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Series GSE1328 Query DataSets for GSE1328
Status Public on Jun 12, 2004
Title VC110+112 mRNA levels in Wild-type versus ddm1 bolting Arabidopsis thaliana plants
Organism Arabidopsis thaliana
Experiment type Expression profiling by genome tiling array
Summary Biological replicate of EV23+24.
The two samples in this series are complementary hybridizations in a dye-swap analysis.
Below is the normalized result of the paired dye swap samples VC110 and VC112.
The ANOVA model of Kerr, Martin and Churchill (2000) was used to analyze the data from the dye-swap experiments, with terms included to account for gene, dye-by-gene, treatment-by-gene, and random error terms.
To account for the number of hypothesis tests being made, and thus provide some level of error rate control, significance was assessed using a false discovery rate (FDR) controlling method. The step-up procedure of Benjamini and Hochberg (1995) was used to control the FDR below alpha = 0.01. For the purposes of this experiment, the hypotheses were assumed to be independent.
Features found to be significantly enriched for DNA methylation after hypothesis-testing with a controlled error rate are flagged in the column.
Standard errors and P-values are not available.
Keywords: other
 
 
Contributor(s) Lippman ZB, Gendrel A, Black M, Vaughn MW
Citation missing Has this study been published? Please login to update or notify GEO.
Submission date Apr 21, 2004
Last update date Mar 15, 2012
Contact name Matthew Wayne Vaughn
E-mail(s) vaughn@tacc.utexas.edu
Phone (512) 232-7124
Organization name University of Texas at Austin
Department Texas Advanced Computing Center
Lab Vaughn
Street address 10100 Burnet Rd
City Austin
State/province TX
ZIP/Postal code 78758
Country USA
 
Platforms (1)
GPL785 Arabidopsis thaliana (ecotype Columbia) chromosome 4 knob genomic tiling array
Samples (2)
GSM21786 VC1110, Wild-type versus ddm1 Arabidopsis thaliana
GSM21787 VC112, Wild-type versus ddm1 Arabidopsis thaliana
This SubSeries is part of SuperSeries:
GSE1354 mRNA levels in Wild-type versus ddm1 Arabidopsis thaliana
Relations
BioProject PRJNA91033

Normalized result of the paired dye swap samples VC110 and VC112 header descriptions
ID_REF Feature name
SOURCE1 Wild-type value
SOURCE2 Mutant value
VALUE Ratio of SOURCE2/SOURCE1
STDERR Standard error for the feature
PVALUE P-value for the feature
FWER 1: Feature was found to be significant via Holm's method
FDR 1: Feature was found to be significant via Benjamini and Hochberg's step-up procedure

Data table
ID_REF SOURCE1 SOURCE2 VALUE STDERR PVALUE FWER FDR
pc01a01F.1000.4.1200143.T10P11_1 8.5662 9.6196 1.1229716793911 0 0 0 0
pc01a02F.999.4.1201129.T10P11_1 7.0748 7.2863 1.02989483801662 0 0 0 0
pc01a03F.1009.4.1202124.T10P11_1 1.2599 1 0.793713786808477 0 0 0 0
pc01a04F.1019.4.1203243.T10P11_1 19.9711 31.9903 1.60182964383534 0 0 0 0
pc01a05F.1002.4.1204327.T10P11_1 13.6673 27.5726 2.01741382716411 0 0 0 0
pc01a06F.923.4.1205524.T10P11_1 10.1895 22.2546 2.18407183865744 0 0 0 0
pc01a07F.967.4.1206542.T10P11_1 2.2581 3.9662 1.75643239891945 0 0 0 0
pc01a08F.995.4.1207488.T10P11_1 1.0905 2.1894 2.00770288858322 0 0 0 0
pc01a09F.1001.4.1208553.T10P11_1 1 1 1 0 0 0 0
pc01a10F.978.4.1209635.T5J8_1 1.0905 1.1892 1.09050894085282 0 0 0 0
pc01a11F.1031.4.1210591.T5J8_1 1 1 1 0 0 0 0
pc01a12F.855.4.1211906.T5J8_1 1 1.251 1.251 0 0 0 0
pc01b01F.991.4.1212715.T5J8_1 1.2968 1.3643 1.05205120296114 0 0 0 0
pc01b02F.980.4.1213666.T5J8_1 1.7067 2.2284 1.30567762348392 0 0 0 0
pc01b03F.972.4.1214603.T5J8_1 1.9511 2.7272 1.39777561375634 0 0 0 0
pc01b04F.986.4.1215711.T5J8_1 3.5839 6.6217 1.84762409665448 0 0 0 0
pc01b05F.990.4.1216676.T5J8_1 4.0431 9.7756 2.41784769112809 0 0 0 0
pc01b06F.984.4.1217785.T5J8_1 1.958 4.1406 2.114708886619 0 0 0 0
pc01b07F.949.4.1218748.T5J8_1 1.1892 1.6683 1.40287588294652 0 0 0 0
pc01b08F.977.4.1219676.T5J8_1 2.2899 2.5188 1.09996069697367 0 0 0 0

Total number of rows: 1720

Table truncated, full table size 104 Kbytes.




Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary data files not provided
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