Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.4.17.21

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.02133	0.331
27DAP/17DAP	8.0872	0.065
39DAP/27DAP	0.64603	0.435
41DAP/39DAP	0.93055	0.597
42DAP/41DAP	1.14246	0.852
43DAP/42DAP	0.76256	0.572
47DAP/43DAP	0.55541	0.055
52DAP/47DAP	5.11635	0.037
57DAP/52DAP	0.69379	0.759

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.26708	0.29
17DAP/reference	0.92885	0.503
27DAP/reference	1.26713	0.055
39DAP/reference	0.92142	0.315
41DAP/reference	0.78013	0.085
42DAP/reference	3.72234	0.001
43DAP/reference	1.02054	1
47DAP/reference	1.09898	0.463
52DAP/reference	1.51335	0.008
57DAP/reference	1.40598	0.022

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.95237	0.442
27DAP/17DAP	0.75709	0.312
39DAP/27DAP	0.87012	0.334
41DAP/39DAP	1.96664	0.037
42DAP/41DAP	0.73113	0.081
43DAP/42DAP	1.81964	0.024
47DAP/43DAP	0.96446	0.833
52DAP/47DAP	5.85629	0.016
57DAP/52DAP	14.2427	0.033
57DAP/7DAP	8.65143	0.249

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87328	0.224
17DAP/reference	0.94279	0.192
27DAP/reference	0.76606	0.024
39DAP/reference	0.81379	0.034
41DAP/reference	1.07051	0.475
42DAP/reference	1.22174	0.534
43DAP/reference	2.573	0.006
47DAP/reference	0.73682	0.066
52DAP/reference	0.77025	0.02
57DAP/reference	2.94873	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.15679	0.758
17DAP/reference	2.13258	0.015
27DAP/reference	1.09865	0.735
39DAP/reference	1.34378	0.182
41DAP/reference	3.15166	0.005
42DAP/reference	1.68426	0.01
43DAP/reference	1.5426	0.079
47DAP/reference	2.13274	0.008
52DAP/reference	1.36789	0.011
57DAP/reference	1.46484	0.104

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.64478	0.034
17DAP/reference	0.96259	0.571
27DAP/reference	1.27597	0.029
39DAP/reference	1.36055	0.33
41DAP/reference	0.97693	0.618
42DAP/reference	1.23949	0.373
43DAP/reference	1.82514	0.009
47DAP/reference	1.25485	0.324
52DAP/reference	1.46006	0.132
57DAP/reference	2.65076	0.013

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.71246	0.021
26DAP/20DAP	0.62816	1
34DAP/26DAP	1.13221	1
51DAP/34DAP	N/A	N/A
52DAP/51DAP	1.71749	0.218
53DAP/52DAP	0.80376	0.329
55DAP/53DAP	1.83647	0.394
57DAP/55DAP	0.93057	0.691
62DAP/57DAP	1.00047	0.994
68DAP/62DAP	1.28912	0.073
68DAP/14DAP	1.34254	0.2

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	2.16766	0.021

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.28429	0.026
Immature Eggplant/Mature Eggplant	4.46952
Ripe Pepper/Ripe Tomato	0.07633	0.224
Mature Eggplant/Ripe Tomato	0.40087	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.9453	0.634
1-1-2/M82	1.02025	1
12-2/M82	N/A	N/A
12-4/M82	1.36975
1-3/M82	0.73085
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	0.92578
3-2/M82	0.86457
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	0.62198	0.447
6-2/M82	1.20195	1
6-3/M82	0.6926
7-1/M82	1.13228
7-2/M82	N/A	N/A
9-3-2/M82	0.63217

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.91265	1
IL2-6/WTpooled	1.07792	1
IL7-5/WTpooled	0.87036	1
IL7-3/WTpooled	0.64966	0.283
IL12-4/WTpooled	0.87372
IL1-4/WTpooled	0.90741	0.834
WT/WTpooled	1.07101	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	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.14924	0.724
DC3000/delta hrp 6h	0.90071
DC3000/delta hrp 12h	1.02012	1
DC3000/delta hrp 24h	0.93693	0.494

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.56091
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	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	0.97323	1
Var 0h	0.96523	1
Var 12h I row2-row1	1.51986	0.58
Var 12h NI row2-row1	1.06641	0.063
Var 36h I row2-row1	1.14941	0.305
Var 36h NI row2-row1	1.03292	1
Var 60h I row2-row1	1.19005	0.543
Var 60h NI row2-row1	1.03425
Time course 0hI-0hNI	1.14891	0.719
Time course 12hI-12hNI	0.85615	0.212
Time course 36hI-36hNI	1.11901	0.166
Time course 60hI-60hNI	1.85082	0.047

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)	1.78522	0.511
transgenic ySAMdc/azygous control (breaker)	0.3069	0.15
transgenic ySAMdc/azygous control (red)	1.55765	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.39451	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.783	1
Manapal/WT (break)	0.48309	0.333
Manapal/WT (red)	0.93422	0.503