Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.1.2.9

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.91867	0.578
27DAP/17DAP	1.54636	0.401
39DAP/27DAP	1.21397	0.635
41DAP/39DAP	0.91561	0.6
42DAP/41DAP	0.93393	1
43DAP/42DAP	1.0357	1
47DAP/43DAP	0.90386	0.671
52DAP/47DAP	0.76212	0.438
57DAP/52DAP	1.11005	0.977

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04482	0.735
17DAP/reference	0.81551	0.013
27DAP/reference	0.96247	0.538
39DAP/reference	1.02913	0.771
41DAP/reference	0.84722	0.026
42DAP/reference	1.1457	0.001
43DAP/reference	1.06552	0.646
47DAP/reference	1.2196	0.018
52DAP/reference	1.13563	0.302
57DAP/reference	1.1158	0.321

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.90782	0.415
27DAP/17DAP	1.22888	0.514
39DAP/27DAP	0.97671	0.844
41DAP/39DAP	0.98677	1
42DAP/41DAP	0.91255	0.322
43DAP/42DAP	1.23277	0.019
47DAP/43DAP	1.01213	0.969
52DAP/47DAP	1.00887	0.991
57DAP/52DAP	0.9506	0.651
57DAP/7DAP	1.14017	0.249

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.08211	0.368
17DAP/reference	1.09432	0.123
27DAP/reference	1.0919	0.197
39DAP/reference	1.03874	0.74
41DAP/reference	1.06207	0.918
42DAP/reference	1.27137	0.03
43DAP/reference	1.16342	0.2
47DAP/reference	1.09648	0.219
52DAP/reference	1.14131	0.229
57DAP/reference	1.06781	0.25

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.24961	0.261
17DAP/reference	1.07507	0.257
27DAP/reference	1.12073	0.367
39DAP/reference	1.05671	0.824
41DAP/reference	1.08977	0.459
42DAP/reference	1.25906	0.059
43DAP/reference	1.10803	0.202
47DAP/reference	1.07805	0.256
52DAP/reference	0.91942	0.143
57DAP/reference	1.07385	0.957

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.13289	0.046
17DAP/reference	1.07436	0.699
27DAP/reference	1.01937	0.967
39DAP/reference	1.04971	0.245
41DAP/reference	1.22405	0.02
42DAP/reference	1.4441	0.011
43DAP/reference	1.37742	0.045
47DAP/reference	1.20924	0.06
52DAP/reference	1.46709	0.053
57DAP/reference	1.42854	0.02

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.21826	0.966
26DAP/20DAP	1.05349	1
34DAP/26DAP	0.96557	0.936
51DAP/34DAP	0.74364	0.158
52DAP/51DAP	0.78411	1
53DAP/52DAP	1.40477	0.221
55DAP/53DAP	0.89756	0.085
57DAP/55DAP	1.42145	0.559
62DAP/57DAP	0.766
68DAP/62DAP	1.35356	0.017
68DAP/14DAP	1.62982	0.17

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	2.35678	0.015

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.92986	0.551
Mature Green Tomato/Ripe Tomato	1.37784	0.053
Immature Eggplant/Mature Eggplant	0.95867	0.594
Ripe Pepper/Ripe Tomato	1.64485	1
Mature Eggplant/Ripe Tomato	0.94376	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.19811	0.455
1-1-2/M82	1.30873	1
12-2/M82	0.88988	0.862
12-4/M82	1.06715	1
1-3/M82	1.3978	0.479
2-1-1/M82	0.85563	0.784
2-1/M82	0.81232	0.322
2-6/M82	1.11245	0.452
3-2/M82	0.9129
4-1-1/M82	1.0776	1
4-1/M82	1.2037
4-3-2/M82	1.47344	0.241
4-3/M82	1.31912	0.268
5-3/M82	1.12417	1
6-2/M82	0.79307	1
6-3/M82	0.97409	1
7-1/M82	0.91701	1
7-2/M82	0.81309	0.578
9-3-2/M82	1.56413	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.30767	0.531
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.80412	0.31
IL12-4/WTpooled	0.98465	1
IL1-4/WTpooled	0.89228
WT/WTpooled	0.99704	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	0.93535	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.09533	0.894
DC3000/delta hrp 6h	0.93805	0.95
DC3000/delta hrp 12h	1.01614	1
DC3000/delta hrp 24h	1.00147	1

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	N/A
DC3000 delta B/DC3000 delta AB	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.44539	1
Exp 36h	1.46473	1
Exp 60h	0.95056	0.994

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01184	1
Var 0h	1.13475	1
Var 12h I row2-row1	0.86077	0.514
Var 12h NI row2-row1	0.87378	0.82
Var 36h I row2-row1	1.19472	0.742
Var 36h NI row2-row1	0.9763	0.852
Var 60h I row2-row1	1.02804	1
Var 60h NI row2-row1	0.88655	0.756
Time course 0hI-0hNI	0.91797	0.28
Time course 12hI-12hNI	1.0003	1
Time course 36hI-36hNI	1.10127	0.248
Time course 60hI-60hNI	2.0396	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)	0.9817	0.567
transgenic ySAMdc/azygous control (breaker)	1.0244	1
transgenic ySAMdc/azygous control (red)	1.12927	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.0443	0.063

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.71223	0.241

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.93831	1
Manapal/WT (break)	0.96248	1
Manapal/WT (red)	0.70146	0.181