Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-7.3.19.18

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.96585	0.728
27DAP/17DAP	1.67391	0.401
39DAP/27DAP	0.87864	0.537
41DAP/39DAP	0.87838	0.566
42DAP/41DAP	0.81138	0.774
43DAP/42DAP	1.10349	1
47DAP/43DAP	0.65411	0.107
52DAP/47DAP	1.21932	0.605
57DAP/52DAP	0.98227	0.971

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.0171	0.844
17DAP/reference	1.04653	0.508
27DAP/reference	0.96293	0.359
39DAP/reference	1.03964	0.524
41DAP/reference	0.93817	0.267
42DAP/reference	1.11364	0.068
43DAP/reference	0.97097	0.631
47DAP/reference	1.08568	0.295
52DAP/reference	1.06633	0.766
57DAP/reference	0.83996	0.015

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.13585	0.736
27DAP/17DAP	0.92011	0.648
39DAP/27DAP	1.0881	0.553
41DAP/39DAP	1.44815	0.016
42DAP/41DAP	1.01639	0.929
43DAP/42DAP	1.34889	0.028
47DAP/43DAP	0.97328	0.815
52DAP/47DAP	1.24012	0.382
57DAP/52DAP	2.35525	0.029
57DAP/7DAP	1.73917	0.23

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03558	1
17DAP/reference	0.86075	0.064
27DAP/reference	0.95016	0.325
39DAP/reference	0.84265	0.034
41DAP/reference	0.91856	0.184
42DAP/reference	0.90416	0.07
43DAP/reference	0.79462	0.034
47DAP/reference	1.07214	0.965
52DAP/reference	0.62386	0.012
57DAP/reference	0.76971	0.022

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96392	0.607
17DAP/reference	1.0661	0.396
27DAP/reference	1.06819	0.471
39DAP/reference	1.02048	1
41DAP/reference	0.98967	0.557
42DAP/reference	1.01726	0.987
43DAP/reference	1.13163	0.272
47DAP/reference	1.00271	0.749
52DAP/reference	0.91029	0.037
57DAP/reference	0.9717	0.549

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.86939	0.104
17DAP/reference	0.94056	0.488
27DAP/reference	0.80919	0.034
39DAP/reference	0.79122	0.015
41DAP/reference	0.88616	0.119
42DAP/reference	0.97978	0.671
43DAP/reference	0.88952	0.256
47DAP/reference	0.99401	0.646
52DAP/reference	0.92331	0.455
57DAP/reference	1.11559	0.73

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.03881	0.966
26DAP/20DAP	1.16143	0.615
34DAP/26DAP	1.26091	0.819
51DAP/34DAP	0.888	0.482
52DAP/51DAP	0.87929	1
53DAP/52DAP	1.00859	0.909
55DAP/53DAP	1.24884	0.712
57DAP/55DAP	1.01059	0.94
62DAP/57DAP	0.89531	0.466
68DAP/62DAP	0.88509	0.579
68DAP/14DAP	1.05112	0.889

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.99815	0.025

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.04046	1
Mature Green Tomato/Ripe Tomato	0.85448	0.317
Immature Eggplant/Mature Eggplant	1.69145	0.05
Ripe Pepper/Ripe Tomato	0.43261	0.224
Mature Eggplant/Ripe Tomato	0.31159	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.19627	0.551
1-1-2/M82	1.07988	1
12-2/M82	1.00037	1
12-4/M82	1.05849	N/A
1-3/M82	N/A	N/A
2-1-1/M82	1.16365	N/A
2-1/M82	0.74947	N/A
2-6/M82	0.72801	N/A
3-2/M82	N/A	N/A
4-1-1/M82	0.86392	1
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	0.94713	1
5-3/M82	1.02184	0.572
6-2/M82	1.59083	0.253
6-3/M82	1.04412	N/A
7-1/M82	1.52079	N/A
7-2/M82	N/A	N/A
9-3-2/M82	0.92556	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.0811	0.659
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.07825	1
IL12-4/WTpooled	1.21543	0.532
IL1-4/WTpooled	1.03957	1
WT/WTpooled	1.02582	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	1.29001	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.9105	1
DC3000/delta hrp 6h	0.94717	0.95
DC3000/delta hrp 12h	1.05559	1
DC3000/delta hrp 24h	0.8695	0.269

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.29482	N/A
DC3000 delta B/DC3000 delta AB	1.17283	0.516

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.14369	1
Exp 36h	0.92141	0.943
Exp 60h	0.92326	0.586

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

hybridization	ratio	FDR (corrected p value)
self-self	0.94536	1
Var 0h	1.08522	1
Var 12h I row2-row1	1.02803	0.795
Var 12h NI row2-row1	1.26151	1
Var 36h I row2-row1	1.2125	0.908
Var 36h NI row2-row1	0.93492	0.743
Var 60h I row2-row1	0.99986	1
Var 60h NI row2-row1	0.97708	1
Time course 0hI-0hNI	1.0429	0.764
Time course 12hI-12hNI	0.91593	0.188
Time course 36hI-36hNI	0.91147	0.295
Time course 60hI-60hNI	1.22649	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)	0.9926	0.789
transgenic ySAMdc/azygous control (breaker)	0.53232	0.15
transgenic ySAMdc/azygous control (red)	0.98781	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.07866	0.077

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.70921	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.8233	1
Manapal/WT (break)	1.21463	0.381
Manapal/WT (red)	1.1191	1