User Manual - フィルジェン株式会社
Contents
1. 0S Windows Xp Windows 2000 Windows98 95 0S lt2. 1 or 1 Copyright C Filgen Inc All Rights Reserved 29 Microarray Data Analysis Tool Wer3 2
3. A Ratio 2 A B C Ratio 2 A Ratio 2 Up A Ratio 2
4. Ratio Filter 0ptions Keyword GAPDH P 29 Per Array Normalization Control gene
5. 0 Log2 P value Ratio calculation Select
6. CodeLinkK Human Mouse Rat Whole Genome Bioarray Pathway GenMAPP or WikiPathways NCBI BioSystems Pathway Gene Ontology ratio 2 0 5
7. Keyword Go Go Pathway 2 Pathway IMm_EGFR1 Signaling_Pathway WP572 21884 Keyword Pathway Changed Genes Total Genes Zscore P value Pathway WikiPathways 41 3118 a No select Beck Row es Mm_Acetylcholine Synthesis WP175 21047 0 6 0 1 gm hm_ACE mhibitor_Pathway_WP3g6 21516 5 Dh 1 Mm_Adipogenesis WP447 28134 128 D 1 him_Alanine_and aspartate_ metabolism WwFP240 21181 11 1 him_Alpha6 Betad Integrin Sijgnaling_Pathway_WP4B8 217065 53 1 him_Androgen_ Receptor Signaling_Pathway_WP252 21209 102 572 39349 Mm_Apoptosis_ Mechanisms WP168 21 33 In 9 1 EGFR1 SS WikiPathways En EESDITET hm_Apoptosis_ Modulation
8. 1 A Ratio 2 A B C Ratio 2 1 A Ratio 2 Up A 1 Ratio 2
9. Quantile Median Scatter Plot Quantile Per Array Normalization Per Gene Normalizatlion 1 Per Gene Normalizatlion Median Control Experiment Q3 Gene 0ntology Pathway
10. GAPDH 8 actin Per Gene Normalization 1Median Per Array Normalized intensity Copyright C Filgen Inc All Rights Reserved 11 Microarray Data Analysis Tool Wer3 2 2 Mean Per Array Normalized intensity 3Control experiment
11. 1 1 Ratio 2 Up A B C 1 Ratio 2 A Ratio 2 Up A B CC Ratiof2 D
12. SearchOption P 34 ScatterPlot Select or OK or or _ ok OK Cancel
13. CSV csv txt select Stanford Eisen Lab _Scatter Plot Plot Window a Fitter Options 3 eg ga EC Filter OL Cluster and TreeView Scatter Plot Scatter Plot Plot Window Scatter Plot Scatter Plot Plot Window
14. Data Name Ignored cells 1 OK lgnored cells Ignored cells lgnored cells lgnored cels
15. CutOff Quality flag intensity 2 Summarized data P 35 Quality ag flag intensity CutOff Quality flag intensity Quality flag P 19 intensity flag 1 1 Test flag Contro flag
16. 1 Gene Ontology Gene Ontology Pathway Pathway External Filter PDF Copyright C Filgen Inc All Rights Reserved 4 Microarray Data Analysis Tool Ver3 2
17. intensity 2 Up 0 5 Down Ratio or 1 Up Normalized intensity Iratio 2 Down 0 5 Normalized intensity llog2ratiol 1 1 Signal Fold Change Ratio Up 2 Down 0 5 Fold Change log2ratio CutOff
18. Gene Ontology Pathway Stanford EisenLab Cluster and TreeView Entrez Gene Ensembl RefSeq Gene 0ntology ID Entrez Gene Ensembl RefSeq UniProt Panorama V Ab Microarray XPRESS Profiler725 Apoptosis Cancer Cell Cycle Cytokine Common Diseases Extracellular Matrix and Adheslon Molecules Neurosclence Signal Iransduction Stem Cel Toxicology and Drug Metabolism etc Ratio CutOff 2 or
19. P 20 CodeLink Bioarray G G Test Control intensity G Test Contro intensity Scatter Plot 2 215 07728 831084 2 2 24966 1 348852 47 87794 D898077 674 44B5G 1 385H 251 12274 924597 295 7043 1 311912 49 1586G 1 3D9704 1504 84958 1 214352 da9 19698 1 244362 222 50952 D799955 1412 78414 923903 518 9844 1 235752 Ol 1 I Ol OI Ol OO Or El I EY 100 000 Copyright C Filgen Inc All Rights Reserved 26 Microarray Data Analysis Tool Wer3 2 ScatterPlot 114 09474 215 07728 831084 132 43582 437042 177 57384 1 458558 2 72 2496 1 348852 160 55908 671947 447 57794 D898077 64 44856 1 385H 251 12274 924597 DD 295 7043 1 311912 dT15856 1 309704 ol Ol Ol Ol Ol Ol Ol Ol Ol Ol Ol 1504 84958 1 214352 Signal Signal 1
20. Per Array Normalized intensity CutOff Per Array Normalized intensity CutOff CutOff lgonored cells 1 Filter Options lgnored cells lgnored cells 1 lgnored cells 0
21. Copyright C Filgen Inc All Rights Reserved 2 2 Microarray Data Analysis Tool Ver3 2 1 CD ROM Microarray Data Analysis Tool CD ROM W Microarray Data hnalysis Tool Ver3 2 FE CE A amp 9 TU 6 5 Web
22. Ratio Group Ratio Group Ratio REE Ratio Group Ratio Per Gene Normalized intensity 6 0OK Ratio Group Ratio lt Fieldl Per Array Normalized intensity Ir Fied TE Fjglda Fieldd Field5 ieldBi
23. Ratio 2 Copyright C Filgen Inc All Rights Reserved 14 Microarray Data Analysis Tool Ver3 2 1 Selee or Block Block Block Column Block Raw Intensity test Raw Intensity Icontrol Background test Background tcontrol Net intensity test Net intensity Icontrol Net intensity suml Normalized intensity test Normalized intensity lcontrol Normalized intensity sum Normalized intensity test controll Normalized intensity ratio Norma
24. Scatter Plot Scatter Plot Scatter Plot BMP ScatterPlot Filter Options 757 Scatter Plot a Scatter Plot Test ws Control No 10 000 100 000 ER i00 00 SE
25. 6 SN oe IP A a Vii C A BE 1 1 1 1 Th a rf ar lin BE 4 BE Pi m MM or pr umi re E 1 Se a 3 B BH 6 1
26. 1 1 3 a 2 6 LL 1 ae bag A A Copyright C Filgen Inc All Rights Reserved 25 Microarray Data Analysis Tool Wer3 2 or CutOff 1 or KeyWord Flag 0 P 18 KeyWord
27. One Sample Ltest 2 1 0 P value 2
28. A Ratio 2 Up A B C Ratio 2 Copyright C Filgen Inc All Rights Reserved 21 Microarray Data Analysis Tool Ver3 2 A Ratio 2 Up A B C Ratio 2 A Ratio 2 Up
29. 1 1 Ratio 2 Up A B C Ratio 2 1 1 1 Ratio 2 A B C 1 Ratio 2
30. Dlgnored cells P value lgnored cells 1 P value 1 FDR Benjamini and Hochberg P value 1 P va
31. Add Signal 2 1 1 Data1 vs Data2 Data1 Data2 1 Signal 1 CndeLink Th Mouse Wholes Ennnm Test 1 CindeLink Th Mouse Whole Genon Test 2 CndeLink Th Mause Whole nn Test 3 CondeLink Th Mouse Whole Genon Test 4 3 Mexxt PCE Experiment Name Control Control Laveling Next intensity
32. http Www genmaDD 0rg 2 http www wikipathways org index php WikiPathways 3 http Wwww ncbinImnih gov sites entrez db biosystems 1 Signal Filter Options Pathway GenMAPP WikiPathways NCBI BioSystems Browser List List List P 43 44 kPathway Filter 0ptions
33. Reference Read External Filter FETErEiCg 0 6 REI IQlign ID lalign_id ly ma omi RB EE EER W Fd Fg Erse rt cllgo ia clen It Enssrr tra homreaeed horalked Ha rgl ed mpre ce iPegithe Ensarril Oi HETTITTTICO
34. ScatterPlot No 2 Filter Optinns Search Option No IL gLp 319 Reset Scatterplot Cancel
35. 1 ca 1 1 1
36. Es 9 3 3 nored cels nored cells Scatternlat Cancel 1 Copyright C Filgen Inc All Rights Reserved 50 Microarray Data Analysis Tool Ver3 2 Q2 Signal A2 Signal Per Array Normalization Per Gene Normalization 2 3 4 Per Array Normalization Median Quantile Median
37. P value 0 05 GO Term Fisher s exact test 2 GO Term GO Term GO Term P value Z score Gene Ontology Gene Ontology Copyright C Filgen Inc All Rights Reserved 4 1 Microarray Data Analysis Tool Wer3 2 9 Pathway Pathway Pathway
38. Z score GO Term P value GO Term P value Two tailed Fisher s exact test GO Term Changed Genes Total Genes GO Term GO Term Changed Genes Total Genes 4 Two tailed Fisher s exact test 2 GO Term GO Term
39. Dra mE Ta Lm glign HEUUUUUZER HO bh HO 4 HO 3 He 1 SG Hun1 D1 HEUJUT Lat HO HE HEUUU1 eh 1 He 11 HEUUUUESBG 1 HEUUU1 BBBG align id EnsermblGe neID HEUUUUUZZR HDL 55ad HEU HDD djGg Hg 1 5 ha Ua51 hguU1 ah hd hguU1 og He OL hEUUIUUEGHBS HEUUU1 EhIEGUUUU Eh GUUUUUUUUHS g Eh GUUUUUUUGU EhIEGUUUUUUU51 UE Eh GUUUUU1 1 Eh GUUUUUUUGdH Eh GUUUU1 1 7 Eh GUUUUU1 1 5 PEPIPIWJsil ahhh rg 1BH8 da EE 51gLU88 dS 1 Bh EH LE ee id GGAs iminlsPe had pe Tedg Rh 7g 52124EH 1129E 12 B dahghdr 14HEHIHTB EPR dh ia HIEBFIG Rd ha grTahHH 5 1 inslmlsil 1 1 E41 F711 1 2 7 dE E transcript EF TO 1 Eh TO1 5 1 Gi EE TIG1 5 EhIS TU 1 5 7 ES TS5 1 Eh TU 4 ES TU T1519 Eh TDIOLILDgL1 H Copyright C Filgen Inc All Rights Reserved Microarray Data Analysis Tool Ver3 2 45 Microarray Data Analysis Tool Ver3 2 External Filter External Filter
40. Exce 1 3 4 CutOff Copyright C Filgen Inc All Rights Reserved 27 Microarray Data Analysis Tool Ver3 2 Summarization g Summarize Options Mean hedian Loeg2Ration Ratio Cancel 1 Summarization EE Filter Options Search Option KeyWuard NestveGortol gt Io 6 0 E 2 ME EE Normalized i Normalized i Normalized in Normalized i Normalized wouality tlae lenored cells First Fla Neeative Control 02 10g541591 11 02362 226565211 ng43994 HI8315 Ilnn 3 EE7
41. 24559 129625 0 530861654862609 0 690120151321392 0 2014071 433204 0556832230146621 0689411332562483 0 J 205699 104053 0000157770563698034 0 00820406931229777 0 P value FDR 0 05 440302 213849 0235178897198282 0679405703017259 0 24691 130399 0275052386532385 0681082099984953 0 283396 150282 0218420345625678 0668109292502074 0 472459 224019 00505584769570973 0525808160353812 0 201581 1m136 0 401039729578549 0719105722002915 0 Copyright C Filgen Inc Al Reserved 36 Microarray Data Analysis Tool Ver3 2 P value Normalized intensity llog2ratiol Signal Per Gene Normalized intensity Student s t test 2
42. Select 5 AND OR OR Quality flag Quality flag Normalized intensity 100 Ratio 2 0 5 le INarmalized intensiy fratio EE BE CE FO AND OR Normalized intensity ratigl rr CE D5 FE AND OR INarmalized intensity festl rl mh BE TF AND FOR Normalized intensity onrol 7 ho BE Ch FF AND TOR Rawitensitesd Ratio 2
43. CD ROM CD ROM oO Microarray Data nalysis Tool Ver3 2 A W MicroArray Name Experiment Name Test Cantral 3 V Copyright C Filgen Inc All Rights Reserved 3 Microarray Data Analysis Tool Wer3 2 3 1 i 1
44. oO Microarray Data nhnalysis Tool Ver3 2 Fileen Inc Wy 9 9 me CadeLink T MM Mouse Whole G Experiment Name Test ws Control Ta t Cu5 Test Control Oy5 Control Ia 4 iso oc ie os corrsocD ek 36227 MicroArra 184435146 905135038 944260976 1849396014 0958564 D061053 GE200017 FIDUCIAL 112515 284861 8560864 11409474 0332748 1587498 LG dn GE1488331 DISCOVERY NM 207255 328977 zs sa 124 8211 631445 6347602 12662052 0994777 D007555 LL 2 GE1461340 DISCOVERY 4 2125055 9761832 11745896 215H7728 0831084 n266933 GG nn GE1415502 DISCOVERY AaKUB054B 320593 5 5 43 7218 B50408 3467256 4317664 0245268 2027567 LL nn GE1560236 DISCOVERY BM115361 74053 6 442013 1354182 3026174 4380356 044749 1160073 EL nn GE155721n DISCOVERY AaK015221 74632 4930428F12Rik 176465156 8839 20486 863682736 1747603222 1023432 nn33415 GG 82 GE200017 FIDUCIAL se 17648 3271 8819 04688 8654 85624 1747390312 1018971 0027113 GG n2 GE200018 FIDUCIAL 5 1264625 8443374 4327286 1277066 1951194 D964357 LL nn GE1409715 DISCOVERY BX6366n3 78025 534201 2089428 7431438 2556685 1 354275 LL nn GE1572262 DISCOVERY AaK047664 1466n
45. No 1 Summarized data Summarization gt Summarize 0ptions OK Summarization Summarization Summarization 1
46. GO Term P value Gene Ontology Browser GO Term List 0K Copyright C Filgen Inc All Rights Reserved 38 Microarray Data Analysis Tool Ver3 2 GO Term Gene Ontology GO Slim 1 Changed Genes Filter 0ptions GO
47. B B B d gt Ii Next Cancel Graup Ratio calculatian Copyright C Filgen Inc All Rights Reserved 12 Microarray Data Analysis Tool Ver3 2 Group Ratio calculation Ratio 05352 Group Ratio calculatlon Ratio calculation Select Ratio A
48. Scatter Plot ScatterPlot Test_02 ws Dant ral Test 3 ws Control 100 000 100 DD 1 1 10 000 ON 1 000 1 000 g 1 100 10U o o 10 10 1 o 1 1 1 0 1 0 1 0 1 100 000 0 1 10 000 100 004 Test D2 est _I3 Test 4 ws Cont rol Test s Control 100 0 100 0 1 10 0100 Os ess dns Ra Esse 3 Sn 0 kd 002
49. GO Term 0 P 41 2 Total Genes GO Term P 41 3 Z score Changed Genes Total Genes Changed Genes GO Term
50. A3 GO Term GO Term GO Term Changed Genes Total Genes Z score P value 4 4 2 Z score P value Z score gt 0 P value lt 0 05 GO Term Gene Ontology P 38 hh TE ES ad gl 1HHE 5 ENSGUUUHUHG1 ENSGUHIHI Blectrnh trahsport LlhII enE ENGGUUHUUUHB1EEH LENSGUHIHI EEratinn ot precursor metabolites arnd EErgy i RgdE EMISGUUHHUH5TEEH ENSGIUHII Iitnchnridrinn dd 4 elg
51. Copyright C Filgen Inc All Rights Reserved 22 Microarray Data Analysis Tool Ver3 2 Ratio 2 Up A B C Ratio 2 1 Ratio 2 A B C 1 Ratio 2
52. One Sample test Student s t test One Way ANOVWD One Sample t test roredH call FDR Benjamini and Hochberg ea FDR Filter 0ptions P 37 0K P value MM Ss2ui 6 TFDR Benjamini and Hochberg FDR 2 8178 0 3145430358276509 0D 62908607655218 0 _ 8 220475 114062 0438865521907218 0633916864977093 0 P value FDR Filter Optlons 295688 156408 0257074353066249 0703571913654997 0
53. ET Summarize Options Mean hledian Log2Ratinn Ratia owee Summarization Summarize Options lgnored cels 1 Quality flag 1
54. Reset Reset _ OK Ok Cance Filter option Ratio 2 Up A B Ratio 2 or or or or
55. or 0 or 4 Gene Ontology GO Slim Pathway Gene Ontology GO Slim Pathway Summarization
56. Select Ignored cells 1 I Per Array Normalization Next Ratio Ratio Group Ratio calculatllon
57. Net intensity 10 10 Per Array Normalization Ratio 1 Median 2 Mean 3 Quantile 4 Control gene
58. Group Edit Next 1 CondeLink Th onuse Whole Ehnn Test 2 Cinrtrol Conde Link Th Mouse Whole Ehnn Test 3 Cinrtrol CondeLink Th ouse Whole Genor Test 4 Cinntrnl Tnun Edit ext CE Copyright C Filgen Inc All Rights Reserved 7 Microarray Data Analysis Tool Wer3 2 Group Edit Group Editl Add gt lt Remove 5 0K
59. Filer option RR Scatterplot ScatterPlot Copyright C Filgen Inc All Rights Reserved 30 Microarray Data Analysis Tool Ver3 2 5 Scatter Plot Plot window Scatter Plot ScatterPlot ScatterPlot Scatter Plot ScatterPlot Normalized intensity Per Array Normalized Intensity XX Normalized intensity Per Array Normalized intensity Y intensity intensity
60. 2 A Ratio 2 Up A Ratio 2 A Ratio 2 Up A 2
61. 0 3 Single Inkage clustering 2 Average Linkage Csteing Complete Linkage Custeing Single Linkage Chsteing 2 or 2 1 Average linkage clustering TreeView cdt gtr TreeViewCluster 4 TreeView cdt 6 Cluster and TreeView
62. Granh Experiment name Sample Sampls name Sample Granh scale Samplg Ratio Ratio Ratio 1 Ratio Flat Scatter Plot Tanh _ OK OK Scatter Plot Scatter Plot Cancel Scatter Plot options Copyright C Filgen Inc All Rights Reserved 33 Microarray Data Analysis Tool Ver3 2 Scatter Plot Scatter Plot
63. Signal 1 Ignored cells 1 0 Search Option Block Row Column or Ratio 2 Ratio 0 5 Ratio 2 0 5 or or Select Block Row Column
64. Olign ID nlign_i 1g HgHHI1a4H1 HaHHI18481 HDODT S73 HaHH 11488 He HgHHIHI4GE HaHH1 7214 HgHHHHBGGH HgHH 1 HaHHI11g81 HaHHIEZEIHH IENSGHHHHUOGH237 ENSEGUHHHHHEH 4 ENSGUHHHHHTE ENSGUHHHHH1938 ENMSGUHHHHHGE1GH ENSEGUHHHHHE 7 ENSEGUHHHHHE 7 ENSGUHHHH1B ENSGUHHHHHG818HI ENMSGUHHHHHEBSHB ENSEGUHHHHHGB 724 PRKWWNK1 NP 79050 HDACGTA EE _HLM MF HH TFP5aBFT HG F149 ST HF SDD 72 TA ENSGUHHHHHGB TET HHM 18gHH 21544 T1558 EPC ET nd dng4 1 PWM 15gHg MM MM 9 13 11 2 15 14 15 42 18 4 18 10 5 geH 13 18 11 14 1 HaaHa ed dg1H 4 TD 115 11 nina T1210 7 818 JH dgdh HBHdB den 1 1 laa Ti Db 12 gg a Eyer lt 1 2 1
65. or Scatter Plot 36227 MicroArray Name CadeLink Bioarray Mouse Who Experiment name Test vs Control Test Oy5 Test Control Cy5 IContol 1870 0 GEss001 DISCOVERY NM 007919 13706 RP23 395H4 4 elastase 2a NW n07919 Mm4516 FNSMUSG000000585 PF a1871 0 GE34488 DISCOVERY NM 008130 14634 Gli3 GLLKruppel family member GLI3 NM 008130 Mm5098 ENSMUSGOn00nH2131 Q 31872 0 GE1462895 DISCOVERY AK035742 Mus musculus adult male urinary bladde a1873 p GE145n479 DISCOVERY BG342824 100040093 100040093 predicted gene 100040093 XM 001474080 Mm206197 31874 2 GE1420139 DISCOVERY 31875 0 GE1493063 DISCOVERY CF577741 AGENCOURT 13211455 updated NIH_M a1876 p GE34306 DISCOVERY NM n08988 immunoglbulin superfamily DCC subclNNM HO8988 Mm 392333 Mm41529 ENSMUSGO0O0003239Q a1877 0 GE33695 DISCOVERY NM 009 20617 Snca synuclein alpha NM 001042451 NM OU Mm17484 ENSMUSGn00025880 S Pl i 31878 0 GE1419052 DISCOVERY N2823 76589 Unc5cl unc 5 homolog C G elsgans like NM152823 Mm311629 ENSMUSGO00004359Q C d t t e O t 1879 0 GE1492233 DISCOVERY BB645934 BB645934 RIKEN fullength enriched n GE1443287 DISCOVET BM119025 Ln919E07 3
66. Group Edit GO Pathway Copyright C Filgen Inc All Rights Reserved 6 Microarray Data Analysis Tool Wer3 2 2 Add ICE Delete
67. ETT 9 select Ww select select West ws Control Cinde Link tT hts ause Whole Genoar Test 1 Ginntrol i Test ws Cptrol CindeLink tT hd Mouse Whole Genoanr Test 2 Cnntrol Copyright C Filgen Inc All Rights Reserved 17 Microarray Data Analysis Tool Ver3 2 4 Filter 0ptions Filter Options Filter Options 1 Signal Search Option or Cor
68. Mean No Median No Log2Ratio Ratio Summarization Log2Ratio 1 Normalized intensity llog2ratiol Signal log2ratio Ratio Ratio 1 Normalized intensity tratiol Signal ratio Log2Ratio Summarization Rati
69. Ratio Fold Change Data Eit Lnwi data treatrment gt gt intensity et intensity HHH HI1 PFgr ray Manrmaligatinn Fer Ene nrmaligatinn Ratio calculation Fahce Copyright C Filgen Inc All Rights Reserved 10 Microarray Data Analysis Tool Wer3 2 Low data treatment intensity Net intensity Net intensity 0 001 0 001 leg Lam data treatment 0 et intengity 1n et intensity DDT EL OD1
70. 1 Summarization Negative Control 2 Filter 0ptlons Keyword Negative Control 3 4 Filter 0ptions CutOff intensity Test Control Normalized intensity lsum CutOff
71. GO Slim ratio 2 0 5 GO Term GO Term 1 Signal Filter 0ptions GO
72. Pathway lt Pathway Pathwayr P value Pathwal OUT PF waluar GenMaPF Fathmaw List 1 2 E 1 Fathwaywg Tntal Gang 1 Fahce Total Gene pathway Pathway Gene Ontology Z score P
73. 2 0 0 GO Term Changed Genes 15 4 GO Term 4 GO Term 15 score GO Term Changed Genes GO Term GO Term Changed Genes Total Genes GO Term GO Term Changed Genes Total Genes 4
74. GO Term List Gene Ontology lt ID Iv cellular component Iv biological process cee Gene Ontology GO Term List Term molecular_ function cellular component biological process GO Term GO Term 1 D intensity ratio D GO Term ID Probe ID Entrez Gene ID 1
75. o 10 1 0 1 1 10 100 1 000 10 000 100 000 0 1 1 10 100 10 000 100 000 Test 04 Test _I1 Plot window Scatter Plot Plot window Plot window or 1 Blank Signal Copyright C Filgen Inc All Rights Reserved 32 ScatterPlot options Microarray Data Analysis Tool Ver3 2 Scatter Plot Scatter Plot options
76. 1 Rgsgt ac Quality flag Fold Change Fold Change Ratio P 13 Copyright C Filgen Inc All Rights Reserved 20 Microarray Data Analysis Tool Ver3 2 canrolystest 1
77. GO Term GO Term Keyword Go GO Term Term Go Term GeneOntology 2 Term lreceptor actiyity Keywuord Term Changed Genes Total Genes Zscore P value molecular function 169d0 19912899 antigxidant actiyity 1 4412 31664 auxiliary transpart protein actiyity 1 27D 21085 2590 374 4328 binding 109d2 14756 21 kh IIU614 1 catalytic activity 105 15 6749888 63 1 48E 13 96802644 chemaattractant actiyity 2 1 9795 chemorepellent activity nD 11112 1 electron carrier activity 226226 1 65E 8 5425139 enzyme reeulator activity 8U 971113 1 metallochaperone activity 10 Dn 1 25 562 1045 molecular transducer activity 281650 2 OD116 energy transducer actiyity DD 1 02 0661 9082 sjghal transducer actiyity 2816240 2 116 1801125 histi
78. 2 P value P value P value Ratio Group Ratio P value One Way ANOVA 2 k 2 P value P value k 3
79. Gene Ontology P 40 Pathway WikiPathways D Copyright C Filgen Inc All Rights Reserved 43 Microarray Data Analysis Tool Ver3 2 Pathway List Pathway Browser Pathway Name System Pathway Name Pathway List 39 WikiPathways 1 iMm Striated Muscle Contraction WP216 21133 4528 UIU315 Entrez Gene 1145g Entrez_Gene 213g3 Entrez_ Gene 21925 E TT Mm_Matrix_ Metalloproteinases WP441 21608 25 2934 04702 Entrez Gene 17386 Entrez Gene 23948 WikiPathways hm _ Ovarian Infertility Genes WP273 21253 gD 2 573 II6381 Entrez_ Gene 12167Entrez_Gene 19217 WikiPathways him_Prostaglandin Synthesis and Reegulation WF374 21465 3D 2 573 Ii6381 Entrez_ Gene 11747 Entrez Gene 19217 WikiPathways hm_Eukarsyoti WikiPathways ranscription Initiation WFPh67 25591 WP7B 20845 WikiPathways him_Nucleotide GPCRs WP207 WikiPathways
80. 1 flag P 20 flag CodeLink Bioarray G 1 Scatter Plot Test 2 WS Control 100 000 84 3795 28 23325 115 95435 95 2847 39 9275 90 7589 103 96375 71 1358 155 5 11 4D 53 5469 94 58GH5 211 21 235 7945 282 1932 392 7168 124 0542 134 5091 126 51735 166 6214 253 72185 194 16U35 DD DD DD 6 5 9 9 DD co oO DD DD rr DD 6 DD rr cl 580 443 827 1831 intensity intensity intensity CutOff intensity 1 CutOff
81. 2 Copyright C Filgen Inc All Rights Reserved 23 Microarray Data Analysis Tool Ver3 2 A B C A B 1 A B Copyright C Filgen Inc All Rights Reserved 24 Microarray Data Analysis Tool Ver3 2 1
82. Copyright C Filgen Inc All Rights Reserved 49 Microarray Data Analysis Tool Ver3 2 13 Q1 Filter Options Excel 2Up 2Down 1 A1 Excel Fold Change Ratio 2 Filter 0ptions 1 2 CutOff 2 CutOff P 26 1 Keyword Flag 0 P 18 Normalized intensity tratiol 2 0 5
83. Cor Filter options EE Filter Options KeyWManrd My Function IE ck Guality flag Chramasnme Pe Peew 3 3 nored cells lgnared cells Scatternlat Cancel Search Option Search Option Keyword P value KeyWord KeyWord 5 KeyWord AND OR KeyWord
84. Range Scatter Plot Auto range Start XEnd X Start YEndY OK Lines Scatter Plot Shnwi fnld charges lines Fold change Ratliop Fold change Fold change Ratio Ratio 2 Ratio Scatter Plot 100 000 Test ws Control 10 000 100 000 Shom Ratin ne catterhlotionptimons Rangg ly Fito ranege tart Start Y End End Lines le Shnm fn charnees lines Lee fnlH charigg 2 lw Shanm Ratin line ma Flnt EE
85. Per Array Normalization Poete sc pry 8 _ ot Ratio Ratio Radio data lt Ratio Signal 2 Ratio 1 IR Ratio calculation SRate es me Ratio 1 Group Ratio calculation BE Group Ratio Group Ratin 1 6
86. snattighnre cell 1 1 33 Cahce lgnored cells Copyright C Filgen Inc All Rights Reserved 47 Microarray Data Analysis Tool Wer3 2 12 Cluster and TreeView Stanford EisenLab Cluster and TreeView Microarray Data Analysis Tool tx Cluster and TreeView Cluster and TreeView http ranalblgov EisenSoftware htm Top page gt Top page software Cluster TreeView Snare windows Al software produced by our as may ba gownissded angu
87. 4 P value Changed Genes Total Genes Changed Genes Total Genes GO Term Changed Genes Total Genes GO Term Z score GO Term Z score Gene Ontology 2 Gene Ontology Browser GO Slim Browser GO Term 2 Gene 0ntology Term GO Term GO Term 3
88. 2 1 A Ratio 2 Up A 1 Ratio 2 1 A Ratio 2 Up A 2 1 2
89. Flag 0 2 0 2 Flag 0 0 2 Excel Copyright C Filgen Inc All Rights Reserved 18 Microarray Data Analysis Tool Ver3 2 Function Panorama Ab Microarray XPRESS Profiler725 or Function Select
90. P 19 2 CutOff 1 Quality flag CutOff Quality flag G P 19 26 2 intensity CutOff Summarized data Normalized intensity suml Summarization Negative Control Excel CutOff P 19 26 lgnored cells lgnored cells P 20 Ratio Ignored cell Filter Options Flag lgnored cells Search Optian KeyWord Flag GE 0 SH 7 Ca I
91. Gene Ontology GO Slim Browser List List List P 39 40 kGO Filer 0ptions G0O Gene ntnlagy ene Ontoalney iene Cntoloegy Eiromser PF walue LL Terml 1T FP walue GU Term List TH QO Termvm Tatal Gene 1 Total Gene
92. P value FDR FDR PID i rh LF lgnored cells lgnored cells 1 Signal 1 lgnored cells 1 0 nrE cgl jnared cells Signal 2 Ratio 18 1
93. DISCOVERTY POSITIVE NEGATIVE FIDUCIAL GenBank Accession NCBI GenBank Accession No http www ncbinImnih gov sites entrez db nucleotide Entrez Gene ID Entrez Gene ID http www ncbinImnih gov sites entrez db gene Gene Symbol Gene Name RefSeq ID RefSeq ID http www ncbinImnih gov sites entrez db nucleotide Unigene ID Unigene ID http www ncbinImnih gov sites entrez2db unigene http www ensemblL org http www uniprotorg Chromosome No Chromosome Position i ee ie http www geneontology org i eile http www geneontology org GO cellular component http www geneontology org Probe Seque
94. we SD Gene Vector gt 2 Atleast 1 Dbservations abs yall gt 12 File Loaded Documents haradald Ys alillesl Mcluster i Load File File Format Help image cluster txt dob Name cluster 147 Faws Dataset has 15 Ca Save Maxyal Minval gt 2 Copyright C Filgen Inc All Rights Reserved 48 Microarray Data Analysis Tool Wer3 2 Hierarchical Clustering mpu ER or Gene Cluster a Ne Arrays Cluster Heataw Dame noamw See FiNer Data Adust Data Krarchical Custein K Means Clustering Sef Organizing Maps PCA MRA 1 Average linkage clustering 2 Calculate Weights Catcuate weights 2 Complete linkage clustering 2 or 2
95. 2 Ce Duehg Copyright C Filgen Inc All Rights Reserved 1 1 7 Microarray Data Analysis Tool Wer3 2 1 Ignored cells or ae ame 30 60
96. Functinh 1 Apoptosis En Ciell Cwcle hclear Cell Stress Cwtnskgletan Ptnskglgtnn EO Quality flag Excel Signal Test Contro CodeLink Test Control G CodeLink Bioarray ality flag lg LLt Chromosome Chromosome
97. 05 intensity 100 Copyright C Filgen Inc All Rights Reserved 19 Microarray Data Analysis Tool Wer3 2 Fold Change Signal Ratio Group Ratio data Fold change Ratio Ratio data intensity Group Ratio Group Ratio data Ratin data E FAND ranun Ratin data S P value FDR P value FDR le Pwalue
98. 2 NGene Ontology 2009 07 06 17 31 Pathway 2009 07 24 11 30 SearchFileDir 2009 07 28 17 18 2009 07 24 10 26 2009 07 24 10 27 MAtoolexe 3436 KB 2009 07 28 13 44 MAtool ini 1KB 2009 08 04 10 44 9 Microarray Data Arnalysis Tool Ver3 2 Use SDIGKE Adobe Acrobat 70 2008 05 30 15 07 2 MAtool exe CD ROM 1
99. Ch oO Tre DCOR 4 Filter Options CutOff 3 ly RE intensity su EMicrosoft Excel Test ys Control xls F GE 0 0 T D 0 00 al 9 Bmlz7u 88 AAQ 2 C D H I J K L N O F Ln a TM miRCURY LNA microRNA Array v 11 0 2 3 labeling sample name 4 Test hanaptrnl mean isumi 11 1 PO CO coartral 2 Down Ratio 5 5 harmalization Net intensity mean 1 Net intensity mean Sumj Ne5WsaCnrtrol meanfsumi 11 CutOff Eh Normalization FHLAG ProbelD _ 9 FN EA EN em gt EE EAE gt EAE gt EEE gt EOE gt rd ir a a micro EE e I microRNA miRE
100. MAtoolexe 1 Signal 3 1 1 2 aera ri TE Pathway 2 a a F i a a Signal
101. Scatter Plot Filter 0ptions Scatter plot 10 000 100 000 ex Test Control Ratio 2 Copyright C Filgen Inc All Rights Reserved 34 Microarray Data Analysis Tool Ver3 2 6 Summarization Summarization Probe ID 1 Summarization
102. 35213 a 1 26 12031687 G 1054715 G 96 2995 G 11653n5 G 79814 32528 ng1n48 01353 n96456 HI52n5 1 2 1 27 2315083 L 2557437 L 56 8393 L 1426163 L 2 45517 1 29583 222251 1 15219 D61603 69893 2a 1 28 6692 49685 G 80073706 G 8639 75488 7421 2125 G 1 29096 0 36845 107898 D10966 1 10886 D14907 2 1 29 7488931 G 87129397 G 99491897 G 8435g647 G 1 28395 ni36n59 114189 D19142 1 08866 D12255 25 1 30 25 35075 L 34 5945 L 1 41997 L 5 431 L nn56n1 4 158n9 DU4105 460661 21423 222274 2 1 1 20 63005 L4413258 L 8096145 L 6244435 L 1 50079 ni58573 D70156 51137 302686 1 59782 1 1 34 33147 L 83416582 L 6295258 Th 34 2358 L 1 22639 0 29442 1 84256 ng8171 666g6 n58434 1 2 1 35 8010 98452 G 8932 84985 G9411 72753 G 9394 80688 G 117485 23248 1 05361 D07534 1 17274 ni22g88 1 2 1 36 7651 54882 G 9240 4302 G 9240 4302 G 9493 2151 G 1 20765 n27221 1 n 1 24069 031114 1 0 1 39 147 09112 G 15607345 G 14895943 G 15788385 G 1 0127 nn1821 95442 H06731 1 7337 10215 a 1 40 40 52577 L 12 6843 L 2912308 L 73 701 L 71863 47668 2 29599 1 19912 1 81862 86284 E no 1 42 713916015 G 8782 92627 G8931 47435 G 864877075 G 1 25105 0 32314 1 01691 nn242 121145 n27674 Cv gt DE 3 Ratio Signal 2 Net intensity Per Array Normalized intensity Quality flag
103. dD 2 045 i10223 Entrez Gene 13871 Entrez Gene 68705 MD MN MM MN mM hm_ Tryptophan_metab 4 1 881 11903 Entrez Gene 11751 Entrez Gene 765507 4 4 ntrez Gene 1 44 2 Prostaglandin Synthe and Regulation Mus musculus WikiPathways Windows Internet Explorer hm_TGF_Beta Sijgnaling_ Pathway_WP11 WikiPathways Mm_Circadian_Exercise_WP544 29533 AD AL2G WikiPathways lt Prostaglandin Synthesis and Regulation M O Mm_Kit Receptor_Signaling_Pathwway_WP407 21538 en bo etn Oko ne r g htp77www wikipathways nrg indexphp PathwayWP374 le _ Log in create account WikiPathways Mm_Prateasnme_Degradatinn_WP519 21770 a DR RRS ource WikiPathways him Cytoplasmic_Ribosomal_Proteins WP163 21023 _ a Prostaglandin Synthesis and Regulation Mus musculus WikiPathways lim Small Ligand GFCRs WwP353 21419 Contents hide WikiPathways Mm_Hedeehog_ Signaling_Pathway WP1165 20927 WikiPathways hm Cytokines_and Inflammatory_Response BioCarta WWP222 21145 WikiPathways Mm_TNF alpha NF kE Signaling_Pathway WwWFP246 21197 3 Bibliography au PA 4 Categories WikiPathways him MAPK Cascade_WP251 21207 ms 5 His
104. 22527 45 n28446 181371 1 6 1 6 12 1952 L 1343 12 L 28 1026 L 8 14265 L 233808 1 22532 20925 1 06523 067745 581g1 1 7 7975n9073 G 876873655 G gn5286133 G 847297098 G 113514 n18287 1 0324 nn46 106243 ni8737 gm 1 8 64898921 G 874525n5 G 83129983 G 743nH6617 G 1 28ng1 n35717 D95057 07313 1 14487 19518 9 1 10 9 32457 L 84 4648 L 1957465 L 46 3403 L 32996 159964 023175 210936 78113 0 35636 1 12 371615 L 5325 12 L 1380325 L 2673362 L 00635 nn913 25922 4778 1 94906 0 96278 1 97 2Q065 4002193 1 L 108 946 G 7509098 L 11198 016324 272216 1 44475 77182 H37366 1 LI _ 1 rn 4 ks Rs G 821876037 G Reatio fe TD I c fa 1 15 7781 83803 G 7717 97508 G 848222703 G 7947 93347 G 1 09 D12433 1 09902 013622 1 02134 nn3n47 1 1 17 24 8589 L 8096748 L 1828317 L 13867 L 073548 44325 5904 76024 205716 1 04065 1 1 18 79 9148 L 72 0002 L 4691085 L 4803578 L n587n1 076854 65154 61808 D6009 783435 16 1 19 21 20818 L 430173 L 2556752 L 179166 L 1 2555 ni26969 ni59435 0 7506 Dn8448 024332 1 20 3365098 L 35 2599 L nn1 L 2724165 L 3E 5 15 3836 3E 5 1510574 809g54 30483 1 21 66453656 G 864877U75 G 923052492 G 7651 54882 G 1 38902 047406 106726 0 09392 115141 02034 9 1 22 6507 734 G 7488931 G 8233 30602 G 6986 72938 G 1 26516 0 33932 1 06251 008748 1 0736 D10246 2m 1 24 3547397 L 4381868 L 46436n5 L 277913 L 1 3 gn2 ni38848 1 06459 ni9n3 78343
105. GO Term 1 1 1 GO Term Go Term List 5353 2 Term 2 33 18569 In 3 98 82 cellular_companent podosome LIUH144 10556 cellular component podosome 2 3 18569 0144 45898 11 426 47 cellular component striated muscle thin filament 3 D 291 8676 024 EE 82 cellular component striated muscle thin filament 30 29d 8676 002 E 97 cellular component striated muscle thin filament 30 291 8676 002 47 cellular component ribonucleoprotein complex 10d 55Q8 4191 DO0071 AN 39 D Bee m sm m cellular component ribonucleoprotein complex 10d 755 Q8 4181 Il GO Term List 1184 10d 755 98 4181 Il 1 10Q 755Q8 4181 0H712 32694 8 303 103 Term 10d 755Q8 4181 0H712 46122 OO 11 428 47 10 755 98 4181 nH7
106. Gls 1299342 4027718 9215864 13243582 0437042 1194157 LG nn GE1537512 DISCOVERY CAB79667 17596 7618 875522072 869709024 17452 31096 1006684 On9611 GG 2 GE200018 FIDUCIAL 162096714 7781 9536 8113 29384 1589524744 D959161 0 060155 GG 2 GE2nnn19 FIDUCIAL 647787 3116752 34 11446 6528198 ng13616 013034 LL nn GE1388n74 DISCOVERY BF160755 382045 Gpr114 1371997 7202178 6708596 13910774 1073575 0102422 nn GE1425706 DISCOVERY BCn41149 208987 BCn25n31 63239 4325134 21 5796 643093 2053919 1038379 LL nn GE1514303 DISCOVERY 822155 218138 Gmds 596232 3546864 2486388 6033252 1 426513 Q512493 LL nn GE1575536 DSCOVERY BC048760 74288 Spemi 166448301 872491036 782909842 1655400878 1 114421 0156294 GG 2 GE200019 FIDUCIAL 155696714 7808 91672 759953526 15408 45198 1 27552 nn39211 GG 2 GE2nn020 FIDUCIAL 9 637897 4384494 21 964 648645B 2085903 160672 LL 2 GE1475586 DISCOVERY a 175404 10534702 7222682 17757384 1 458558 0544543 GL nn GE1564544 DISCOVERY AKD18340 76245 653n415H11Rik 2 370239 2577728 11 79214 3756942 2185971 11 128274 LL nn GE1566322 DSCOVERY NM 146178 232821 Ocdc106 2g 16426 2417 8093 4 8093 4 16186 8 1 n GG l2 GE200020 FIDUCIAL 2 17961 3995 8789 9211 9140 74142 17930 66252 D96162 0 056461 GG 02 GE200021 FIDUCIAL 5 33 3539 34 77864 non1 3477964 34778 64 15085914 LL nn GE1488008 DISCOVERY AMI45825 69378 1700013G23Rik 2 672184 4433764 23 85022 6818786 1859003 D894529 LL on GE1549778 DISCOVERY NM_181529 319508 Syt
107. HPLKITHP te LT ELE EF TO Pe li re ETL i EC HE NCC FN Eh Ets TO 1 1413 1 13 1W th EE EC HBnrmi a 1 ET Ga FTHHI It Eh hE TM EE ll FEHIIT SD53 3 1 EE MM LlHeoon he 1 ENSGOOOO BNSTOCO9 gg16277 Q791B41 033672 Q 0 HeOCOH 155 ENSGOOGG on is FL LI EP MN HL EE TN URI JHH 1 ST EE HHLILLH LET E5I Li WI BllHaoootes h30OQ1 7 ENSGOO00I EMBTOOOO 192 71BB 1 041605 O00547 0 0 HSoonl B87 EEO er Bj tz IPLLIT TE ESN Eh TI dL TP 1 5 EL TE EE e0002B27 ELE EAL ES TEN EE Et Li FE ng E EGRH 11 PTECTHE JP TB 1255 DBSHBWH D HEPTITITEPEMRT Copyright C Filgen Inc All Rights Reserved 46 Microarray Data Analysis Tool Wer3 2 11 Stanford EisenLab Cluster and TreeView
108. NIA Mouse Newborn Kidney ScatterPlot GE1401847 DisgOvERY CB181674 16709 Ktn1 kinectin 1 NM 008477 Mm3110 ENSMUSGOOO0002184 Q GE94328 DISCOVERY NM 007920 13709 EIf1 E74 like factor 1 NM 007920 Mm20938 ENSMUSGn00003646Q Test vs Cont rol GE34492 DISCOVERY NM 008136 14670 Gnall guanine nucleotide binding protein like NM O08136 Mm335754 ENSMUSGOOO0002442 P 100 000 ee GEM7368 DISCOVERY BB368592 69276 Sec62 SEC62 homolog cerevisiae NM 027016 Mm26017 ENSMUSGOO000027700 E1431809 DISCOVERY BE981092 UIM CG0 bcu c 06 0 UTs1 NIH BMA GE1486458 DISCOVERY Bx524760 BX524760 Soares mouse NML Mus mus GE34307 DISCOVERY NM 008989 19290 Pura purine rich element binding protein A NM 008989 Mm 231802 Mm39245 ENSMUSGO0On04399F GE33697 DISCOVERY BU938100 545182 ENSMUSGOOOODO predicted gene ENSMUSGOOOOOOE1848 XM 619421 Mm 446488 ENSMUSGOOOOODE184 Q GE1429882 DISCOVERY BY185413 14042 Ext1 exastoses muliple 1 NM 010162 Mm 309395 ENSMUSGOOO0006173 Pt GE1456353 DISCOVERY AKD35678 60533 ENSMUSGOOONNN1G49Q GE42197 DISCOVERY NM 139306 230379 m458684 ENSMUSGn00H3800Q GE38503 DISCOVERY NM 025431 66225 ENSMUSGOn000H2022Q GE39160 DISCOVERY CK787647 27410 J Parameter ENSMUSGONOONN2413Q GE130089 DISCOVERY NM 144850 223864 H Test vs Contral ENSMUSGOH00002246Q GE130341 DISCOVERY NM _144901 229663 d Me 31970 ENSMUSGn00006882Q GE37395 DISCOVERY NM 19453 54483 ENSMUSGOn0002253Q GE37560 DISCOVERY AKO82128 56349 m468637 ENSMUSGOn0nOH2121 Q
109. TE mi Li TiF pm T IE sc Cmmihml Next Normalized intensity llog2ratio 7 0K 1 Fieldl Narmalized intensity ftest le Field2 hormalized intensity IEnntrnl dd le Fieldd hor
110. by HSP70 WwP1656 21029 15 Dh 1 NE Ee hways org ndexphp PattmayWP57 lt gt MMm_Beta_Qxidatinn_Meta_Pathway WP141 28195 I 1 hm_Beta Oxidation of Unsaturated Fatty Acids wF204 21109 I 4 D 1 Mm_Biogenic_ Amine Synthesis WP522 217756 Dh 14 D 1 Mm_Blood Clotting Cascade WPA460 21648 Dh 18 D 1 I him_B Cell Receptor Signaling_Pathway WP274 21255 1 148 0682 1 EGFR1 Signaling Pathway Mus musculus hm Calcium_Reegulation_in the Cardiac Cell WPB53 21844 2 1465 II58 0I806 Ahpanaey hm CR RET_metabalism LTVER_WPB56 20795 In In Dh 1 Mm CAR RET_metabolism RPE WwP283 21275 In Dh D 1 hm CAR RET_metabolism BiGCaT WP223 21147 hn In D Samon him Cell cycle WP190 21079 In 83 D 1 naa him Cholesterol Bigsynthesis_WP1U3 20899 15 D 1 Home 3 Bibliography hm Circadian Exercise WP544 29533 2 dT D14093 him Complement_ Activation Classical Pathway WwFP200 21101 14 D 1 1 a Mm Complement_and Coagulatinn_ Cascades_KEGG_WP449 22601 Dh 58 D 1 1 en la HE pasNodes hm Cytokines_and jmflammataory_Respanse_BigCarta WP222 21145 1 23 ZD Download Mm_Cytonlasmic_Ribosnmal_Proteins_WP163 21023 2 Bs gz 229965 1 MMm_Delta Natch_Signaling_Pathwway_WP265 21237 6 In IE hm DNA Replication WP150 20997 Dn Dn 3 a 3 167 D546 048275 commun Mm_Eicosanoid Synthesis WP318 21349 0 22 Dn 1 F 30 him_Electron_ Transport Chain_WP295 21301 1 54 D174 D57596 Howio cit him_ESC Pluripotency_Pathways WP339 265
111. 04 2 108 49 65281 him_Eukaryotic_ Transcription Initiation WFP567 25591 2 dD 2 046 10223 Mm_F AS pathway_and Stress_induction of_ HSFP regulation WP571 21882 0 7 Dl UU Develonment Related changes Permanentlink Download Gene Ontology Pathway Pathway WikiPathways Pathway Z score P value Z Pathway List P value P value GO Term List
112. 12 49986 OC 12 464 55 cellular component podosome 2 3 18569 D000144 GES15878 GES8029 LU OO 50814 CO 0 2 15 cellular_component striated muscle thin filament 3 29 8676 000O249 GE57960GEB15878 GEBg029 19 5508 4181 IOO0072 52821 O 12 490 53 cellular component ribonucleoprotein complex 1n 55 98 4 181 000712 a 100 75508 8 DUDORZ 5374 12 99 102 cellular component MHC protein complex 30 54 0 6147 In137 7 54 ai BN 10605 3 A biological process pathogenesis 2 133 8192 In188 WS 5 cellular_companent muscle thin filament tropomyosin 2 1505 8112 19 0 lt cellular component filamentous actin 2 19d9 7151 no029 ID molecular function MHC class I receptor activity 26 21 1 6 759 In35 malecular_functian calcium dependent protein binding 26 211 6759 035 GE57960iGE59915 cellular component microsome 5 262262 3 991 DO0367 GE57499GE57696 GE61115C cellular component MHC class I protein complex 2 2363 6447 In41 GE61021 GE81120 cellular_component yesicular fractian 5 2797 3 805 DO0476 GE57499GE57696 GE61115C biological process icosanaid metabolic process 30 562 4 654 Un492 GE61115GE8U456 GE86136 malecular_functign TRNA binding 2 27 22 5 889 Un554 GE61347GE686746 biological process antigen processing and presentation of peptide or polysaccharic 22 2423 5881 Inh564 GE61021 GE8112D biglogical pracess positiye regulatian of innate immune response 20 2406
113. 15 64 8659 343697 31 11904 65 48874 1 104459 n14334 LL nn GE1568161 DISCOVERY BP757047 2 18071 4746 898803164 90291701 1801720174 0995444 0006588 GG 2 GE200021 FIDUCIAL 29 17828 252 9284 3385 832251338 17606 85188 1 115569 015778 GG 02 GE200022 FIDUCIAL a 2689089 156 3421 11590756 27224966 1 348852 0431732 GG nn GE1408499 DISCOVERY CB233063 mm 7335 1279628 6052292 733192 0211429 2241757 LL nn GE1403966 DISCOVERY CF751807 10041953 ENSMUSGOOOOC 17655 0459 8851 48692 861480116 17466 28808 1027474 0039102 GG oi2 GE200022 FIDUCIAL lt gt or 1 PE Excel Excel 2Up 2D0wn Filter 0ptions P 18 P 50 1 1
114. 24 0 747317 GG DD 881904688 8654 85624 1 018971 GG 0 B403 24982 8654 85624 D970929 GG 10 59 44632 4327286 1 373755 LL 84 43374 4327286 1 951194 LL 19 73472 43 27286 0 456053 EE 12 13 82414 20 89428 6G1623 LL Dn 53 4201 20 89428 2 556G85 LL 1391136 20 89428 0 665798 LL 13 97 08904 92 15864 1 053499 GG D 40 27718 92 15864 0 437042 LG 10889826 92 15864 1 181639 GG 14 7088 4173 8697 09024 815033 GG DD 8755 22072 8697 09024 1 006684 GG Dn 8476 117 8697 09024 0 974592 GG n 15 7847 7126 8113 29384 96726G GG 0 7781 9536 8113 29384 959161 GG 0 B569592356 8113 29384 1 056241 GG Di 17 25 05378 34 11445 0 734404 LL Dn 31 16752 34 11445 913616 LL 1841116 34 11445 539688 LL 18 79 93184 57 08596 1 191484 EE D 72 02178 67 08596 1 073575 LL 47 08226 5657 08596 0 70182 EE 19 21 394 21 05796 1 015958 LL 43 25134 21 05796 2 053919 LL In 25 76918 21 05796 1 223726 LL 20 33 857652 24 86388 1 361719 LL D 35 46854 24 86388 1 426513 LL In1 24863G8 4E 5 21 55637 7082 7829 09842 847825 GG 0 872491036 7829 09842 1 114421 GG 0 9274 56338 7829 09842 1 184636 GG 22 565487 14686 7599 53526 0 853624 GG 0 7808 91672 7599 53526 1 027552 GG 0 8322 51338 7599 53526 1 095135 GG DD 24 35 67918 21 01964 1 697421 LL 43 84494 21 01964 2 085903 LL 46 6007 21 01964 2 217008 LL 26 120 2035 72 22682 1 56425 GL 105 34702 72 22682 1 458558 GL 95 80044 72 22682 1 326383 GL 27 23 345655 11 79214 1 979764 I D 25 77728 11 79214 2 185971 LL 56 98256 11 79214 4 532249 LL 2
115. 5881 HUU564 GE6U158 GE79982 molecular function oxidareductase actiyity acting on CH OH group of donors 4D 181 3 962 II5 GE7938HGEB5489GE86136C malecular_functian structural cnnstituent of ribosnme 55 2g5295 363 HIU6HG GE545368GE58363 GE61347 lt gt Copyright C Filgen Inc All Rights Reserved 40 Microarray Data Analysis Tool Ver3 2 GO Term GO Term ID Probe ID Entrez Gene ID ID D GO Term GO Term Gene Ontology GO Term GO Term Changed Genes Total Genes
116. 8 5687 50802 8093 4 0 826292 GG D 8093 4 8093 4 1 GG 0 8716 75566 8093 4 1 07702 GG 29 7808 91672 9140 74142 854298 GG D0 8789 9211 9140 74142 96162 GG 0 9958 33106 9140 74142 1 089445 GG n 30 25 55156 in1 25551 56 LL 34 77864 1 34778 64 LL 1 43902 In1 1439 02 LL D 1 20 79854 23 85022 872048 LL D 4433J4 23 85022 1 859003 LL 31 16218 23 85H22 1 306578 LL 34 51 5076 31 11904 1 65518 EE D 34 3697 31 11904 1 104459 LL 5653 01084 31 11904 2 024832 LL 35 80965716 9029 1701 896713 GG 0 8988 03164 9029 1701 995444 GG 0 9438 6289 9029 1701 1 045348 GG 36 7707 98222 8322 51338 92616 GG 0 92843385 8322 51338 1 115569 GG 0 92843385 8322 51338 1 115569 GG DD 39 147 38594 115 90756 1 271582 GG Dn 156 3421 115 90756 1 348852 GG 149 2217 115 90756 1 28742 GG Ell 40 7618 50 52292 0 673494 EE Dn 12 79628 650 52292 211429 LL 29 2932 552292 0 484002 EE 42 7141 11318 8614 80116 0 828935 GG DD 8851 48692 861480116 1 027474 GG 89g85 GI8 861480116 1 043043 GG 0 O us i uu lt gt 2 lt 1 Copyright C Filgen Inc All Rights Reserved 3 2 lw Microarray ata Analysis Tool Ver3 2 Signal Signal 2
117. Data Analysis Tool Wer3 2 4 mw ea fmm iTesta ws Cantral TestB ws Cantral TestC ws Contral TestD ws Contral TestE ws Cantral Cancel careel Signal Scatter Plot Signal 4 Scatter Plot 1 Filter 0ptions
118. E 5 ENGGUHUUHHHHUEGHB ENGGUHHIH sndoplasmic reticulum TED OT ENSGUHHHHH5ET1HB E MSDN ecCeptor actieity 1315H 1 2 OT ES ENSGUHHHHHHBGHH E MSO Ehal transducer actreity 1550 45 2 3 OT ENSGUHHHHHHBGHH E isa 1 HH11 525 525ij ghBg HH18ii UClEus 131 2 9 2 182g HHgHHB ENSGHHUHHHHHH ENSIGHHIHH ElBEtFn CaFTIET actreitsy GO Term G0 Term Copyright C Filgen Inc All Rights Reserved 51 14 Microarray Data Analysis Tool Ver3 2 2005 2005 10 2006 4 2006 9 2007 6 2008 3 2009 9 Ver 1 0 Ver 1 1 Ver 1 2 Ver 1 4 Ver 2 0 Ver 3 0 Ve 3 2 Copyright C Filgen Inc All Rights Reserved 52
119. Filgen inc hip nannfilrm hnnl 1 Microarray ata Analysis Tool Ver3 2 User Manual 2069 5 456 0032 15 1 Tel 052 624 4388 9 00 17 00 Fax 052 624 4389 E Mail biosupport filgen jp http www filgen jp Copyright C Filgen Inc All Rights Reserved I ON 2 Microarray Data Analysis Too
120. GE40022 DISCOVERY AaKO16906 654409 GE40232 DISCOVERY NM 010936 18171 Row ENSMUSGOOODND22800 2 NM 007919 elastase 2A Sa199 DISCOVERY NM _138648 108078 Cnlumn 1 000 10 000 100 000 Plot window Scatter Plot Signal 1 X Y Signal Signal X Y 4 Copyright C Filgen Inc All Rights Reserved 31 Microarray
121. ac Copyright C Filgen Inc All Rights Reserved 13 Microarray Data Analysis Tool Ver3 2 Signal Signal Ratio calculation Group Ratio calculation Ratio Log2rallio BY Microarray Data Analysis Tool Ver3 2 Filgen Inc A CD i a EE 36227 Micraarray Name CodeLinkTM Mouse Whale G Experiment Name Test Oantral CC co co so el cui eae Og oe 1 8036 41822 G 9000 90503 G8524 6211 G7772 55698 G 1 06075 D08508 94708 007843 96717 004816 1 2 py 28 3082 L 73 6891 L 1005945 G 078976 34051 ds 1 07812 D10852 6 sa 1 35 86518 63 0875 L 60 8776 L 33 02553 L 1 6974 076333 ni96497 05144 ng282 0119 1 Mi G 1 356242 G 96 52367 L D981632 1R4 tio 8072 76083 0 39435 5 1 8 41135 L 7443 L 9 3986 L
122. ase EE microR 10 358 48 3 13 14 5831215 18 3025665 32 5763455 0 7436138256 0 4273745 II Empt Empty Empty 7217 d8 1 2 8U 364G5 46643317 1256 2000285 161 34545 6g33Bn5 5 4040 hsa iR MMATUHHU4 mmu miR 9 MIMATOODODODT 4 rno mif 12 g280 43 5 15 T6512739 6582g35 14466116 1 1g193123 02533n1 4390 mmu miR 7b MIMATOODDEGT rno mif ll 7U22 37 1 2 1 122611 52 323935 123 4465465 0D 980497937 H284135 4610 hsa miR 126 hilhdATOOODDS mmu miR 126 MIMATOOODODT 3 rno mif 14 7615 1 10 51 5566875 62 2725435 1241292315 1 028510841 D040557 Il 4700 hsa miR 140 MihAATOODDS mmu miR 1 4 MIM TUUUH15rna mif 1 7420 1 10 202 4649685 188 002766 3872814285 1 0894 5686 123534 5250 hsa miR 105 MMATHHHH1n2 7225 1 10 160 3630575 155 5281245 3195749395 D0 9394807456 HHBUU645 5730 hsa miR 208e hihiATOODD mmu miR 2UE MIMATOODODSZ rno mif rm Excel Nm CutOff C
123. dine phosphotransfer kinase a liu 1 morphogen activity Dn nD 1 quUorum Sensing response regulator nn 1 qUOrUM Sensing SjEhal generator a nD 1 TBCBDtnf actiyity 7 24482556 DOO0533 receptor sighalinrotein actiyity 15326 D14456 SH3 SH2 adaptor ativity ial 23293 1 twn cnmpanent response reeulator 2 1 two component sensor ctivity 1 50G0 Ii35n51 hutrient reserwoir actiyity nD Lia 1 vI EA proteasome regulatar activity iR 1 protein tag 1 structural mnlecule activity HU2G4 transcrintinn regulatar actiyity ik 5G925 translation regulatar activity 1 1513 H 1 transporter activity 116 1398 48 1 cellular component 168163 20458Nd1903 0 1 biological process 1608 18321976 1 Copyright C Filgen Inc All Rights Reserved 39 Microarray Data Analysis Tool Wer3 2 GO Term List GO Term P value P value GO Term
124. l Ver3 2 Filter option Scatter Plot Summarization Gene Ontology Pathway External Filter Cluster and TreeView Copyright C Filgen Inc All Rights Reserved P 2 P 4 17 P 18 30 P 31 34 P 35 P 36 37 P 38 41 P 42 44 P 45 46 P 47 P 48 49 P 50 51 P 52 Microarray Data Analysis Tool VeI3 2 or or
125. lized intensity test Normalized intensity control Normalized intensity log2ratio Normalized intensity fratio log2 Quality flag Ignored cells 0 1 P value P value Benjamine amp Hochberg False Discovery Rate Raw intensity intensity Backgrounmd intensity Net intensity Raw intensity Background Net intensity ltes1 Net intensity controll Normalization Net intensity Signal Solect or Block Block Block Column Block Raw Intensity Raw intensity jntensity Background Background intensity Net intensity Net intensity Raw Intensity Background Per Array Normalized intensity Per Array Normaliza
126. lue FDR False Discovery Rate P value FDR Benjamini amp Hochberg 1995 Filter 0ptions FDR Copyright C Filgen Inc All Rights Reserved 37 Microarray Data Analysis Tool Wer3 2 8 Gene Ontology Gene Ontology Gene Ontology GO molecular func
127. malized intensity ratin le FieldH Iauality flag Field TE Fi uml Frey nce Copyright C Filgen Inc All Rights Reserved 8 Microarray Data Analysis Tool Wer3 2 8D Microarray Data nnalysis Tool Ver3 2 TT SA Filgen Inc 36227 1 8121 97266 94426096 8Gn141 0 9gU51 35H38 9442 60976 95854 BU65B53 9442 60976 0 911459 2 93 10072 85 60864 1 087515 GG 28 4861 85 U8G4 332748 LGS 73 5989 85 60864 0 560882 LG 3 35 0745 653 47602 D568317 LL Dn 63 1445 653 47602 0 994777 LL 60 96014 53 476502 0 960365 LL 4 126 88808 11745896 1 0802765 GG 97 61832 117 45896 0D 831084 GG D103 47784 117 45896 0 88097 GG 5 33 24344 34 57255 958782 LL D 8 50408 34 57255 245268 LL D 7 5337 34 57255 0217281 LL 5 12 1511 30 26174 0 401533 LL Dn 13 54182 30 26174 0 44749 LL 28 28814 30 26174 0 934782 EE 7 BU5651126 8636 82736 0 932809 GG 0 883920486 B636 82736 1 023432 GG 0 D938 B636 82736 1 053808 GG Di 8 6467 9214 B654 856
128. nce CodeLink Human Whole Genome Bioarray or Copyright C Filgen Inc All Rights Reserved 16 Microarray Data Analysis Tool Ver3 2 ce or 1 Blank Select Filter 0ption Select Select Select CUTT 7 select
129. o Copyright C Filgen Inc All Rights Reserved 35 Microarray Data Analysis Tool VeI3 2 7 Signal 1 P value FDR re oe
130. sed veutabie ang or Source cede requre 2 Icone Wo rm Stan ed SETUP EXE Eisen Lab Uh rsity For informa do n haw to eS alic MM lt fac Cluster exe SI use nf the GMEP s SR Re a 2 fram IN gt uster 6XC raord anee 1 NN 0 tL PE Te rm a a NE NG 0 00 0 _ TreeView exe LM i functional Register He transcription factor nding st Regis 5 and js a 9 track usage and to nrnvid sftvar wpda ate a egistr lo not required to download softw Cster 1 Microarray Data Analysis Tool cluster txt Microarray Data Analysis Tool FS RDO eit Ril og2
131. tion biological process cellular component 3 3 Apoptosis cell division GO Term 1 GO Term GO Term CodeLinkK Human Mouse Rat Whole Genome Bioarray GO Gene Ontology GO Term Gene Ontology GO Slim GO
132. tion intensity Per Gene Normalized intensity Per Gene Normalization Intensity ratio Per Array Normalized intensity log2ratlo ratio log2 Quality flag Ignored cells 0 1 P value FDR P value Benjamine amp Hochberg False Discovery Rate microRNA Summarization Raw Raw intensity Background Copyright C Filgen Inc All Rights Reserved 15 Microarray Data Analysis Tool Ver3 2 or or Terms Descriptions Probe Name Applied Microarray Probe Type
133. tory WikiPathways Mm_TC Cycle WP434 21594 6 Pathway Info lt Download overview Recent Changes MostViewed MostEdited New Pathways Log in to edit pathway _ not working Download wv Curation Tags Gene Ontology Pathway Name ID Probe ID Entrez Gene ID ER D D Changed Genes Total Genes Gene Ontology Pathwa
134. utOff 1 P 20 2 CutOff 100 200 2 100 CutOff Signal Signal Normalization Copyright C Filgen Inc All Rights Reserved 28 Microarray Data Analysis Tool Ver3 2 Signal Test Control Normalized intensity IsumD Normalization intensity Per Array Normalized intensity CutOff
135. value Gene Ontology P 39 Changed Genes Total Genes Gene Ontology P 44 Copyright C Filgen Inc All Rights Reserved 42 Microarray Data Analysis Tool Wer3 2 Gene Ontology 2 GenMAPP or WikiPathways NCBI BioSystems Pathway Browser 2 Pathway Pathway
136. y Name Pathway WikiPathways score Gene Ontology Gene Ontology P 38 P value Gene Ontology Gene Ontology P 38 Pathway Pathway Copyright C Filgen Inc All Rights Reserved 44 10 External Filter External Filter 2 2
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