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Series GSE1353 Query DataSets for GSE1353
Status Public on Sep 01, 2004
Title splitplotnestedANOVA
Organism Zea mays
Experiment type Expression profiling by array
Summary Determination of significant differential expression was undertaken with analysis of variance (ANOVA) style models. From the ideas provided by Kerr and Churchill (2001) and Wolfinger, et al. (2001), and based on the specific design of this experiment, the following ANOVA models were constructed:

Model (1)

y_gijklr = \mu + L_i + A(L)_j(i) + T_k + LT_ik + D_l + AD_jl + \epsilon_gijklr


Model (2)

r_gijklr = GL_gi + GA(L)_gj(i) + GT_gk + GLT_gik + GD_gl + GS(A)_gr(j) + \epsilon_gijklr


In model (1), y is the logarithm (base 2) of the intensity for a particular spot. L, T and D are global effects due to differences in lines (Mo17 and B73), treatments (control and UV exposure) and dyes, respectively, while LT represents interaction between lines and treatments. The AD interaction term is present as suggested by Wolfinger et al. to account for intensity scaling done on the two channels. The nested term, A(L), accounts for variation across replicate arrays in a slightly different fashion than that set forth in Kerr and Churchill's ANOVA models. Their approach considered connected designs; however, in this experiment, lines are not connected because no array has samples from two different lines hybridized to it. The output from model (1) is given in the file "standardized".Model (2) takes residuals from model (1) as normalized response values and includes gene specific effects. Additionally, it models replicate spot variation via the GS(A) term.
Both models were fit using the SAS/STAT® software's MIXED procedure, with model (2) being fit gene by gene. Observed significance levels for all effects tests were adjusted for multiplicity of testing by use of the Sidak method. Significance was assessed based on an experiment-wise significance level of 0.05.
The levels of expression of the SP10 negative controls were used to determine the log-ratio level for expression above background. All cDNAs with all levels below the SP10 median were set to background, thus diminishing their influence on the final list of genes. Ten genes, that may have been otherwise called significant, were removed from the 5366 total using this criterion. There are still 201 genes with at least one very low level; however, these were retained for significance testing as some may have significant expression level alterations in one line or condition. There were six cDNAs with significant differences between lines but not interaction or treatment; these genes were not analyzed further. A table of summary information for all genes is included as Table S1. Cluster analysis on gene expression levels was performed using the SAS v. 8 Enterprise Miner software Cluster node, using the default settings except for specifying input cluster number as equal to the total sample number. Clustering was performed separately on genes significant by interaction (Table S2) and genes significant by treatment (Table S3); the output cluster number is listed for each gene name in these tables.

The entire model (1) output file can be obtained by within the citation below.
 
 
Contributor(s) Blum JE, Casati P, Walbot V, Stapleton AE
Citation Split-plot microarray design allows sensitive detection of expression differences after ultraviolet radiation in the inbred parental lines of a key maize mapping population. BLUM, J. E.1; CASATI, P.2; WALBOT, V.2; STAPLETON, A. E. Plant, Cell & Environment, Volume 27, Number 11, November 2004 , pp. 1374-1386(13). DOI: 10.1111/j.1365-3040.2004.01230.x.
Submission date Apr 29, 2004
Last update date Mar 15, 2012
Contact name Ann Stapleton
E-mail(s) stapletona@uncw.edu
Phone 910 962-7267
Organization name University of North Carolina Wilmington
Department Biological Sciences
Street address 601 S. College
City Wilmington
State/province NC
ZIP/Postal code 29403
Country USA
 
Platforms (1)
GPL1208 Zea mays Unigene01_01_04
Samples (8)
GSM21917 B73Ch1greencontrol1
GSM21918 B73Ch1greenControl2
GSM21919 B73Ch1greenUV1
Relations
BioProject PRJNA90101

Table S1. All Genes That Passed Quality Control Standardized log2 median data after evaluation of Model (2) is shown; B73 and Mo17 ratios are median UV minus median control header descriptions
name (control ID number or Genbank number)
B73 control median log2 expression level
B73 UV median log2 expression level
Mo17 control median log2 expression level
M017 UV median log2 expression level
treatment P value
line P value
interaction P value
significance call
ratio B73 expression (control-UV)
ratio Mo17expression (control-UV)
TUC ID
Homolog1 PID
Homolog1 Desccription
Homolog 1 Species
Homolog2 PID
Homolog2 Description
Homolog2 Species
Homolog3 PID
Homolog3 Description
Homolog3 Species

Data table
name (control ID number or Genbank number) B73 control median log2 expression level B73 UV median log2 expression level Mo17 control median log2 expression level M017 UV median log2 expression level treatment P value line P value interaction P value significance call ratio B73 expression (control-UV) ratio Mo17expression (control-UV) TUC ID Homolog1 PID Homolog1 Desccription Homolog 1 Species Homolog2 PID Homolog2 Description Homolog2 Species Homolog3 PID Homolog3 Description Homolog3 Species
AI649528 -0.894013669 -0.787597191 -1.039641054 -1.334756913 0.962366328 1 0.002054712 interaction 0.106416478 -0.295115859
AI855296 2.08020197 2.122113872 -1.630711197 -2.087207863 0.330866096 1 0.000210169 interaction 0.041911902 -0.456496666 ZMtuc03-08-11.6542
AI947648 -2.600460083 -2.529414291 -2.504908655 -2.631563091 1 1 0.009379088 interaction 0.071045793 -0.126654436 ZMtuc03-08-11.18719
AI947977 -2.999748535 -2.918620398 -2.64448605 -3.022108155 0.078268104 1 0.006397473 interaction 0.081128137 -0.377622105 ZMtuc03-04-07.12014
AI948033 -2.178241571 -1.824936525 -2.339733259 -2.587048296 1 1 1.72196E-08 interaction 0.353305046 -0.247315037 ZMtuc03-08-11.3288 O-methyltransferase Zea mays Putative o-methyltransferase ZRP4 Oryza sativa Putative to o-methyltransferase ... Oryza sativa
AI948047 -2.238326613 -2.356790448 -2.215426235 -2.481409285 0.990554943 1 0.007798367 interaction -0.118463835 -0.26598305
AI948163 -2.332803495 -2.247472714 -2.420404542 -2.603365228 1 1 0.008635237 interaction 0.085330781 -0.182960685 Q8S052 P0678F11.26 protein Oryza sativa OJ1485_B09.3 Oryza sativa P0678F11.32 Oryza sativa
AW062052 0.580658281 0.691606201 -2.39549755 -2.997139055 0.999999843 1 0.011752451 interaction 0.110947919 -0.601641505 ZMtuc03-08-11.6571 Psst70 Pisum sativum 70 kDa heat shock protein Pisum sativum heat shock protein 70 Triticum aestivum
AW066000 -0.228603038 -0.089867909 -1.351740352 -1.524728297 1 1 0.000610977 interaction 0.138735129 -0.172987945 ZMtuc03-08-11.28761 hypothetical protein~similar to ... Oryza sativa unnamed protein product Solanum tuberosum putative protein Arabidopsis thaliana
AW191188 -2.817416248 -2.651850241 -2.411972302 -2.741132567 1 1 0.004896529 interaction 0.165566007 -0.329160265 ZMtuc03-08-11.25318 putative protein kinase Oryza sativa serinethreonine-protein kinase-l... Arabidopsis thaliana putative serine threonine-protei... Arabidopsis thaliana
AW191426 -0.957881605 -0.464622371 -2.022428872 -2.379029896 1 1 4.72299E-06 interaction 0.493259234 -0.356601024 ZMtuc03-08-11.13187
AW191766 -0.852652702 -0.686353568 -2.285053252 -2.633351903 0.338859589 1 0.000379671 interaction 0.166299134 -0.34829865 ZMtuc03-08-11.26809
AW215932 -0.589794504 -0.471592001 -2.275823864 -2.97057877 1 1 0.007571685 interaction 0.118202504 -0.694754906 ZMtuc03-08-11.23232
AW216013 -2.804482352 -2.694345106 -2.573281445 -2.725245321 1 1 0.003649094 interaction 0.110137246 -0.151963877
AW216078 0.381460085 0.679151585 -1.056554685 -1.277862582 1 1 0.015657649 interaction 0.297691499 -0.221307897 ZMtuc03-04-07.8032 protein phosphatase 2A regulator... Lolium perenne protein phosphatase 2A A subunit Oryza sativa phosphatase 2A regulatory A subu... Oryza sativa
AW216255 -0.63559673 -0.003302946 -1.48211385 -1.16549507 0.970924453 1 0.013243116 interaction 0.632293783 0.31661878 ZMtuc03-08-11.5750 OJ1081_B12.5 Oryza sativa F1N21.14 Arabidopsis thaliana At1g67325 Arabidopsis thaliana
AW224892 0.898210338 1.213185995 -0.845843705 -1.421632317 1 1 0.000471544 interaction 0.314975656 -0.575788612 P29193 "Phosphoenolpyruvate carboxylase, housek" Saccharum sp. Q8S0I7 Putative phosphoenolpyruvate carboxylase (E Oryza sativa O23946 Phosphoenolpyruvate carboxylase 1 (EC 4.1.1 Gossypium hirsutum
AW224973 -2.708845094 -2.449453633 -2.459078697 -2.624320053 0.365985804 1 2.65E-07 interaction 0.259391461 -0.165241356
AW224979 -2.483944325 -2.335733252 -2.255271069 -2.549726546 1 1 1.14778E-05 interaction 0.148211073 -0.294455477 ZMtuc03-08-11.1372 putative RNA-binding like protein Oryza sativa putative RNA-binding like protein Oryza sativa RNA-binding like protein Arabidopsis thaliana
AW231441 -1.703639133 -1.780689782 -2.006878304 -2.365479821 0.776938365 1 0.000921059 interaction -0.077050649 -0.358601517 zein Zea mays zein Zea mays 19kD alpha zein B3 Zea mays

Total number of rows: 5366

Table truncated, full table size 989 Kbytes.




Table S2. Manually Classified List of Genes Significant by Interaction and Treatment Interaction header descriptions
CLONE_ID
B73control log2 median
B73UV log2 median
Mo17control log2 median
Mo17UV log2 median
interaction P value
significance call
ratio B73 expression levels (UV minus control)
ratio Mo17 expression levels (UV minus contol)
line difference in expression change (ratio B73 minus ratio Mo17)
TUC_ID
Homolog1_PID
Homolog1_Desc
Homolog1_Species
Cluster Number

Data table
CLONE_ID B73control log2 median B73UV log2 median Mo17control log2 median Mo17UV log2 median interaction P value significance call ratio B73 expression levels (UV minus control) ratio Mo17 expression levels (UV minus contol) line difference in expression change (ratio B73 minus ratio Mo17) TUC_ID Homolog1_PID Homolog1_Desc Homolog1_Species Cluster Number
Total manually classified: 63
Translation:5
BE128853 -2.764788787 -2.729014467 -2.275107577 -2.579094142 1.87039E-05 treatment interaction 0.03577432 -0.303986565 0.339760885 ZMtuc02-12-23.6682 ribosomal protein L30 Argopecten irradians 6
AW787726 -0.572374758 -1.52569967 -0.42596059 -0.756993624 0.00491014 treatment interaction -0.953324911 -0.331033035 -0.622291876 ZMtuc03-08-11.12821 putative chloroplast 50S ribosom... Oryza sativa 13
AW066279 0.201089191 -1.035730865 0.764769865 -0.080553648 0.006343343 treatment interaction -1.236820057 -0.845323513 -0.391496544 ZMtuc03-08-11.25607 chloroplast ribosomal L1-like pr... Arabidopsis thaliana 13
AW147172 1.068360206 2.58970672 1.355807957 2.478318404 0.000757644 treatment interaction 1.521346514 1.122510447 0.398836067 protein disulfide isomerase Zea mays 12
AW352521 -0.119198007 -1.299987392 0.281072829 0.007040176 1.41349E-06 treatment interaction -1.180789385 -0.274032652 -0.906756733 ZMtuc02-12-23.8031 chloroplast RelA homologue 2 Oryza sativa 13
Metabolism: 13
AW331644 -3.569364277 -1.445633649 -2.915778228 -3.063030624 5.17162E-10 treatment interaction 2.123730628 -0.147252396 2.270983023 ZMtuc03-08-11.10115 putative UDP-glucose dehydrogenase Oryza sativa 2
AW313328 1.305333415 0.148960829 1.384074927 1.20025372 2.88099E-06 treatment interaction -1.156372586 -0.183821206 -0.97255138 ZMtuc03-08-11.22398 Q41739 "Thiazole biosynthetic enzyme 1-2, chlor" Zea mays 11
AW356013 1.148744777 0.385473767 1.232241589 1.211118521 0.006400737 treatment interaction -0.76327101 -0.021123068 -0.742147942 ZMtuc03-08-11.22399 thiamine biosynthetic enzyme Zea mays 11
AW360565 0.158441738 0.467788049 -1.03023439 -1.378199208 0.009243396 interaction 0.309346312 -0.347964818 0.65731113 putative stearoyl-acyl-carrier p... Oryza sativa 16
AW225182 -0.187838326 -1.350677227 -0.182125728 -0.562737535 0.004049456 treatment interaction -1.162838901 -0.380611807 -0.782227094 ZMtuc03-08-11.13029 putative aspartate aminotransfer... Oryza sativa 13
AW455631 1.024323218 0.232357005 0.347784186 0.841517991 7.65898E-05 interaction -0.791966213 0.493733805 -1.285700018 ZMtuc03-08-11.22545 putative alanine transaminase Oryza sativa 11
AW224892 0.898210338 1.213185995 -0.845843705 -1.421632317 0.000471544 interaction 0.314975656 -0.575788612 0.890764269 P29193 "Phosphoenolpyruvate carboxylase, housek" Saccharum sp. 8
AW216244 -0.93226785 -0.037541004 -0.599691129 -0.580448023 3.74541E-06 treatment interaction 0.894726847 0.019243106 0.875483741 ZMtuc03-08-11.6650 NADH dependent Glutamate Synthase Oryza sativa 7
AW424534 0.816833458 0.03318335 0.638759121 0.45126771 3.71631E-08 treatment interaction -0.783650108 -0.187491411 -0.596158697 chloroplastic aldolase Oryza sativa 13
BE056237 -1.160189205 -1.279673511 -0.734814191 -0.486228855 0.014055502 interaction -0.119484306 0.248585336 -0.368069643 ZMtuc02-12-23.6638 "2-oxoglutarate dehydrogenase, E1..." Arabidopsis thaliana 4
AW330974 0.758770703 0.186755483 0.78704823 0.743666264 0.009779814 treatment interaction -0.57201522 -0.043381966 -0.528633254 aldolase Oryza sativa 11
AW787230 -1.411853004 -0.871121187 -1.007500862 -1.005458084 0.004215304 treatment interaction 0.540731817 0.002042778 0.53868904 aldehyde dehydrogenase Oryza sativa 4

Total number of rows: 179

Table truncated, full table size 27 Kbytes.




Table S3. Manually Classified List of Genes Significant by Treatment header descriptions
CLONE_ID
B73control log2 median
B73UV log2 median
Mo17control log2 median
Mo17UV log2 median
treatment P value
significance call
ratio B73 expression levels (UV minus control)
ratio Mo17 expression levels (UV minus contol)
line difference in expression change (ratio B73 minus ratio Mo17)
TUC_ID
Homolog1_PID
Homolog1_Desc
Homolog1_Species
Cluster Number

Data table
CLONE_ID B73control log2 median B73UV log2 median Mo17control log2 median Mo17UV log2 median treatment P value significance call ratio B73 expression levels (UV minus control) ratio Mo17 expression levels (UV minus contol) line difference in expression change (ratio B73 minus ratio Mo17) TUC_ID Homolog1_PID Homolog1_Desc Homolog1_Species Cluster Number
Total manually classified: 446
Translation: 59
Ribosomal proteins:32
AW585293 0.93808127 1.565819834 1.357137586 1.759856203 2.14597E-09 treatment 0.627738564 0.402718617 0.51522859 ZMtuc03-04-07.16583 40S ribosomal protein S2 Picea abies 32
AW324592 -0.785020108 -0.437960174 -0.682290618 -0.491776601 0.005501332 treatment 0.347059934 0.190514017 0.268786976 ZMtuc03-04-07.16587 40S ribosomal protein S2 homolog Arabidopsis thaliana 13
AW461060 1.181305145 1.374706051 1.313487681 1.633037523 0.007387521 treatment 0.193400906 0.319549841 0.256475374 ZMtuc03-04-07.4990 40S ribosomal protein S24 Zea mays 32
AW424505 1.192678938 1.532901493 1.150190705 1.779992944 4.86842E-05 treatment 0.340222555 0.629802239 0.485012397 ZMtuc03-04-07.20939 40S ribosomal protein S27 homolog Zea mays 32
AW231530 0.210829696 0.697442837 -0.08819041 0.533577776 1.8332E-12 treatment 0.486613141 0.621768187 0.554190664 ZMtuc03-04-07.14126 60S acidic ribosomal protein P0 Zea mays 5
AW231758 1.416862187 1.716780055 1.135163754 1.679346631 1.79392E-06 treatment 0.299917868 0.544182877 0.422050373 ZMtuc03-04-07.14127 60S acidic ribosomal protein P0 Zea mays 32
AW330871 -0.955536066 -0.791574752 -0.912630011 -0.622487036 0.000119716 treatment 0.163961315 0.290142974 0.227052145 ZMtuc03-04-07.14163 60S ribosomal protein L17 Oryza sativa 72
AW438254 1.705297203 1.959267388 1.550252619 1.815308061 0.001105188 treatment 0.253970185 0.265055442 0.259512814 ZMtuc03-04-07.21868 60S ribosomal protein L21 Oryza sativa 67
AW330593 -1.046268739 -2.063866855 -0.503505993 -1.214740371 6.8691E-08 treatment -1.017598117 -0.711234378 -0.864416247 ZMtuc02-12-23.8184 chloroplast ribosomal L1-like pr... Arabidopsis thaliana 60
AW455717 1.165296452 2.161192783 1.262994745 2.072176061 6.10623E-15 treatment 0.995896331 0.809181317 0.902538824 ZMtuc03-04-07.10994 Putative 40S Ribosomal protein Oryza sativa 31
AW225068 0.935740425 1.345169687 1.007005392 1.588333541 0.010129281 treatment 0.409429262 0.581328149 0.495378705 ZMtuc03-04-07.10991 Putative 40S Ribosomal protein Oryza sativa 32
AI649536 -0.43516148 0.115157713 -0.793926999 -0.292810996 1.29996E-11 treatment 0.550319193 0.501116003 0.525717598 ZMtuc03-04-07.4125 putative 40S ribosomal protein S19 Arabidopsis thaliana 53
AW438242 0.522821671 0.94187086 1.050767225 1.316345126 0.004755206 treatment 0.419049189 0.2655779 0.342313545 ZMtuc03-04-07.21815 putative 60S ribosomal protein Oryza sativa 79
AW331529 -0.987857596 -0.527192855 -1.024897435 -0.283374204 0.000105114 treatment 0.460664741 0.741523231 0.601093986 ZMtuc03-04-07.9502 putative 60S ribosomal protein Arabidopsis thaliana 13
AW400322 0.942128421 1.79514827 0.837952193 2.100278294 1.11022E-15 treatment 0.853019849 1.262326101 1.057672975 ZMtuc03-04-07.12982 putative 60S ribosomal protein L1 Arabidopsis thaliana 4
BE055937 -1.846259348 -1.42422925 -1.545534629 -1.004068963 0.000101251 treatment 0.422030098 0.541465666 0.481747882 ZMtuc03-04-07.20467 putative 60S ribosomal protein L38 Oryza sativa 23
AI948043 -0.521270188 -0.782644602 0.05165496 -0.254519277 6.98444E-06 treatment -0.261374414 -0.306174237 -0.283774325 ZMtuc03-04-07.8200 putative chloroplast 50S ribosom... Oryza sativa 41

Total number of rows: 972

Table truncated, full table size 151 Kbytes.




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