实战--酵母基因表达数据的聚类分析

Posted 2021-01-17 lokwongho

背景：酵母会在一定的时期发生diauxic shift，有一些基因的表达上升，有一些基因表达被抑制，通过聚类算法，将基因表达的变化模式聚成6类。

ORF	Name	R1.Ratio	R2.Ratio	R3.Ratio	R4.Ratio	R5.Ratio	R6.Ratio	R7.Ratio
1	YDR025W	RPS18A	0.136061549576028	-0.111031312388744	-0.189033824390017	-0.782408564927373	-0.75702324650746	-0.855989697308481	-2.30451104180995
2	YDR031w		-0.286881147788162	-0.0840642647884746	0.184424571137428	0.136061549576028	0.535331732996556	2.32192809488736	1.25153876699596
3	YDR060w		-0.0426443374084937	-0.0976107966264223	-0.0143552929770701	-0.799087306074004	-0.839959587489532	-2.24792751344359	-2.38681094647222
4	YDR064W	YS15	-0.0565835283663676	-0.124328135002202	-0.070389327891398	-0.545968369105293	-0.55581615506164	-2.10433665981474	-2.36737106564853
5	YDR070c		0.0144995696951152	0.0740005814437768	0.0588936890535686	0.0144995696951152	0.251538766995964	2.39592867633114	1.68965987938785
6	YDR144C	MKC7	0.136061549576028	-0.0426443374084937	-0.298658315564515	-0.871843648509318	-1.14404636961671	-2.42223300068305	-2.72246602447109
7	YDR171W	HSP42	0.0740005814437768	0.136061549576028	0.434402824145775	0.836501267717121	0.943416471633632	3.64385618977472	3.32192809488736
8	YDR178W	SDH4	-0.189033824390017	-0.028569152196771	0.599462070416271	0.888968687611256	0.836501267717121	2.55639334852439	2.64385618977472
9	YDR258C	HSP78	-0.250961573533219	0.136061549576028	-0.22650852980868	0.862496476250065	0.62148837674627	2.55639334852439	2.39592867633114
10	YBL015W	ACH1	-0.111031312388744	0.0588936890535686	0.0144995696951152	0.104697378666693	0.3040061868901	2.73696559416621	3.32192809488736
11	YDR272W	GLO2	-0.028569152196771	-0.0976107966264223	0.358453970912476	0.434402824145775	0.377069649079823	2.55639334852439	1.25153876699596
12	YDR272W		0.0740005814437768	0.3040061868901	0.494109070270043	0.473931188332412	0.377069649079823	2.32192809488736	1.47393118833241
13	YDR342C	HXT7	0.184424571137428	0.434402824145775	0.943416471633632	1.51457317282976	1.64385618977472	2.32192809488736	1.59946207041627
14	YDR343C	HXT6	0.15200309344505	0.761213140412884	1.28630418515664	1.94341647163363	1.51457317282976	2.18442457113743	2.64385618977472
15	YBL027W	RPL19A	0.0439433475875972	0.0144995696951152	0.395928676331139	-0.16349873228288	-0.27500704749987	-1.11103131238874	-2.44360665147561
16	YDR382W	RPLA4	0.104697378666693	0.15200309344505	0.104697378666693	0.0588936890535686	0.0439433475875972	-0.604071323668861	-2.36457243229586
17	YDR398W		-0.0143552929770701	-0.0840642647884746	-0.124328135002202	-1.03562390973072	-1.1243281350022	-2.02147972741045	-2.799087306074
18	YDR417C		0.321928094887362	0.120294233717712	0.0892673380970873	-0.344828496997441	-0.250961573533219	-1.64616265715789	-2.54596836910529
19	YDR418W	RPL15A	0.200912693925996	0.168122758808327	0.286304185156641	-0.20163386116965	-0.20163386116965	-1.75274859140713	-2.99638874644762
20	YDR516C		-0.137503523749935	0.2688167584278	0.415037499278844	0.785875194647153	0.713118852211838	2.32192809488736	1.02914634565952
21	YBL043W		-0.516015147003665	0.0740005814437768	0	-0.214124805352847	-0.53605290024021	1.94341647163363	2.32192809488736
22	YDR529C	QCR7	0.168122758808327	0.0291463456595165	0.377069649079823	0.862496476250065	0.810966175609983	2.18442457113743	2.55639334852439
23	YDR533C		-0.070389327891398	0.0588936890535686	0.577766999316952	0.415037499278844	0.0144995696951152	2.73696559416621	2.39592867633114
24	YBL045C	COR1	0.0740005814437768	0	0.68965987938785	0.514573172829758	0.15200309344505	1.68965987938785	2.47393118833241
25	YEL011w	GLC3	-0.286881147788162	0.120294233717712	0.494109070270043	0.836501267717121	0.494109070270043	2.64385618977472	2.83650126771712
26	YEL012w	UBC8	-0.0840642647884746	-0.298658315564515	0.0740005814437768	0.0740005814437768	-0.356143810225275	1.32192809488736	2.32192809488736
27	YEL024w	RIP1	0.0892673380970873	0.2688167584278	0.556393348524385	0.888968687611256	0.943416471633632	1.94341647163363	2.32192809488736
28	YBL048W		-0.250961573533219	0.104697378666693	-0.150559676575381	-0.22650852980868	-0.356143810225275	2.55639334852439	2.18442457113743
29	YBL049W		-0.584962500721156	0.168122758808327	0.184424571137428	-0.150559676575381	-0.823749360308273	2.47393118833241	2.64385618977472
30	YEL054c	RPL15A	0.200912693925996	0.0892673380970873	0.321928094887362	-0.321928094887362	-0.475084882948783	-1.64154602908752	-2.46466826700344
31	YER024w		-0.27500704749987	-0.150559676575381	0.168122758808327	-0.356143810225275	-0.495695162624069	1.12029423371771	3.18442457113743
32	YER053c		-0.189033824390017	0.358453970912476	1.02914634565952	1.51457317282976	1.64385618977472	2.18442457113743	2.64385618977472
33	YER065c	ICL1	0.120294233717712	0.168122758808327	0.535331732996556	0.0892673380970873	-0.150559676575381	0.535331732996556	3.64385618977472
34	YER067w		-0.070389327891398	0.15200309344505	0.761213140412884	1.02914634565952	0.377069649079823	3.18442457113743	2.55639334852439
35	YBL064C		0.377069649079823	0.0439433475875972	0.736965594166206	0.888968687611256	0.761213140412884	3.47393118833241	2.83650126771712
36	YER131w	RPS26B	0.358453970912476	0.136061549576028	0.473931188332412	0.0439433475875972	-0.0143552929770701	-1.36737106564853	-2.48800077083407
37	YER150w		-0.0143552929770701	0.184424571137428	1.15200309344505	1.51457317282976	1.59946207041627	3.47393118833241	3.32192809488736
38	YAL003W	TEF5	0.234465253637023	0	-0.0426443374084937	-0.641546029087524	-0.933572638261024	-1.53605290024021	-2.33342373372519
39	YFL014W	HSP12	-0.150559676575381	0.377069649079823	0.62148837674627	1.59946207041627	2.25153876699596	3.64385618977472	3.47393118833241
40	YFL054C		-0.678071905112638	-0.36737106564853	-0.137503523749935	-0.27500704749987	-0.176322772640463	2.47393118833241	0.971430847803229
41	YBL078C		-0.400537929583729	-0.16349873228288	0.136061549576028	0.234465253637023	0.321928094887362	2.32192809488736	2.12029423371771
42	YFR015C	GSY1	-0.22650852980868	0.0439433475875972	0.415037499278844	1.55639334852439	1.02914634565952	2.73696559416621	2.73696559416621
43	YFR033C	QCR6	0.0588936890535686	-0.111031312388744	0.0291463456595165	0.321928094887362	0.62148837674627	2.39592867633114	1.88896868761126
44	YFR053C	HXK1	0.184424571137428	0.321928094887362	0.395928676331139	1	1.47393118833241	2.55639334852439	0.377069649079823
45	YGL031C	RPL30A	0.0291463456595165	0	0.0439433475875972	-0.137503523749935	0	-0.669026765509631	-2.31324585178756
46	YGL037C		0.200912693925996	0.377069649079823	0.286304185156641	1.15200309344505	1.47393118833241	2.83650126771712	1.83650126771712
47	YGL076C	RPL6A	0.0740005814437768	-0.411426245726465	-0.028569152196771	-0.790772037862	-0.839959587489532	-1.6959938131099	-2.78868571061353
48	YGL078C		-0.0143552929770701	-0.250961573533219	0.321928094887362	-0.831877241191673	-0.831877241191673	-1.46988597627446	-2.4594316186373
49	YGL102C		0.0291463456595165	-0.0976107966264223	0.168122758808327	0	-0.028569152196771	-1.39506279951758	-2.55090066464752
50	YBL100C		0.136061549576028	0.217591435072627	0.415037499278844	0.577766999316952	0.888968687611256	1.28630418515664	2.39592867633114
51	YGL191W	COX13	0.0439433475875972	-0.070389327891398	0.0291463456595165	0.0291463456595165	0.888968687611256	2.47393118833241	2.32192809488736
52	YBL108W		0.0439433475875972	0.0892673380970873	0.395928676331139	0.217591435072627	0.971430847803229	0.888968687611256	2.39592867633114
53	YGL259W		-0.137503523749935	-0.070389327891398	0.473931188332412	0.643856189774725	0.377069649079823	1.68965987938785	2.83650126771712
54	YGR008C	STF2	-0.0565835283663676	0.0439433475875972	0.494109070270043	1.12029423371771	1.05889368905357	2.73696559416621	2.05889368905357
55	YGR043C		-0.432959407276106	-0.7311832415722	-0.0565835283663676	-0.111031312388744	-0.16349873228288	3.47393118833241	2.64385618977472
56	YGR067C		0.0439433475875972	-0.0976107966264223	0.168122758808327	-0.344828496997441	-0.37851162325373	0.599462070416271	2.39592867633114
57	YGR088W	CTT1	0.15200309344505	0.0588936890535686	0.217591435072627	0.736965594166206	0.971430847803229	3.64385618977472	2.94341647163363
58	YGR103W		0.15200309344505	-0.0565835283663676	0.321928094887362	-0.903038270112912	-1.10433665981474	-1.64154602908752	-2.56315813040281
59	YGR148C	RPL30B	0.200912693925996	0.104697378666693	0.0588936890535686	-0.286881147788162	-0.27500704749987	-1.81966818349646	-2.61588707391606
60	YGR160W		0.321928094887362	0.104697378666693	-0.250961573533219	-1.48542682717024	-1.48026512205446	-2.50842865253186	-3.21412480535285
61	YGR214W	NAB1A	0.2688167584278	0.15200309344505	0.454031630894707	-0.36737106564853	-0.286881147788162	-1.66902676550963	-2.45154083301783
62	YGR236C		-0.124328135002202	-0.189033824390017	-0.298658315564515	-0.495695162624069	-0.641546029087524	3.47393118833241	2.83650126771712
63	YGR243W		-0.344828496997441	-0.27500704749987	-0.37851162325373	-0.20163386116965	-0.411426245726465	3.18442457113743	2.47393118833241
64	YGR244C		0.0439433475875972	0.2688167584278	0.761213140412884	0.943416471633632	1.47393118833241	2.39592867633114	2.05889368905357
65	YGR248W		-0.298658315564515	-0.389566811762726	0.434402824145775	0.666576266274808	1.39592867633114	4.05889368905357	2.47393118833241
66	YGR264C	MES1	0.415037499278844	0.434402824145775	0	-0.722466024471091	-0.815575428862572	-2.55581615506164	-2.08746284125034
67	YHL015W	URP2	0.168122758808327	0.321928094887362	0.104697378666693	-0.0840642647884746	-0.176322772640463	-1.80322703643493	-2.85598969730848
68	YHL021C		-0.443606651475615	0.120294233717712	0.643856189774725	1	0.785875194647153	2.94341647163363	2.47393118833241
69	YHL033C	RPL4A	0.340075441597622	0.217591435072627	0.184424571137428	-0.176322772640463	-0.505890929729957	-1.56559717585423	-2.51349074558812
70	YBR032W		0	0.15200309344505	0.395928676331139	0.136061549576028	-0.0565835283663676	-1.09761079662642	-2.39780296186249
71	YAL012W	CYS3	0.104697378666693	-0.0143552929770701	0.556393348524385	-0.575312330687437	-0.7311832415722	-1.25096157353322	-2.52105073690096
72	YHR051W	COX6	0.200912693925996	0.0291463456595165	0.200912693925996	0.415037499278844	0.761213140412884	2.18442457113743	2.47393118833241
73	YHR087W		-0.411426245726465	-0.422233000683048	-0.111031312388744	0.104697378666693	0.888968687611256	2.94341647163363	0.971430847803229
74	YHR089C	GAR1	-0.20163386116965	-0.333423733725192	-0.137503523749935	-0.713695814843359	-0.464668267003444	-2.16992500144231	-2.63459326844576
75	YHR096C	HXT5	-0.124328135002202	-0.0426443374084937	0.666576266274808	0.321928094887362	-0.321928094887362	1.43440282414577	3.05889368905357
76	YHR104W		0.286304185156641	0.2688167584278	0.556393348524385	0.643856189774725	0.577766999316952	2.39592867633114	1.25153876699596
77	YHR128W	FUR1	0.234465253637023	0.0740005814437768	0.234465253637023	-0.713695814843359	-0.669026765509631	-1.87184364850932	-2.34482849699744
78	YBR048W	RPS18B	0.120294233717712	0.200912693925996	0.0740005814437768	-0.411426245726465	-0.992768430768924	-1.51601514700366	-2.48026512205446
79	YBR051W		-0.150559676575381	0.200912693925996	0	-0.400537929583729	-0.941106310946431	0.321928094887362	2.64385618977472
80	YIL018W	RPL5A	0.3040061868901	0.0892673380970873	0.2688167584278	-0.214124805352847	-0.176322772640463	-1.37295209791183	-2.33913738491959
81	YIL053W	GPP1	0.2688167584278	-0.0143552929770701	-0.22650852980868	-0.941106310946431	-1.23878685958712	-2.32768736417605	-2.95791459863299
82	YIL069C	RP50B	-0.0565835283663676	-0.495695162624069	-0.411426245726465	-0.641546029087524	-0.704871964456353	-1.9560566524124	-2.44625622988956
83	YIL111W	COX5B	-0.0840642647884746	0.136061549576028	0.666576266274808	1.08926733809709	1.47393118833241	2.94341647163363	1.08926733809709
84	YIL113W		-0.333423733725192	-0.356143810225275	-0.298658315564515	0.0439433475875972	-0.0840642647884746	2.39592867633114	1.28630418515664
85	YIL125W	KGD1	0.234465253637023	0.556393348524385	0.377069649079823	0.120294233717712	0.494109070270043	1.43440282414577	2.94341647163363
86	YIL136W	OM45	-0.978195629681652	-0.263034405833794	0.217591435072627	-0.250961573533219	1.32192809488736	3.47393118833241	1.78587519464715
87	YIL162W	SUC2	0.0588936890535686	0.377069649079823	0.785875194647153	0.377069649079823	0.0439433475875972	2.73696559416621	1.35845397091248
88	YBR072W	HSP26	-0.0143552929770701	0.395928676331139	0.358453970912476	1	1.43440282414577	3.47393118833241	2.83650126771712
89	YJL045W		-0.333423733725192	-0.189033824390017	0.415037499278844	-0.0840642647884746	-0.485426827170242	1	2.32192809488736
90	YJL089W	SIP4	-0.632268215499513	-0.344828496997441	-0.238786859587116	-0.189033824390017	-0.250961573533219	1.12029423371771	3.05889368905357
91	YJL109C		-0.0840642647884746	0.0291463456595165	-0.111031312388744	-1.17632277264046	-1.08406426478847	-3.23419472295381	-1.98913900736823
92	YJL136C	RPS25B	0.184424571137428	-0.0840642647884746	0.340075441597622	-0.070389327891398	-0.475084882948783	-1.46466826700344	-2.35895882583233
93	YJL148W		0.0892673380970873	-0.20163386116965	0.168122758808327	-0.75702324650746	-0.678071905112638	-1.29278174922785	-2.41413553298445
94	YJL177W	RPL20B	0.340075441597622	0.136061549576028	0.136061549576028	-0.422233000683048	-0.622930350920177	-1.93357263826102	-2.38956681176273
95	YJL190C	RPS24A	0.120294233717712	-0.189033824390017	0.340075441597622	0.0892673380970873	-0.0840642647884746	-1.4594316186373	-2.32481060342048
96	YJR095W	ACR1	-0.613531652917927	-0.464668267003444	1.08926733809709	-0.124328135002202	-0.176322772640463	1.35845397091248	3.64385618977472
97	YJR096W		-0.411426245726465	0.217591435072627	0.200912693925996	0.340075441597622	0.943416471633632	2.83650126771712	1.43440282414577
98	YJR123W	RPS5	0.104697378666693	0.0892673380970873	0.168122758808327	-0.37851162325373	-0.411426245726465	-1.85598969730848	-2.48026512205446
99	YJR145C	RPS7B	0.0740005814437768	0.0588936890535686	-0.250961573533219	-0.565597175854225	-0.422233000683048	-1.53605290024021	-2.61353165291793
100	YKL009W		-0.150559676575381	-0.443606651475615	-0.0976107966264223	-0.790772037862	-1.07724299893246	-2.03913839390696	-2.52105073690096
101	YKL026C		-0.189033824390017	-0.150559676575381	0.0291463456595165	0.2688167584278	0.535331732996556	3.64385618977472	2.73696559416621
102	YBR116C		-0.16349873228288	0.184424571137428	0.0439433475875972	-0.22650852980868	-0.422233000683048	1.78587519464715	2.39592867633114
103	YBR117C	TKL2	0.358453970912476	0.643856189774725	0.68965987938785	0.0439433475875972	-0.27500704749987	1.64385618977472	2.47393118833241
104	YKL081W	TEF4	0.0740005814437768	-0.150559676575381	-0.0143552929770701	-0.925999418556223	-0.722466024471091	-2.15704371014558	-2.43562859405209
105	YKL085W	MDH1	0.0439433475875972	0.0144995696951152	0.286304185156641	0.915935735211525	1.35845397091248	2.83650126771712	2.55639334852439
106	YKL103C	LAP4	-0.070389327891398	0.377069649079823	0.473931188332412	0.888968687611256	1.32192809488736	2.39592867633114	1.68965987938785
107	YKL109W	HAP4	0.234465253637023	0.577766999316952	1.02914634565952	0.666576266274808	0.62148837674627	2.55639334852439	3.18442457113743
108	YKL141W	SDH3	0.358453970912476	0.168122758808327	0.643856189774725	0.785875194647153	1.15200309344505	1.94341647163363	2.64385618977472
109	YKL142W	MRP8	-0.070389327891398	0.217591435072627	0.234465253637023	0.494109070270043	1.02914634565952	2.47393118833241	1.15200309344505
110	YKL151C		-0.124328135002202	0.234465253637023	0.577766999316952	0.62148837674627	0.251538766995964	2.55639334852439	1.78587519464715
111	YKL187C		0.0439433475875972	0.0740005814437768	0.200912693925996	-0.16349873228288	-0.400537929583729	2.12029423371771	3.32192809488736
112	YKL193C	SDS22	-0.0565835283663676	-0.124328135002202	-0.263034405833794	0.184424571137428	0.514573172829758	2.47393118833241	1.43440282414577
113	YKL217W	JEN1	-0.485426827170242	-0.070389327891398	0.0439433475875972	-0.333423733725192	0.120294233717712	3.47393118833241	3.83650126771712
114	YKR059W	TIF1	0.217591435072627	0.0740005814437768	0.473931188332412	-0.27500704749987	-0.505890929729957	-1.44360665147561	-2.3305584000308
115	YBR139W		0.120294233717712	0.514573172829758	0.434402824145775	1.08926733809709	0.888968687611256	2	2.39592867633114
116	YKR097W	PCK1	-0.124328135002202	-0.176322772640463	0.434402824145775	-0.0840642647884746	-0.250961573533219	0.415037499278844	3.83650126771712
117	YLL026w	HSP104	0.0144995696951152	0.0144995696951152	-0.189033824390017	0.836501267717121	1	2.39592867633114	2.64385618977472
118	YBR147W		-0.0976107966264223	0.340075441597622	-0.028569152196771	0.0740005814437768	0.251538766995964	3.05889368905357	2.47393118833241
119	YLL041c	SDH2	-0.0565835283663676	-0.0976107966264223	0.494109070270043	1.05889368905357	1.43440282414577	2.55639334852439	2.64385618977472
120	YLL044W		0.286304185156641	0.0144995696951152	-0.16349873228288	-0.443606651475615	-0.713695814843359	-2.09085343045111	-2.53356334821451
121	YLL045c	RPL4B	0.184424571137428	-0.176322772640463	-0.0840642647884746	-0.111031312388744	-0.111031312388744	-1.94860084749336	-3.06522762277562
122	YLR048w	NAB1B	0.321928094887362	0.234465253637023	0.454031630894707	-0.111031312388744	-0.344828496997441	-1.9297909977186	-2.58736499093646
123	YLR062C		0.184424571137428	-0.0565835283663676	0.0588936890535686	-0.356143810225275	-0.0976107966264223	-1.91073266190291	-2.86591881455221
124	YLR076C		0.217591435072627	-0.0426443374084937	0.0892673380970873	0.0740005814437768	-0.31034012061215	-1.49569516262407	-2.32481060342048
125	YLR129w	DIP2	-0.344828496997441	-0.37851162325373	-0.286881147788162	-0.887525270741588	-0.863938450423972	-2.81147103052984	-2.09423606984577
126	YLR142w	PUT1	-0.176322772640463	-0.464668267003444	-0.505890929729957	-0.263034405833794	-0.20163386116965	0.514573172829758	2.39592867633114
127	YLR149C		-0.263034405833794	-0.124328135002202	-0.189033824390017	0.599462070416271	0.286304185156641	2.47393118833241	2.73696559416621
128	YLR174W	IDP2	-0.111031312388744	-0.286881147788162	0.713118852211838	0.120294233717712	-0.137503523749935	1.28630418515664	3.32192809488736
129	YLR178C	TFS1	-0.22650852980868	-0.214124805352847	-0.0565835283663676	0.761213140412884	1.25153876699596	2.64385618977472	1.78587519464715
130	YLR180W	SAM1	0.184424571137428	0.2688167584278	0.217591435072627	-0.925999418556223	-1.0703893278914	-2.54596836910529	-3.06350294230616
131	YLR186W		0.0740005814437768	-0.0426443374084937	-0.298658315564515	-1	-0.687060688339892	-1.38956681176273	-2.42223300068305
132	YLR196W	PWP1	0.251538766995964	0.0892673380970873	0.2688167584278	-0.855989697308481	-0.925999418556223	-1.53605290024021	-2.78240856492737
133	YLR198C		0.3040061868901	0.0144995696951152	0.454031630894707	-0.150559676575381	-0.22650852980868	-1.36176835941915	-2.47767732756531
134	YLR249W	YEF3	0.0588936890535686	0.0291463456595165	0.120294233717712	-0.765534746362977	-0.0565835283663676	-1.47508488294878	-2.76128527336162
135	YLR258W	GSY2	0.104697378666693	0.434402824145775	0.454031630894707	1.88896868761126	2	3.32192809488736	2.55639334852439
136	YLR267W		-0.124328135002202	0.120294233717712	0.2688167584278	-0.111031312388744	-0.485426827170242	1.64385618977472	2.73696559416621
137	YLR270W		0.104697378666693	-0.028569152196771	0.217591435072627	0.62148837674627	0.377069649079823	3.05889368905357	1.51457317282976
138	YLR304C	ACO1	0.200912693925996	0.556393348524385	0.494109070270043	1.02914634565952	1.21759143507263	1.94341647163363	2.64385618977472
139	YLR312C		-0.613531652917927	-0.659924558402378	0	0.184424571137428	-0.27500704749987	1.25153876699596	2.32192809488736
140	YBR181C	RPS101	0.184424571137428	0.217591435072627	0.200912693925996	0.0892673380970873	0.120294233717712	-1.58496250072116	-2.56803210477128
141	YLR325C		0.0439433475875972	0.0144995696951152	0.120294233717712	0.0291463456595165	-0.298658315564515	-1.54596836910529	-2.59454854955035
142	YLR327C		-0.189033824390017	-0.333423733725192	0.0892673380970873	0.915935735211525	1.08926733809709	3.32192809488736	2.64385618977472
143	YLR339C		0.321928094887362	0.473931188332412	0.3040061868901	-0.214124805352847	-0.669026765509631	-1.78240856492737	-2.55826763405574
144	YLR340W	RPLA0	0.200912693925996	0.321928094887362	0.473931188332412	-0.0840642647884746	-0.443606651475615	-1.8073549220576	-2.77610398807316
145	YBR183W		-0.36737106564853	-0.400537929583729	0.395928676331139	1.05889368905357	0.862496476250065	2.55639334852439	1.43440282414577
146	YLR344W	RPL33A	-0.0840642647884746	-0.176322772640463	-0.356143810225275	-0.704871964456353	-0.505890929729957	-1.56559717585423	-2.37851162325373
147	YLR355C	ILV5	0.358453970912476	0.0588936890535686	-0.454175893185802	-1.24488705912353	-1.22032995487956	-2.39231742277876	-2.13422093976063
148	YLR356W		-0.111031312388744	0.599462070416271	0.535331732996556	0.862496476250065	0.810966175609983	2.83650126771712	1.88896868761126
149	YLR377C	FBP1	-0.22650852980868	-0.028569152196771	0.251538766995964	-0.16349873228288	-0.124328135002202	0.473931188332412	3.83650126771712
150	YBR189W	SUP46	-0.028569152196771	-0.31034012061215	0.0291463456595165	-0.27500704749987	-0.545968369105293	-1.97819562968165	-2.65535182861255
151	YLR413W		0.217591435072627	0.358453970912476	0.535331732996556	-0.650764559116902	-0.669026765509631	-2.4032677223393	-2.82781902461732
152	YBR191W	URP1	0.0740005814437768	-0.250961573533219	0.0588936890535686	-0.238786859587116	-0.55581615506164	-1.73552217729654	-2.66902676550963
153	YLR448W	YL16B	0.340075441597622	0.0291463456595165	-0.214124805352847	-0.613531652917927	-0.704871964456353	-1.89530262133331	-2.32768736417605
154	YLR449W		-0.0426443374084937	-0.028569152196771	0.136061549576028	-1.19534759832222	-0.970853654340484	-2.61353165291793	-2.20789285164133
155	YML054C	CYB2	-0.575312330687437	-0.0976107966264223	0.434402824145775	-0.111031312388744	-0.0426443374084937	2.32192809488736	2.94341647163363
156	YML063W	RP10B	0.217591435072627	0.217591435072627	0.395928676331139	0.0144995696951152	-0.028569152196771	-1.58014548442338	-2.48542682717024
157	YML128C		-0.124328135002202	0.200912693925996	0.971430847803229	1.55639334852439	1.35845397091248	4.32192809488736	3.47393118833241
158	YMR090W		-0.176322772640463	0.0892673380970873	0.577766999316952	0.321928094887362	0.971430847803229	2.32192809488736	1.02914634565952
159	YMR093W		0.0740005814437768	0	-0.454175893185802	-1.27500704749987	-1.33913738491959	-1.85199883711245	-2.46205231879643
160	YMR105C	PGM2	0.136061549576028	0.535331732996556	0.713118852211838	1.73696559416621	1.47393118833241	3.18442457113743	2.64385618977472
161	YMR107W		-0.411426245726465	-0.263034405833794	-0.20163386116965	-0.298658315564515	-0.111031312388744	2.32192809488736	2.32192809488736
162	YMR121C	RPL13B	0.340075441597622	-0.0426443374084937	0.340075441597622	0.321928094887362	-0.111031312388744	-1.36176835941915	-2.4594316186373
163	YMR131C		0.217591435072627	0.104697378666693	0.321928094887362	-0.411426245726465	-0.831877241191673	-1.33342373372519	-2.59693514238723
164	YMR170C	ALD2	0.184424571137428	0.234465253637023	0.200912693925996	0.434402824145775	0.713118852211838	3.64385618977472	2.25153876699596
165	YMR191W		-0.0143552929770701	0.15200309344505	0.599462070416271	0.514573172829758	0.377069649079823	1.83650126771712	2.32192809488736
166	YMR217W	GUA1	0.15200309344505	0.120294233717712	0.184424571137428	-1.07724299893246	-1.27500704749987	-1.62293035092018	-2.7311832415722
167	YMR250W		-0.0840642647884746	0.473931188332412	1.02914634565952	1.78587519464715	2.12029423371771	3.05889368905357	3.18442457113743
168	YMR290C		0.120294233717712	-0.22650852980868	-0.238786859587116	-1.15704371014558	-1.40599235967584	-2.67129337248158	-3
169	YNL002C	RLP7	-0.0976107966264223	-0.36737106564853	-0.250961573533219	-1.18269229751619	-0.871843648509318	-2.8011586560937	-2.38956681176273
170	YBR238C		0.15200309344505	0.943416471633632	0.377069649079823	-0.782408564927373	-0.978195629681652	-1.50080205305716	-2.33913738491959
171	YNL015W	PBI2	-0.070389327891398	-0.321928094887362	0.514573172829758	0.810966175609983	0.915935735211525	3.05889368905357	2.25153876699596
172	YBR241C		-0.978195629681652	0.0588936890535686	0.415037499278844	0.184424571137428	-0.189033824390017	2.47393118833241	1.55639334852439
173	YNL052W	COX5A	-0.238786859587116	-0.238786859587116	-0.0976107966264223	0.0892673380970873	0.643856189774725	1.78587519464715	2.32192809488736
174	YNL065W		0	0.286304185156641	-0.214124805352847	-0.992768430768924	-0.214124805352847	-2.19219416528334	-2.39780296186249
175	YNL067W	RPL9B	0.0439433475875972	-0.36737106564853	-0.137503523749935	-0.389566811762726	-0.22650852980868	-0.722466024471091	-2.38681094647222
176	YNL069C	RP23	-0.0976107966264223	-0.0426443374084937	0.3040061868901	-0.20163386116965	-0.0840642647884746	-1.10433665981474	-2.74631276642546
177	YNL096C		0.120294233717712	-0.028569152196771	-0.321928094887362	-0.495695162624069	-0.400537929583729	-2.19534759832222	-2.790772037862
178	YBR247C	ENP1	-0.028569152196771	-0.214124805352847	-0.070389327891398	-1.17632277264046	-1.03562390973072	-1.20789285164133	-2.76553474636298
179	YNL117W	MLS1	-0.31034012061215	-0.0426443374084937	0.713118852211838	-0.298658315564515	-0.263034405833794	0.761213140412884	3.18442457113743
180	YNL119W		0.136061549576028	-0.028569152196771	0.3040061868901	-0.214124805352847	-0.20163386116965	-1.15704371014558	-2.79701297783614
181	YBR249C	ARO4	0.15200309344505	0.0439433475875972	0.136061549576028	-0.432959407276106	-0.594548549550354	-2.02147972741045	-2.36176835941915
182	YNL134C		0.136061549576028	0.0892673380970873	0.0740005814437768	0.104697378666693	0.2688167584278	2.32192809488736	2.05889368905357
183	YNL141W		-0.16349873228288	-0.0426443374084937	-0.070389327891398	-1.25701061820602	-1.19534759832222	-2.81557542886257	-3.13093086982645
184	YNL160W	YGP1	0.234465253637023	0.340075441597622	1.12029423371771	1.47393118833241	1.73696559416621	3.05889368905357	2.83650126771712
185	YNL173C		-0.070389327891398	-0.250961573533219	0.104697378666693	0.862496476250065	0.785875194647153	2.64385618977472	1.68965987938785
186	YNL174W		0.0588936890535686	-0.214124805352847	0.0144995696951152	-0.963474123974886	-0.879705766282288	-2.38681094647222	-1.18903382439002
187	YNL175C		0.200912693925996	-0.189033824390017	0.120294233717712	-0.650764559116902	-0.903038270112912	-1.70043971814109	-2.62293035092018
188	YNL194C		-0.286881147788162	0.0291463456595165	0.136061549576028	-0.16349873228288	0.3040061868901	3.83650126771712	3.32192809488736
189	YNL195C		-0.321928094887362	-0.238786859587116	-0.111031312388744	-0.150559676575381	0.0291463456595165	0.761213140412884	2.32192809488736
190	YNL200C		-0.22650852980868	-0.028569152196771	0.358453970912476	1.25153876699596	1.51457317282976	3.83650126771712	2.55639334852439
191	YNL274C		0.0144995696951152	0.0588936890535686	0.358453970912476	0.643856189774725	0.494109070270043	2.73696559416621	1.68965987938785
192	YNL301C	RP28B	0.217591435072627	-0.124328135002202	0.251538766995964	-0.298658315564515	-0.545968369105293	-1.89917563048051	-2.48284828306847
193	YNL303W		-0.389566811762726	-0.748461233004036	-0.344828496997441	-0.613531652917927	-1.11103131238874	-2.56315813040281	-2.49569516262407
194	YNL305C		-0.124328135002202	0.104697378666693	0.494109070270043	0.136061549576028	0.888968687611256	2.39592867633114	1.12029423371771
195	YNR001C	CIT1	0.184424571137428	0.454031630894707	0.643856189774725	0.713118852211838	1.21759143507263	2.64385618977472	3.18442457113743
196	YAL054C	ACS1	-0.669026765509631	-0.189033824390017	0	-0.189033824390017	-0.298658315564515	1.47393118833241	3.64385618977472
197	YNR053C		0.200912693925996	0.415037499278844	0.286304185156641	-0.495695162624069	-0.594548549550354	-1.73984810269933	-2.39506279951758
198	YOL120C	RP28A	0.2688167584278	-0.0840642647884746	0.395928676331139	-0.16349873228288	-0.594548549550354	-1.8073549220576	-2.41683974191283
199	YOL032W		-0.070389327891398	-0.028569152196771	0.286304185156641	0.184424571137428	0.0892673380970873	2.55639334852439	1.68965987938785
200	YOL039W	RPLA2	0.0740005814437768	-0.028569152196771	0.104697378666693	0	0	-0.16349873228288	-2.30158764660319
201	YOL040C	RPS21	0.104697378666693	0.0588936890535686	-0.137503523749935	-0.411426245726465	-0.55581615506164	-1.53106949272595	-2.65535182861255
202	YOL053C	DDR2	-0.111031312388744	-0.16349873228288	0.0892673380970873	0.888968687611256	0.915935735211525	2.55639334852439	1.78587519464715
203	YOL084W		-0.31034012061215	0.120294233717712	0.434402824145775	0	-0.070389327891398	1.32192809488736	2.64385618977472
204	YOR065W	CYT1	0.168122758808327	0.104697378666693	0.321928094887362	0.286304185156641	0.943416471633632	1.68965987938785	2.39592867633114
205	YOR178C	GAC1	-0.189033824390017	-0.070389327891398	0.473931188332412	0.2688167584278	0.136061549576028	2.32192809488736	2.05889368905357
206	YOR215C		0.0740005814437768	0	0.377069649079823	0.785875194647153	0.943416471633632	3.47393118833241	2.83650126771712
207	YOR234C	RPL37B	0.0740005814437768	0.0740005814437768	-0.124328135002202	-0.36737106564853	-0.485426827170242	-1.6959938131099	-2.30158764660319
208	YOR309C		0.200912693925996	0.0291463456595165	0.234465253637023	-0.641546029087524	-0.37851162325373	-2.09761079662642	-2.96347412397489
209	YOR310C		0.15200309344505	-0.0143552929770701	0.340075441597622	-0.604071323668861	-0.641546029087524	-1.81966818349646	-3.09592441999854
210	YCL025C		0	-0.028569152196771	0.434402824145775	0.0439433475875972	0.643856189774725	0.666576266274808	2.47393118833241
211	YOR312C	RPL18B	0.234465253637023	-0.0143552929770701	0.251538766995964	-0.422233000683048	-0.454175893185802	-1.51601514700366	-2.53106949272595
212	YOR374W		0	0.494109070270043	0.340075441597622	1	1.32192809488736	2.47393118833241	2.47393118833241
213	YPL012W		0.0892673380970873	-0.27500704749987	-0.150559676575381	-1.17632277264046	-1.58496250072116	-2.9560566524124	-3.07553263116736
214	YCL035C		0.0291463456595165	0.321928094887362	0.535331732996556	0.666576266274808	0.2688167584278	2.55639334852439	1.51457317282976
215	YPL131W	RPL1	0.0588936890535686	0.0892673380970873	0.15200309344505	-0.823749360308273	-0.22650852980868	-1.65535182861255	-2.53356334821451
216	YPL220W	SSM1A	0.0439433475875972	-0.0143552929770701	0.395928676331139	-0.356143810225275	-0.0426443374084937	-1.60407132366886	-2.76765479823735
217	YPL226W		0.0439433475875972	0.0740005814437768	-0.0976107966264223	-0.839959587489532	-1.17632277264046	-1.88752527074159	-2.45680614923047
218	YPR137W		0.0740005814437768	-0.176322772640463	-0.20163386116965	-0.887525270741588	-0.918386234446348	-1.6959938131099	-2.95419631038688
219	YPR149W	NCE2	0.15200309344505	0.120294233717712	0.395928676331139	0.810966175609983	0.915935735211525	2.05889368905357	2.32192809488736
220	YPR184W	GDE	-0.238786859587116	-0.0840642647884746	-0.27500704749987	0.200912693925996	0.556393348524385	1.51457317282976	2.64385618977472
221	YDL215C	GDH2	-0.070389327891398	0.0439433475875972	0.0439433475875972	-0.464668267003444	-0.0565835283663676	0.3040061868901	2.32192809488736
222	YDR258C	HSP78	-0.214124805352847	-0.0840642647884746	-0.263034405833794	0.666576266274808	0.915935735211525	2.18442457113743	2.47393118833241
223	YCR010C		-0.485426827170242	-0.36737106564853	0.234465253637023	-0.36737106564853	-0.422233000683048	0.535331732996556	2.64385618977472
224	YCR021c	HSP30	-0.790772037862	0.0144995696951152	1.88896868761126	1.55639334852439	0.862496476250065	3.64385618977472	3.32192809488736
225	YDL083C		0.104697378666693	-0.286881147788162	-0.189033824390017	-0.650764559116902	-0.799087306074004	-1.17632277264046	-2.40053792958373
226	YDL085w		-0.111031312388744	1	0.0588936890535686	-0.124328135002202	-0.27500704749987	2.05889368905357	2.83650126771712
227	YDL136w		-0.070389327891398	-0.0143552929770701	-0.0426443374084937	-0.36737106564853	-0.214124805352847	-1.55090066464752	-2.56315813040281
228	YDL199c		-0.0426443374084937	0.494109070270043	0.415037499278844	0.184424571137428	-0.344828496997441	1.73696559416621	2.32192809488736
229	YDL204w		-0.36737106564853	0.915935735211525	-0.505890929729957	0.2688167584278	0.0892673380970873	4.05889368905357	3.05889368905357
230	YDL208W	NHP2	0.0439433475875972	-0.150559676575381	0.0439433475875972	-0.575312330687437	-0.485426827170242	-2.14404636961671	-2.63691458035588

230个基因的表达水平变化

 

算法1 Lloyd Algorithm  k_mean clustering
* Centers to Clusters: After centers have been selected, assign each data point to the cluster corresponding to its nearest center; ties are broken arbitrarily.
* Clusters to Centers: After data points have been assigned to clusters, assign each cluster’s center of gravity to be the cluster’s new center.

 程序利用Lloyd算法，随机选取起始的Centers，并进行2000次迭代，选取最佳结果。

python源码

  1 from os.path import dirname
  2 import numpy as np
  3 import math
  4 import random
  5 import matplotlib.pyplot as plt
  6 
  7 def  square_EuclideanDistance(vId,wId,Centers):
  8     s = 0
  9     for i in range(m):
 10         s += (points[vId][i]-Centers[wId][i])**2
 11     return s
 12 
 13 def Centers_to_Clusters(Centers):
 14     global Cluster
 15     Cluster = [[] for i in range(k)]
 16     Distortion = 0
 17     for i in range(len(points)):
 18         minVal = INF
 19         minId = -1
 20         for c in range(k):
 21             tmp = square_EuclideanDistance(i, c,Centers)
 22             if tmp < minVal:
 23                 minVal = tmp
 24                 minId = c
 25         Cluster[minId].append(i)
 26         Distortion += minVal
 27     return Distortion/points_num
 28             
 29 def Clusters_to_Centers():
 30     #print(Cluster)
 31     Centers = []
 32     for i in range(k):
 33         coordinate = [0 for i in range(m)]
 34         for pId in Cluster[i]:
 35             for j in range(m):
 36                 coordinate[j] += points[pId][j]        
 37         if len(Cluster[i])==0:
 38             coordinate = [0.5 for item in coordinate]
 39         else:
 40             coordinate = [item/len(Cluster[i]) for item in coordinate]
 41         Centers.append(coordinate)
 42     #print(Centers)
 43     return Centers
 44 
 45 def LloydClustering():
 46     global Cluster
 47     Centers = random.sample(points,k)
 48     minDistortion = INF    
 49     Distortion = Centers_to_Clusters(Centers)
 50     i = 0
 51     while(Distortion < minDistortion):
 52         i += 1
 53         #print(‘*%d iteration*...‘%i)
 54         minDistortion = Distortion
 55         Centers = Clusters_to_Centers()
 56         Distortion = Centers_to_Clusters(Centers)        
 57     return [Centers,Distortion]
 58 
 59 if __name__ == ‘__main__‘:
 60     INF = 999999
 61     dataset = open(dirname(__file__)+‘230genes_log_expression.txt‘).read().strip().split(‘
‘)
 62     dataset = [line.split() for line in dataset]
 63     name = [item[1] for item in dataset[1:]]
 64     k = 6 # 分成 6 类
 65     m = 7 # 数据的维度
 66     #print(m)
 67     # print(m,k)
 68     points = []
 69     for line in dataset[1:]:
 70         if(len(line)==10):
 71             points.append(list(map(float,line[3:])))
 72         elif(len(line)==9):
 73             points.append(list(map(float,line[2:])))
 74     
 75     points_num = len(points)
 76     out_Distortion = INF
 77     out_Centers = []
 78     out_i = -1
 79     for i in range(2000):
 80         [Centers,Distortion] = LloydClustering() #Distortion 精确度
 81         if Distortion<out_Distortion:
 82             out_Distortion = Distortion
 83             out_Centers = Centers
 84             out_i = i
 85     
 86     print(out_i,out_Distortion)
 87     
 88     for c in out_Centers:
 89         for i in range(len(c)):
 90             if i != 0:
 91                 print(‘ ‘,end=‘‘)
 92             print(‘%.3f‘%c[i],end=‘‘)
 93         print(‘‘)
 94     
 95     x = [i for i in range(1,8)]
 96     
 97     plt.rcParams[‘figure.figsize‘]=(12,8)
 98     for i in range(len(points)):
 99             plt.plot(x,points[i],color=‘#C0C0C0‘,linewidth=1.5,linestyle=‘-‘,marker=‘.‘)
100 
101     for i in range(k):
102         plt.plot(x,Centers[i],linewidth=1.5,linestyle=‘-‘,marker=‘.‘)
103     plt.show()

 运行结果：