Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.1.9.16

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.73906	0.178
27DAP/17DAP	1.17879	1
39DAP/27DAP	0.88683	0.641
41DAP/39DAP	1.32103	0.67
42DAP/41DAP	1.14843	0.873
43DAP/42DAP	0.74932	0.554
47DAP/43DAP	0.97695	0.729
52DAP/47DAP	1.29613	0.584
57DAP/52DAP	1.12893	0.912

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96118	0.412
17DAP/reference	0.99931	0.957
27DAP/reference	0.93175	0.314
39DAP/reference	1.01244	1
41DAP/reference	0.92504	0.341
42DAP/reference	0.88176	0.017
43DAP/reference	0.85285	0.135
47DAP/reference	0.98373	0.503
52DAP/reference	1.03863	1
57DAP/reference	1.08238	0.291

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.05601	1
27DAP/17DAP	0.8914	0.684
39DAP/27DAP	1.03141	0.742
41DAP/39DAP	1.13808	0.663
42DAP/41DAP	0.88366	0.404
43DAP/42DAP	0.85325	0.28
47DAP/43DAP	1.20059	0.563
52DAP/47DAP	0.82091	0.226
57DAP/52DAP	1.07066	0.67
57DAP/7DAP	1.79353

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.81119	0.088
17DAP/reference	0.83512	0.015
27DAP/reference	0.82372	0.01
39DAP/reference	0.85389	0.027
41DAP/reference	0.76243	0.019
42DAP/reference	0.74242	0.01
43DAP/reference	0.72302	0.02
47DAP/reference	0.73301	0.101
52DAP/reference	0.73273	0.028
57DAP/reference	0.82205	0.057

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98129	0.756
17DAP/reference	0.91802	0.253
27DAP/reference	0.97661	0.554
39DAP/reference	0.89942	0.159
41DAP/reference	0.84747	0.087
42DAP/reference	0.80023	0.061
43DAP/reference	1.03151	1
47DAP/reference	0.88585	0.116
52DAP/reference	0.99316	0.619
57DAP/reference	0.98469	0.68

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.85134	0.061
17DAP/reference	0.90014	0.286
27DAP/reference	0.91158	0.085
39DAP/reference	0.84304	0.011
41DAP/reference	0.93965	0.167
42DAP/reference	0.82536	0.019
43DAP/reference	0.94936	0.334
47DAP/reference	0.72827	0.023
52DAP/reference	0.86376	0.174
57DAP/reference	0.97545	0.643

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.74661	0.545
26DAP/20DAP	1.14894	0.493
34DAP/26DAP	0.97251	0.954
51DAP/34DAP	0.93155	0.674
52DAP/51DAP	0.90262	1
53DAP/52DAP	1.05446	0.961
55DAP/53DAP	1.10562	0.547
57DAP/55DAP	0.99582	0.961
62DAP/57DAP	0.9517	0.994
68DAP/62DAP	1.15866	0.491
68DAP/14DAP	1.07638

Experiment: Tomato (breaker-stage) vs. Pepper (breaker-stage)

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.81037	0.108

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.64169
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.76517	0.293
Mature Eggplant/Ripe Tomato	0.69362	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.2051
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	0.90473	0.319
1-3/M82	1.12145
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	0.74976
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	1.10018
4-3-2/M82	N/A	N/A
4-3/M82	1.18016
5-3/M82	0.89442	1
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.6574
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	0.89441	0.834
WT/WTpooled	N/A	N/A

Experiment: Transcriptional changes determined by expression of the Xanthomonas AvrRxv effector in resistant tomato plants

hybridization	ratio	FDR (corrected p value)
10 h post inoculation	1.02283	1

Experiment: Time course of DC3000 vs delta hrp on tomato Prf-3

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.92278	0.941
DC3000/delta hrp 6h	0.91578	0.95
DC3000/delta hrp 12h	1.23495	1
DC3000/delta hrp 24h	1.18713	0.37

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.32596	0.384
DC3000 delta B/DC3000 delta AB	1.11754

Experiment: Matt's wild cherry tomato vs. Phytophthora infestans

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.90672	1
Exp 36h	1.63953	0.693
Exp 60h	N/A	N/A

Experiment: Gene expression profiling of infection of tomato by Phytophthora infestans in the field

hybridization	ratio	FDR (corrected p value)
self-self	1.00902	1
Var 0h	1.15024	0.374
Var 12h I row2-row1	1.14411	0.235
Var 12h NI row2-row1	1.62382	0.649
Var 36h I row2-row1	0.95666	1
Var 36h NI row2-row1	0.79095	0.522
Var 60h I row2-row1	0.89582	0.292
Var 60h NI row2-row1	1.01013	1
Time course 0hI-0hNI	0.92144	0.381
Time course 12hI-12hNI	1.22193	0.087
Time course 36hI-36hNI	1.73923	0.004
Time course 60hI-60hNI	2.28757	0.008

Experiment: Transcriptional profiling of the tomato fruit pericarp tissue: fruits overexpressing yeast ySAMdc gene and controls

hybridization	ratio	FDR (corrected p value)
transgenic ySAMdc/azygous control (mature green)	0.90978	0.324
transgenic ySAMdc/azygous control (breaker)	0.96334	1
transgenic ySAMdc/azygous control (red)	1.07728	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.93115	0.064

Experiment: Microarray Analysis on Salt Stress Affected Genes in Tomato Seedlings

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.08827	0.237

Experiment: Transcriptional Profiling of high pigment-2dg Tomato Mutant Fruit

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.84637	0.172
Manapal/WT (break)	0.90724	0.333
Manapal/WT (red)	1.194	0.413