030c,YBR023c,YMR307w,YGL027c,YML115c, YGL200c,YPR159w
26	9.5	17	78	YNL298w,YDR388w,YER111c,YNL271c,YLR330w,YHR030c,YBL061c,YBR023c,YNL322c,YMR307w,YLR039c,YLR262c,YGR229c,YLR342w,YJR073c, YJL183w,YKL190w
27	8.6	14	56	YLR039c,YPL051w,YLR262c,YJL154c,YDR126w,YGL005c,YOR132w,YOR069w,YNL051w,YHL031c,YNL041c,YOR070c,YML071c,YBR164c
28	8.5	14	55	YOL012c,YLR039c,YLR262c,YLR085c,YLR418c,YAL011w,YAL013w,YMR263w,YJL168c,YML041c,YGL244w,YPL181w,YDR334w,YOR123c
29	7.7	13	46	YNL051w,YHL031c,YPL051w,YOR070c,YNL041c,YLR262c,YML071c,YDR126w,YKL190w,YLR039c,YBR164c,YKR001c,YMR004w
30	7.6	11	39	YBR023c,YKL190w,YNL322c,YHR030c,YGR229c,YMR307w,YJR073c,YLR262c,YDR162c,YLR039c,YDL006w
31	7.5	13	45	YNL051w,YML071c,YPL051w,YOR070c,YNL041c,YLR262c,YOL018c,YDR126w,YHL031c,YBR164c,YLR039c,YNL238w,YLL040c
39	6	17	51	YBR200w,YNL298w,YOR127w,YHR061c,YHL007c,YER149c,YGR152c,YLL021w,YPL115c,YLR319c,YDR309c,YBL085w,YAL041w,YER114c,YOR188w, YMR273c,YLR229c
40	6	8	25	YCR088w,YOR284w,YGR268c,YDR388w,YBL007c,YNL094w,YNL243w,YHR016c
42	6	7	18	YER155c,YAL040c,YDL047w,YKR028w,YJL098w,YFR040w,YKR072c
43	5.8	10	27	YMR263w,YOR123c,YLR085c,YGL244w,YML041c,YJL168c,YAL013w,YLR418c,YBL008w,YOR038c
48	5.5	8	26	YIL144w,YDR201w,YFL008w,YOL069w,YFR031c,YEL043w,YDL074c,YJL074c
50	5.3	17	55	YLR347c,YNL189w,YML064c,YLR082c,YLR245c,YDR321w,YPL070w,YBR176w,YNL044w,YNL331c,YPL124w,YER023w,YLR423c,YJR056c,YEL066w, YJL218w,YNR012w
51	5.3	9	26	YOR284w,YJL199c,YNL189w,YML064c,YBR176w,YLR245c,YPL070w,YLR291c,YHL018w
55	4.9	8	18	YHR066w,YPL093w,YER006w,YPL211w,YMR049c,YMR290c,YNL002c,YGR103w
56	4.9	8	17	YGL244w,YLR039c,YLR262c,YOR216c,YLR085c,YLR418c,YIR005w,YGL174w
59	4.5	17	49	YML064c,YNL189w,YLR347c,YGR010w,YKL067w,YFR047c,YGL175c,YOR020c,YLR328w,YLR335w,YGL040c,YGL037c,YNL333w,YFL059w,YPL111w, YGR267c,YLR377c
60	4.5	5	11	YFL059w,YNL333w,YMR322c,YMR095c,YMR096w
61	4.5	5	10	YNL214w,YDR244w,YGL153w,YDR142c,YLR191w
65	4.4	6	12	YLR310c,YLL016w,YAL024c,YNL098c,YAR019c,YOR101w
70	4.3	7	16	YML064c,YPL124w,YLR423c,YPL070w,YDR148c,YER086w,YDL239c
71	4.3	7	14	YDL226c,YGR172c,YLR324w,YGL198w,YDR425w,YGL161c,YPL095c
73	4.3	7	14	YLR347c,YMR047c,YKL068w,YBR216c,YML007w,YER107c,YDL207w
74	4.3	7	14	YLR039c,YPL234c,YKL190w,YLR262c,YER081w,YHR060w,YGR020c
77	4	5	11	YER093c,YJL058c,YJR066w,YKL203c,YNL006w
78	4	5	12	YKL203c,YJR066w,YNL006w,YHR186c,YPL180w
82	4	5	8	YLR039c,YLR262c,YCR020c-a,YPR051w,YEL053c
90	4	5	8	YAR019c,YGR092w,YDL047w,YPR111w,YIL106w
93	4	5	8	YLR039c,YOR070c,YBR036c,YMR272c,YPL057c
94	4	5	8	YMR197c,YHL031c,YLR026c,YKL006c-a,YKL196c