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Series GSE1327

Query DataSets for GSE1327

Status

Public on Jun 12, 2004

Title

EV39+40 mRNA levels in Wild-type versus ddm1 Arabidopsis thaliana seedlings

Organism

Arabidopsis thaliana

Experiment type

Expression profiling by genome tiling array

Summary

Technical replicate of EV33+34.
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 EV39 and EV40.
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

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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)

Arabidopsis thaliana (ecotype Columbia) chromosome 4 knob genomic tiling array

Samples (2)

GSM21779	EV39, Wild-type versus ddm1 seedlings
GSM21780	EV40, Wild-type versus ddm1 seedlings

This SubSeries is part of SuperSeries:

mRNA levels in Wild-type versus ddm1 Arabidopsis thaliana

Relations

BioProject

Normalized result of the paired dye swap samples EV39 and EV40 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	1355.9731	1363.4319	1.00550069909204	0	0	0	0
pc01a02F.999.4.1201129.T10P11_1	770.7288	715.7334	0.928644939698633	0	0	0	0
pc01a03F.1009.4.1202124.T10P11_1	3.8632	5.7554	1.48980120107683	0	0	0	0
pc01a04F.1019.4.1203243.T10P11_1	1382.0281	1176.46	0.851256208176954	0	0	0	0
pc01a05F.1002.4.1204327.T10P11_1	220.3608	206.9886	0.939316793186447	0	0	0	0
pc01a06F.923.4.1205524.T10P11_1	232.686	223.3854	0.960029395838168	0	0	0	0
pc01a07F.967.4.1206542.T10P11_1	110.6884	116.6934	1.05425139400335	0	0	0	0
pc01a08F.995.4.1207488.T10P11_1	98.7514	88.1708	0.892856202544977	0	0	0	0
pc01a09F.1001.4.1208553.T10P11_1	4.3107	7.7601	1.80019486394321	0	0	0	0
pc01a10F.978.4.1209635.T5J8_1	6.8139	15.2658	2.24039096552635	0	0	0	0
pc01a11F.1031.4.1210591.T5J8_1	4.739	10.3663	2.18744460856721	0	0	0	0
pc01a12F.855.4.1211906.T5J8_1	11.3748	12.3915	1.0893817913282	0	0	0	0
pc01b01F.991.4.1212715.T5J8_1	11.915	8.1976	0.688006714225766	0	0	0	0
pc01b02F.980.4.1213666.T5J8_1	9.4833	8.862	0.934484831229635	0	0	0	0
pc01b03F.972.4.1214603.T5J8_1	5.1899	7.5015	1.44540357232317	0	0	0	0
pc01b04F.986.4.1215711.T5J8_1	62.3559	63.0188	1.01063091062754	0	0	0	0
pc01b05F.990.4.1216676.T5J8_1	42.7755	41.5421	0.971165737396407	0	0	0	0
pc01b06F.984.4.1217785.T5J8_1	120.3307	81.556	0.677765524508708	0	0	0	0
pc01b07F.949.4.1218748.T5J8_1	193.317	169.4264	0.876417490443158	0	0	0	0
pc01b08F.977.4.1219676.T5J8_1	89.0171	63.4606	0.712903475849022	0	0	0	0

Total number of rows: 1724

Table truncated, full table size 120 Kbytes.

Download family	Format
SOFT formatted family file(s)	SOFT
MINiML formatted family file(s)	MINiML
Series Matrix File(s)	TXT

Supplementary data files not provided

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