Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.1.12.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.80233	0.107
27DAP/17DAP	1.00324	0.994
39DAP/27DAP	1.27729	0.603
41DAP/39DAP	0.99195	0.925
42DAP/41DAP	1.13911	0.898
43DAP/42DAP	0.91931	0.697
47DAP/43DAP	0.84177	0.51
52DAP/47DAP	0.85263	0.637
57DAP/52DAP	1.02003	1

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00585	1
17DAP/reference	0.93847	0.24
27DAP/reference	0.86288	0.024
39DAP/reference	0.95679	0.446
41DAP/reference	0.92347	0.154
42DAP/reference	0.90923	0.045
43DAP/reference	0.95358	0.287
47DAP/reference	0.92469	0.025
52DAP/reference	0.90111	0.177
57DAP/reference	0.96481	0.262

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.07289	0.34
27DAP/17DAP	0.91677	0.312
39DAP/27DAP	0.89749	0.17
41DAP/39DAP	1.12908	0.362
42DAP/41DAP	0.94047	0.478
43DAP/42DAP	0.95125	0.206
47DAP/43DAP	1.04088	0.681
52DAP/47DAP	0.96505	0.763
57DAP/52DAP	0.93015	0.342
57DAP/7DAP	0.94421	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99382	0.758
17DAP/reference	0.93204	0.094
27DAP/reference	0.90942	0.014
39DAP/reference	0.83426	0.014
41DAP/reference	0.86578	0.018
42DAP/reference	0.90803	0.011
43DAP/reference	0.80757	0.011
47DAP/reference	0.8818	0.168
52DAP/reference	0.80711	0.012
57DAP/reference	0.80468	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97643	0.669
17DAP/reference	0.90714	0.143
27DAP/reference	1.02893	0.888
39DAP/reference	0.77104	0.028
41DAP/reference	0.88791	0.141
42DAP/reference	0.90129	0.032
43DAP/reference	0.89737	0.066
47DAP/reference	0.91945	0.129
52DAP/reference	0.7179	0.003
57DAP/reference	0.74044	0.002

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.09781	0.138
17DAP/reference	1.12078	0.241
27DAP/reference	1.06372	0.143
39DAP/reference	0.98587	0.544
41DAP/reference	0.91604	0.077
42DAP/reference	0.78285	0.032
43DAP/reference	0.77711	0.038
47DAP/reference	0.68637	0.004
52DAP/reference	0.80659	0.105
57DAP/reference	0.75774	0.019

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.92884	1
26DAP/20DAP	1.15055	0.62
34DAP/26DAP	0.91354	0.596
51DAP/34DAP	0.94647	0.681
52DAP/51DAP	0.96361	1
53DAP/52DAP	0.95791	0.758
55DAP/53DAP	1.22421	0.537
57DAP/55DAP	0.93898	0.718
62DAP/57DAP	1.08832	0.8
68DAP/62DAP	0.89796	0.505
68DAP/14DAP	0.90609	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.0358	0.7

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.18341	0.113
Mature Green Tomato/Ripe Tomato	1.12659	0.752
Immature Eggplant/Mature Eggplant	1.53258	0.05
Ripe Pepper/Ripe Tomato	1.03253	1
Mature Eggplant/Ripe Tomato	1.29419	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.88091	0.571
1-1-2/M82	1.0457	1
12-2/M82	1.15462	1
12-4/M82	0.93167	1
1-3/M82	1.38275	0.479
2-1-1/M82	1.20985
2-1/M82	1.16739	1
2-6/M82	1.2264	0.395
3-2/M82	1.12512	0.717
4-1-1/M82	0.93083	1
4-1/M82	0.85895
4-3-2/M82	1.25247	1
4-3/M82	1.24758	1
5-3/M82	0.84844	0.642
6-2/M82	1.20524	1
6-3/M82	1.05005	1
7-1/M82	1.12908
7-2/M82	1.33806	0.385
9-3-2/M82	1.27769	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.84196	0.247
IL2-6/WTpooled	0.85502	0.383
IL7-5/WTpooled	0.7136	1
IL7-3/WTpooled	0.97767	1
IL12-4/WTpooled	1.04164	0.595
IL1-4/WTpooled	1.04561	0.426
WT/WTpooled	0.96057	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	1.078	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.90578	0.807
DC3000/delta hrp 6h	1.0073	0.95
DC3000/delta hrp 12h	1.00511	1
DC3000/delta hrp 24h	0.6795	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.65332	0.042
DC3000 delta B/DC3000 delta AB	0.45831	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.02901	1
Exp 36h	0.84833	0.623
Exp 60h	0.67689	0.266

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01668	1
Var 0h	0.83524	0.933
Var 12h I row2-row1	0.84087	0.338
Var 12h NI row2-row1	0.95719	0.82
Var 36h I row2-row1	0.88771	0.575
Var 36h NI row2-row1	1.08574	0.482
Var 60h I row2-row1	1.34342	0.543
Var 60h NI row2-row1	1.02864	0.904
Time course 0hI-0hNI	1.03209	0.799
Time course 12hI-12hNI	0.98374	0.906
Time course 36hI-36hNI	0.85966	0.045
Time course 60hI-60hNI	0.17863	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)	1.01152	0.863
transgenic ySAMdc/azygous control (breaker)	0.82936	0.251
transgenic ySAMdc/azygous control (red)	0.92264	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.76822	0.073

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	3.21039	0.222

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.24261	0.14
Manapal/WT (break)	0.85314	1
Manapal/WT (red)	0.82585	0.183