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Series GSE1324

Query DataSets for GSE1324

Status

Public on Jun 12, 2004

Title

EV23+24 mRNA levels in Wild-type versus ddm1/+ backcross bolting Arabidopsis thaliana plants

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 EV23 and EV24.
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 both family-wise error rate (FWER) and false discovery rate (FDR) controlling methods. The step-down multiple comparisons procedure of Holm (1979) was used to control the FWER below alpha = 0.01, while 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 last two columns.
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)

GSM21773	EV23, Wild-type versus ddm1/+ backcross mRNA
GSM21774	EV24, Wild-type versus ddm1/+ backcross mRNA

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 EV23 and EV24 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	1367.1748	1257.5424	0.919810985398502	0.10062	0.40708	0	0
pc01a02F.999.4.1201129.T10P11_1	1171.1202	1098.4588	0.937955642811045	0.075574	0.42853	0	0
pc01a03F.1009.4.1202124.T10P11_1	19.5674	17.9104	0.915318335599007	0.7382	0.40174	0	0
pc01a04F.1019.4.1203243.T10P11_1	2277.9915	1954.8925	0.858164966813967	0.11479	0.33355	0	0
pc01a05F.1002.4.1204327.T10P11_1	1204.2574	1100.946	0.914211529860643	0.084831	0.40043	0	0
pc01a06F.923.4.1205524.T10P11_1	689.9285	690.0655	1.00019857130123	0.18271	0.49978	0	0
pc01a07F.967.4.1206542.T10P11_1	256.9696	253.5173	0.986565336911448	0.1028	0.48483	0	0
pc01a08F.995.4.1207488.T10P11_1	159.9506	149.6577	0.93564950678522	0.065992	0.42581	0	0
pc01a09F.1001.4.1208553.T10P11_1	16.0358	14.3229	0.893182753588845	0.37846	0.37537	0	0
pc01a10F.978.4.1209635.T5J8_1	10.6875	9.09	0.850526315789474	0.74447	0.32446	0	0
pc01a11F.1031.4.1210591.T5J8_1	6.4682	4.7685	0.73722210197582	0.38352	0.19565	0	0
pc01a12F.855.4.1211906.T5J8_1	24.3946	19.549	0.801365876054537	0.51839	0.26674	0	0
pc01b01F.991.4.1212715.T5J8_1	6.6225	4.5641	0.689180822952057	0.50669	0.1476	0	0
pc01b02F.980.4.1213666.T5J8_1	25.7431	17.3709	0.674778872785329	0.4221	0.13432	0	0
pc01b03F.972.4.1214603.T5J8_1	10.5683	7.9409	0.751388586622257	0.50384	0.21076	0	0
pc01b04F.986.4.1215711.T5J8_1	134.3419	146.9699	1.09399896830401	0.14538	0.40027	0	0
pc01b05F.990.4.1216676.T5J8_1	92.7644	92.0432	0.992225465803692	0.34772	0.49124	0	0
pc01b06F.984.4.1217785.T5J8_1	149.02	163.642	1.09812105757616	0.19425	0.39619	0	0
pc01b07F.949.4.1218748.T5J8_1	168.8097	179.2442	1.06181220628909	0.13579	0.43303	0	0
pc01b08F.977.4.1219676.T5J8_1	110.389	105.1572	0.952605784996694	0.13537	0.4457	0	0

Total number of rows: 1724

Table truncated, full table size 143 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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