Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.3.1.13

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.80965	0.217
27DAP/17DAP	0.73763	0.307
39DAP/27DAP	0.85031	0.507
41DAP/39DAP	0.86831	0.503
42DAP/41DAP	1.29874	0.647
43DAP/42DAP	1.03587	1
47DAP/43DAP	1.23209	0.727
52DAP/47DAP	0.9917	0.89
57DAP/52DAP	1.14312	0.946

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90988	0.277
17DAP/reference	0.89588	0.208
27DAP/reference	0.9412	0.428
39DAP/reference	0.82565	0.013
41DAP/reference	0.8278	0.267
42DAP/reference	0.86274	0.011
43DAP/reference	0.99424	0.882
47DAP/reference	0.96431	0.345
52DAP/reference	1.08131	0.912
57DAP/reference	1.10542	0.321

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.16538	0.515
27DAP/17DAP	1.03918	0.988
39DAP/27DAP	0.79844	0.243
41DAP/39DAP	1.09601	0.817
42DAP/41DAP	0.99956	0.899
43DAP/42DAP	0.95053	0.641
47DAP/43DAP	1.08674	0.69
52DAP/47DAP	1.2218	0.474
57DAP/52DAP	1.24653	0.199
57DAP/7DAP	1.37756	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04331	1
17DAP/reference	0.97772	0.447
27DAP/reference	1.20205	0.16
39DAP/reference	1.10505	0.237
41DAP/reference	0.95814	0.431
42DAP/reference	1.22372	0.233
43DAP/reference	1.00235	0.727
47DAP/reference	0.99976	1
52DAP/reference	1.0039	0.74
57DAP/reference	1.0761	0.41

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.05093	0.823
17DAP/reference	0.78844	0.013
27DAP/reference	1.02171	0.948
39DAP/reference	0.79939	0.012
41DAP/reference	0.93422	0.262
42DAP/reference	0.82861	0.027
43DAP/reference	0.95896	0.494
47DAP/reference	0.9343	0.284
52DAP/reference	0.93866	0.203
57DAP/reference	0.83471	0.043

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.36578	0.046
17DAP/reference	0.99822	0.81
27DAP/reference	1.09815	0.179
39DAP/reference	0.94163	0.328
41DAP/reference	0.92002	0.293
42DAP/reference	1.02452	0.961
43DAP/reference	0.91261	0.131
47DAP/reference	0.97701	0.478
52DAP/reference	1.54531	0.363
57DAP/reference	1.00752	0.828

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.2057	0.966
26DAP/20DAP	1.08208	0.707
34DAP/26DAP	0.9383	0.988
51DAP/34DAP	1.19124	0.496
52DAP/51DAP	1.10703	0.542
53DAP/52DAP	0.7526	0.056
55DAP/53DAP	0.66707	0.111
57DAP/55DAP	1.17263	0.077
62DAP/57DAP	1.1471	0.8
68DAP/62DAP	1.17536	0.85
68DAP/14DAP	1.89243	0.249

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.42274	0.019

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.89068	0.41
Mature Green Tomato/Ripe Tomato	1.05946	0.715
Immature Eggplant/Mature Eggplant	0.81917	0.096
Ripe Pepper/Ripe Tomato	1.11631	1
Mature Eggplant/Ripe Tomato	1.96593	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.38705
1-1-2/M82	1.02228	1
12-2/M82	1.07597
12-4/M82	0.88279	1
1-3/M82	N/A	N/A
2-1-1/M82	0.84542	0.465
2-1/M82	0.78944	1
2-6/M82	1.07006	0.695
3-2/M82	1.09067	0.967
4-1-1/M82	1.15841
4-1/M82	N/A	N/A
4-3-2/M82	1.31751	0.284
4-3/M82	1.2082	1
5-3/M82	0.97148	1
6-2/M82	1.14035	1
6-3/M82	0.94077	1
7-1/M82	1.00411
7-2/M82	1.07556	1
9-3-2/M82	0.80131	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.25411	0.493
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.93422
IL12-4/WTpooled	0.89248	1
IL1-4/WTpooled	0.82403
WT/WTpooled	1.21894	1

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	0.86387	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.96811	1
DC3000/delta hrp 6h	1.04756	1
DC3000/delta hrp 12h	0.89269	1
DC3000/delta hrp 24h	0.62235	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.62136	0.023
DC3000 delta B/DC3000 delta AB	0.7079	0.026

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.81599	1
Exp 36h	0.92482	0.699
Exp 60h	0.84832	0.29

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99227	1
Var 0h	0.71561	0.933
Var 12h I row2-row1	0.84525	0.338
Var 12h NI row2-row1	1.11732	1
Var 36h I row2-row1	0.84078	1
Var 36h NI row2-row1	1.47965	1
Var 60h I row2-row1	0.7629
Var 60h NI row2-row1	1.13247	0.904
Time course 0hI-0hNI	0.90969	0.489
Time course 12hI-12hNI	1.01131	0.888
Time course 36hI-36hNI	0.85974	0.159
Time course 60hI-60hNI	0.32438	0.006

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)	1.29983	0.238
transgenic ySAMdc/azygous control (breaker)	1.43086	0.166
transgenic ySAMdc/azygous control (red)	1.07443	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.11177	0.1

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.11109	0.237

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.92119	0.093
Manapal/WT (break)	1.76275	0.183
Manapal/WT (red)	1.09542	0.222