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Series GSE1325 Query DataSets for GSE1325
Status Public on Jun 12, 2004
Title EV33+34 mRNA levels in Wild-type versus ddm1 Arabidopsis thaliana seedlings
Organism Arabidopsis thaliana
Experiment type Expression profiling by genome tiling array
Summary 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 EV33 and EV34.
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)
GSM21776 EV33, Wild-type versus ddm1 mRNA
GSM21777 EV34, Wild-type versus ddm1 mRNA
This SubSeries is part of SuperSeries:
GSE1354 mRNA levels in Wild-type versus ddm1 Arabidopsis thaliana
Relations
BioProject PRJNA91027

Normalized result of the paired dye swap samples EV33 and EV34 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_1 911.8115 1121.5696 1.23004546444084 0 0 0 0
pc01a02F.999.4.1201129.T10P11_1 846.1243 1152.1395 1.36166695602526 0 0 0 0
pc01a03F.1009.4.1202124.T10P11_1 12.5192 9.5307 0.76128666368458 0 0 0 0
pc01a04F.1019.4.1203243.T10P11_1 371.234 563.8231 1.51878087675159 0 0 0 0
pc01a05F.1002.4.1204327.T10P11_1 391.6414 556.7462 1.42157136605068 0 0 0 0
pc01a06F.923.4.1205524.T10P11_1 421.7148 559.3735 1.32642605855901 0 0 0 0
pc01a07F.967.4.1206542.T10P11_1 176.4807 251.8631 1.42714245807049 0 0 0 0
pc01a08F.995.4.1207488.T10P11_1 109.1008 146.4367 1.34221472253182 0 0 0 0
pc01a09F.1001.4.1208553.T10P11_1 8.0901 9.2552 1.14401552514802 0 0 0 0
pc01a10F.978.4.1209635.T5J8_1 7.5285 8.3644 1.11103141396028 0 0 0 0
pc01a11F.1031.4.1210591.T5J8_1 2.0528 2.9938 1.4583982852689 0 0 0 0
pc01a12F.855.4.1211906.T5J8_1 9.0972 10.1458 1.11526623576485 0 0 0 0
pc01b01F.991.4.1212715.T5J8_1 8.2757 8.0252 0.969730657225371 0 0 0 0
pc01b02F.980.4.1213666.T5J8_1 11.9287 11.6455 0.976258938526411 0 0 0 0
pc01b03F.972.4.1214603.T5J8_1 10.2473 10.2714 1.00235183902101 0 0 0 0
pc01b04F.986.4.1215711.T5J8_1 97.4036 117.3148 1.20441954917477 0 0 0 0
pc01b05F.990.4.1216676.T5J8_1 137.5456 133.7296 0.972256473489519 0 0 0 0
pc01b06F.984.4.1217785.T5J8_1 122.9722 134.3976 1.09291043016226 0 0 0 0
pc01b07F.949.4.1218748.T5J8_1 204.1552 262.239 1.28450806053434 0 0 0 0
pc01b08F.977.4.1219676.T5J8_1 82.1788 87.9204 1.06986716768802 0 0 0 0

Total number of rows: 1724

Table truncated, full table size 120 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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