Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.1.12.16

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.88082	0.285
27DAP/17DAP	1.22763	0.815
39DAP/27DAP	1.18868	0.825
41DAP/39DAP	1.13439	0.386
42DAP/41DAP	1.03696	0.994
43DAP/42DAP	0.93052	0.7
47DAP/43DAP	0.94805	0.788
52DAP/47DAP	1.49742	0.239
57DAP/52DAP	1.00578	0.995

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.06011	0.32
17DAP/reference	0.98606	0.63
27DAP/reference	1.0057	0.966
39DAP/reference	0.992	0.874
41DAP/reference	1.03462	0.338
42DAP/reference	1.01245	1
43DAP/reference	0.97007	0.331
47DAP/reference	1.01769	0.627
52DAP/reference	1.04008	0.878
57DAP/reference	0.93458	0.082

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.03803	0.605
27DAP/17DAP	0.99822	0.969
39DAP/27DAP	1.06049	0.519
41DAP/39DAP	1.04359	0.861
42DAP/41DAP	0.97162	0.717
43DAP/42DAP	0.94172	0.321
47DAP/43DAP	0.98767	0.933
52DAP/47DAP	1.02463	0.907
57DAP/52DAP	1.02759	0.858
57DAP/7DAP	1.05563	0.249

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91287	0.203
17DAP/reference	0.94186
27DAP/reference	0.8771	0.031
39DAP/reference	0.963	0.146
41DAP/reference	0.97671	0.357
42DAP/reference	1.01233	0.686
43DAP/reference	0.97367	0.202
47DAP/reference	0.91522	0.066
52DAP/reference	0.9602	0.077
57DAP/reference	0.97241	0.314

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03077	0.634
17DAP/reference	1.04327	0.311
27DAP/reference	1.01969	0.875
39DAP/reference	0.99385	0.603
41DAP/reference	0.93832	0.284
42DAP/reference	0.97362	0.482
43DAP/reference	1.0831	0.38
47DAP/reference	0.95892	0.246
52DAP/reference	1.02813	0.223
57DAP/reference	1.07268	0.26

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.85703	0.249
17DAP/reference	0.88298	0.118
27DAP/reference	0.97283	0.416
39DAP/reference	1.01693	0.935
41DAP/reference	1.01506
42DAP/reference	0.94448	0.018
43DAP/reference	0.97499	0.568
47DAP/reference	0.98455	0.558
52DAP/reference	0.93443	0.551
57DAP/reference	0.85718	0.017

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.9818	1
26DAP/20DAP	0.99026	1
34DAP/26DAP	0.95637	0.795
51DAP/34DAP	0.98061	0.835
52DAP/51DAP	1.04518	0.579
53DAP/52DAP	1.03897	0.768
55DAP/53DAP	0.99922	0.951
57DAP/55DAP	0.94197	0.724
62DAP/57DAP	0.98018	0.994
68DAP/62DAP	0.95957	0.747
68DAP/14DAP	0.9623	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.04916	0.439

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.78809	0.241
Mature Green Tomato/Ripe Tomato	0.93387	0.522
Immature Eggplant/Mature Eggplant	2.21991	0.05
Ripe Pepper/Ripe Tomato	0.90283	1
Mature Eggplant/Ripe Tomato	0.88414	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.99152	0.961
1-1-2/M82	0.91419	1
12-2/M82	1.04321	1
12-4/M82	0.91963	1
1-3/M82	0.94681	0.501
2-1-1/M82	1.08188	0.689
2-1/M82	N/A	N/A
2-6/M82	0.94029	1
3-2/M82	1.03614	0.967
4-1-1/M82	0.98418	1
4-1/M82	1.10994	1
4-3-2/M82	0.96801	1
4-3/M82	1.08147	1
5-3/M82	0.9716	1
6-2/M82	0.93928	1
6-3/M82	0.98357	1
7-1/M82	1.08869	1
7-2/M82	1.03727	1
9-3-2/M82	0.88843	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.98665	1
IL2-6/WTpooled	1.08654	0.788
IL7-5/WTpooled	0.68764	1
IL7-3/WTpooled	0.87869	0.294
IL12-4/WTpooled	1.03857	1
IL1-4/WTpooled	0.91787	0.415
WT/WTpooled	1.19984	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	1.7366	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.93629	1
DC3000/delta hrp 6h	1.05838	1
DC3000/delta hrp 12h	0.97909	1
DC3000/delta hrp 24h	1.01725	0.76

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.09122	0.094
DC3000 delta B/DC3000 delta AB	1.01157	0.703

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.14454	1
Exp 36h	1.8459	0.489
Exp 60h	1.329	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	0.97592	1
Var 0h	0.73724	0.933
Var 12h I row2-row1	1.18615	0.211
Var 12h NI row2-row1	1.06497	1
Var 36h I row2-row1	1.04067	1
Var 36h NI row2-row1	0.92446	0.645
Var 60h I row2-row1	1.08041	1
Var 60h NI row2-row1	0.89999	0.69
Time course 0hI-0hNI	1.08485	0.833
Time course 12hI-12hNI	1.04286	0.785
Time course 36hI-36hNI	1.16588	0.031
Time course 60hI-60hNI	1.42423	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)	1.28	0.254
transgenic ySAMdc/azygous control (breaker)	0.87856	0.49
transgenic ySAMdc/azygous control (red)	1.31159	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.99673	0.712

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.70137	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.68918	1
Manapal/WT (break)	0.8464	1
Manapal/WT (red)	0.69214	0.274