实战--利用Lloyd算法进行酵母基因表达数据的聚类分析
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
from os.path import dirname
import numpy as np
import math
import random
import matplotlib.pyplot as plt def square_EuclideanDistance(vId,wId,Centers):
s = 0
for i in range(m):
s += (points[vId][i]-Centers[wId][i])**2
return s def Centers_to_Clusters(Centers):
global Cluster
Cluster = [[] for i in range(k)]
Distortion = 0
for i in range(len(points)):
minVal = INF
minId = -1
for c in range(k):
tmp = square_EuclideanDistance(i, c,Centers)
if tmp < minVal:
minVal = tmp
minId = c
Cluster[minId].append(i)
Distortion += minVal
return Distortion/points_num def Clusters_to_Centers():
#print(Cluster)
Centers = []
for i in range(k):
coordinate = [0 for i in range(m)]
for pId in Cluster[i]:
for j in range(m):
coordinate[j] += points[pId][j]
if len(Cluster[i])==0:
coordinate = [0.5 for item in coordinate]
else:
coordinate = [item/len(Cluster[i]) for item in coordinate]
Centers.append(coordinate)
#print(Centers)
return Centers def LloydClustering():
global Cluster
Centers = random.sample(points,k)
minDistortion = INF
Distortion = Centers_to_Clusters(Centers)
i = 0
while(Distortion < minDistortion):
i += 1
#print('*%d iteration*...'%i)
minDistortion = Distortion
Centers = Clusters_to_Centers()
Distortion = Centers_to_Clusters(Centers)
return [Centers,Distortion] if __name__ == '__main__':
INF = 999999
dataset = open(dirname(__file__)+'230genes_log_expression.txt').read().strip().split('\n')
dataset = [line.split() for line in dataset]
name = [item[1] for item in dataset[1:]]
k = 6 # 分成 6 类
m = 7 # 数据的维度
#print(m)
# print(m,k)
points = []
for line in dataset[1:]:
if(len(line)==10):
points.append(list(map(float,line[3:])))
elif(len(line)==9):
points.append(list(map(float,line[2:]))) points_num = len(points)
out_Distortion = INF
out_Centers = []
out_i = -1
for i in range(2000):
[Centers,Distortion] = LloydClustering() #Distortion 精确度
if Distortion<out_Distortion:
out_Distortion = Distortion
out_Centers = Centers
out_i = i print(out_i,out_Distortion) for c in out_Centers:
for i in range(len(c)):
if i != 0:
print(' ',end='')
print('%.3f'%c[i],end='')
print('') x = [i for i in range(1,8)] plt.rcParams['figure.figsize']=(12,8)
for i in range(len(points)):
plt.plot(x,points[i],color='#C0C0C0',linewidth=1.5,linestyle='-',marker='.') for i in range(k):
plt.plot(x,Centers[i],linewidth=1.5,linestyle='-',marker='.')
plt.show()
运行结果：
实战--利用Lloyd算法进行酵母基因表达数据的聚类分析的更多相关文章
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