Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.3.16.9

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.95543	0.699
27DAP/17DAP	0.64097	0.098
39DAP/27DAP	0.77405	0.487
41DAP/39DAP	0.93585	0.828
42DAP/41DAP	1.11836	0.937
43DAP/42DAP	1.62258	0.202
47DAP/43DAP	0.68613	0.185
52DAP/47DAP	0.93809	0.812
57DAP/52DAP	1.51579	0.853

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.8751	0.064
17DAP/reference	0.88001	0.091
27DAP/reference	0.91595	0.215
39DAP/reference	0.88737	0.106
41DAP/reference	0.83733	0.026
42DAP/reference	0.88276	0.001
43DAP/reference	0.8864	0.045
47DAP/reference	1.00892	1
52DAP/reference	1.05037	0.548
57DAP/reference	1.14478	0.132

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.0174	0.871
27DAP/17DAP	1.21781	0.238
39DAP/27DAP	0.63579	0.068
41DAP/39DAP	0.58593	0.026
42DAP/41DAP	1.11458	1
43DAP/42DAP	1.47646	0.094
47DAP/43DAP	0.8282	0.018
52DAP/47DAP	0.82462
57DAP/52DAP	0.97754	0.773
57DAP/7DAP	0.3717	0.186

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01454	0.98
17DAP/reference	1.17318	0.147
27DAP/reference	1.0019	0.748
39DAP/reference	1.00112	0.745
41DAP/reference	1.06761	0.524
42DAP/reference	0.97596	0.355
43DAP/reference	0.98817	0.555
47DAP/reference	0.94579	0.383
52DAP/reference	0.88964	0.232
57DAP/reference	0.89583	0.017

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.89035	0.248
17DAP/reference	0.86584	0.075
27DAP/reference	0.89957	0.134
39DAP/reference	0.85776	0.099
41DAP/reference	0.85014	0.031
42DAP/reference	0.91165	0.169
43DAP/reference	0.79262	0.042
47DAP/reference	0.88242	0.079
52DAP/reference	0.90681	0.037
57DAP/reference	0.86075	0.012

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.0964	0.258
17DAP/reference	1.12964	0.431
27DAP/reference	1.19805	0.088
39DAP/reference	1.02767	0.752
41DAP/reference	1.083	0.537
42DAP/reference	1.14895	0.184
43DAP/reference	0.93597	0.305
47DAP/reference	0.90006	0.231
52DAP/reference	0.89504	0.2
57DAP/reference	1.05192	0.878

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.1293	1
26DAP/20DAP	1.22236	0.312
34DAP/26DAP	1.05551	1
51DAP/34DAP	1.49464	0.032
52DAP/51DAP	0.80031	0.151
53DAP/52DAP	0.91501	0.52
55DAP/53DAP	0.62261	0.021
57DAP/55DAP	0.79389	0.297
62DAP/57DAP	1.23643	0.35
68DAP/62DAP	2.23422	0.225
68DAP/14DAP	1.43261	0.211

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.21647	0.02

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	9.03369	0.015
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	N/A	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	0.8882
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	N/A	N/A
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	N/A	N/A
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.40553	0.277
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	1.12099	0.792
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	0.76864	0.415
WT/WTpooled	N/A	N/A

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	0.79221	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.86092	1
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	0.85569	1
DC3000/delta hrp 24h	0.91142	0.447

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.44149	0.023
DC3000 delta B/DC3000 delta AB	0.48086	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.89669	1
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	0.99379	1
Var 0h	1.11208	1
Var 12h I row2-row1	0.7387	0.338
Var 12h NI row2-row1	0.90642	0.488
Var 36h I row2-row1	0.76884	0.805
Var 36h NI row2-row1	1.34566	0.276
Var 60h I row2-row1	1.06853	0.562
Var 60h NI row2-row1	1.06849	1
Time course 0hI-0hNI	0.97855	0.93
Time course 12hI-12hNI	1.02572	0.842
Time course 36hI-36hNI	0.77328	0.027
Time course 60hI-60hNI	0.1174	0.005

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)	1.56329	0.699
transgenic ySAMdc/azygous control (breaker)	1.16669	1
transgenic ySAMdc/azygous control (red)	1.01832	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.97882	0.343

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.26542	0.239

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	N/A	N/A
Manapal/WT (break)	1.08833	1
Manapal/WT (red)	N/A	N/A