Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.4.7.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.85483	0.19
27DAP/17DAP	0.86882	0.597
39DAP/27DAP	1.12521	0.61
41DAP/39DAP	1.17663	0.58
42DAP/41DAP	1.14903	0.777
43DAP/42DAP	0.87723	0.55
47DAP/43DAP	0.79832	0.395
52DAP/47DAP	1.48275	0.31
57DAP/52DAP	0.95409	0.919

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97464	0.412
17DAP/reference	0.99612	0.904
27DAP/reference	0.97612	0.497
39DAP/reference	1.01975	0.747
41DAP/reference	1.0216	0.516
42DAP/reference	0.92942	0.025
43DAP/reference	1.00497	0.957
47DAP/reference	0.95095	0.161
52DAP/reference	1.00903	1
57DAP/reference	0.94222	0.176

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.87862	0.08
27DAP/17DAP	0.99002	0.943
39DAP/27DAP	1.0367	0.663
41DAP/39DAP	0.98731	1
42DAP/41DAP	1.04005	0.795
43DAP/42DAP	1.02153	0.746
47DAP/43DAP	1.0139	0.926
52DAP/47DAP	0.86248	0.247
57DAP/52DAP	0.87418	0.366
57DAP/7DAP	0.79625

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97533	0.445
17DAP/reference	0.96549	0.124
27DAP/reference	1.03343	0.371
39DAP/reference	0.94196	0.011
41DAP/reference	0.97558	0.341
42DAP/reference	1.05169	0.233
43DAP/reference	0.90677	0.013
47DAP/reference	0.92182	0.101
52DAP/reference	0.92067	0.013
57DAP/reference	0.95131	0.162

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03647	0.712
17DAP/reference	1.04019	0.311
27DAP/reference	1.05358	0.463
39DAP/reference	1.14241	0.272
41DAP/reference	1.14631	0.362
42DAP/reference	0.92459	0.05
43DAP/reference	1.21295	0.159
47DAP/reference	0.97197	0.39
52DAP/reference	1.0798	0.085
57DAP/reference	1.05525	0.868

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94189	0.05
17DAP/reference	0.99976	0.9
27DAP/reference	1.00032	1
39DAP/reference	0.9579	0.033
41DAP/reference	1.01604	0.889
42DAP/reference	0.9863	0.816
43DAP/reference	0.91303	0.032
47DAP/reference	0.99537	0.667
52DAP/reference	0.91699	0.2
57DAP/reference	0.83426	0.016

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.98945	1
26DAP/20DAP	0.98382	1
34DAP/26DAP	0.91368	0.693
51DAP/34DAP	0.99778	0.946
52DAP/51DAP	1.06747	0.42
53DAP/52DAP	1.14278	0.261
55DAP/53DAP	1.17949	0.054
57DAP/55DAP	0.94625	0.825
62DAP/57DAP	1.02471	0.868
68DAP/62DAP	1.07989	0.872
68DAP/14DAP	0.9673	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.42171	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.42164	0.287
Mature Green Tomato/Ripe Tomato	1.14481	0.053
Immature Eggplant/Mature Eggplant	1.12122	0.334
Ripe Pepper/Ripe Tomato	1.24274	1
Mature Eggplant/Ripe Tomato	1.98224	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.09661	0.877
1-1-2/M82	0.75411	0.958
12-2/M82	1.09567	1
12-4/M82	1.17942	1
1-3/M82	0.79206
2-1-1/M82	1.17523
2-1/M82	N/A	N/A
2-6/M82	1.0207	1
3-2/M82	1.15157	0.84
4-1-1/M82	0.80552
4-1/M82	0.96568	1
4-3-2/M82	1.00015
4-3/M82	N/A	N/A
5-3/M82	1.03463	1
6-2/M82	N/A	N/A
6-3/M82	1.01443	1
7-1/M82	1.14704
7-2/M82	0.99141	1
9-3-2/M82	0.92564	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.89815	0.473
IL7-5/WTpooled	0.75541	1
IL7-3/WTpooled	1.05866	1
IL12-4/WTpooled	0.83164	0.581
IL1-4/WTpooled	0.88055
WT/WTpooled	1.11712	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	1.18072	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.9209	1
DC3000/delta hrp 6h	0.8702	0.95
DC3000/delta hrp 12h	0.97277	1
DC3000/delta hrp 24h	0.97455	0.897

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.16638	0.102
DC3000 delta B/DC3000 delta AB	1.06145	0.535

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	N/A	N/A
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	1.00524	1
Var 0h	0.92677	1
Var 12h I row2-row1	1.06648	0.348
Var 12h NI row2-row1	0.97102	0.82
Var 36h I row2-row1	1.05678	0.908
Var 36h NI row2-row1	1.0314	1
Var 60h I row2-row1	0.88824	0.439
Var 60h NI row2-row1	1.04632	0.904
Time course 0hI-0hNI	1.00456	1
Time course 12hI-12hNI	1.04786	0.55
Time course 36hI-36hNI	1.08312	0.166
Time course 60hI-60hNI	1.47733	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)	0.91882	0.246
transgenic ySAMdc/azygous control (breaker)	1.06802	0.248
transgenic ySAMdc/azygous control (red)	1.08165	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.02683	0.35

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.90417	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.00862	1
Manapal/WT (break)	0.97101	1
Manapal/WT (red)	1.24325	0.222