Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.3.16.4

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.21879	0.827
27DAP/17DAP	2.16559	0.215
39DAP/27DAP	3.95017	0.026
41DAP/39DAP	1.38388	0.504
42DAP/41DAP	1.24403	0.582
43DAP/42DAP	1.38761	0.823
47DAP/43DAP	1.6413	0.213
52DAP/47DAP	0.89987	0.702
57DAP/52DAP	2.20525	0.731

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.59864	0.029
17DAP/reference	0.64302	0.007
27DAP/reference	0.75507	0.013
39DAP/reference	1.13733	0.771
41DAP/reference	0.83264	0.031
42DAP/reference	1.37002	0.002
43DAP/reference	1.18585	0.014
47DAP/reference	2.10978	0.001
52DAP/reference	1.56425	0.013
57DAP/reference	1.56958	0.009

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.66283	0.65
27DAP/17DAP	1.31896	0.794
39DAP/27DAP	1.47338	0.603
41DAP/39DAP	0.79416	0.465
42DAP/41DAP	1.84341	0.327
43DAP/42DAP	1.46678	0.072
47DAP/43DAP	1.29829	0.221
52DAP/47DAP	1.07438	0.991
57DAP/52DAP	1.65555	0.274
57DAP/7DAP	1.32267

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.78129	0.088
17DAP/reference	0.79515	0.072
27DAP/reference	1.04875	0.664
39DAP/reference	1.18288	0.12
41DAP/reference	1.55902	0.01
42DAP/reference	1.46855	0.016
43DAP/reference	1.1896	0.188
47DAP/reference	1.2431	0.124
52DAP/reference	1.77205	0.009
57DAP/reference	3.36453	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.49378	0.006
17DAP/reference	0.45827	0.003
27DAP/reference	0.74228	0.025
39DAP/reference	0.82158	0.016
41DAP/reference	1.08817	0.459
42DAP/reference	1.06631	0.664
43DAP/reference	0.75212	0.039
47DAP/reference	2.95639	0.008
52DAP/reference	1.11482	0.085
57DAP/reference	1.27616	0.277

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9231	0.335
17DAP/reference	0.77605	0.141
27DAP/reference	0.91844	0.056
39DAP/reference	1.36053	0.016
41DAP/reference	1.25197	0.012
42DAP/reference	1.35878	0.027
43DAP/reference	1.38315	0.014
47DAP/reference	2.53624	0.005
52DAP/reference	2.8582	0.028
57DAP/reference	1.67827	0.058

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.08648	0.966
26DAP/20DAP	1.32201	0.262
34DAP/26DAP	1.91299	0.542
51DAP/34DAP	3.21078	0.023
52DAP/51DAP	0.69641	0.151
53DAP/52DAP	1.70016	0.033
55DAP/53DAP	0.42241	0.021
57DAP/55DAP	0.73784	0.066
62DAP/57DAP	2.77754	0.003
68DAP/62DAP	1.0485	0.914
68DAP/14DAP	3.27535	0.022

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.01026	1

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.02785	0.036
Mature Green Tomato/Ripe Tomato	0.32128	0.019
Immature Eggplant/Mature Eggplant	38.1683	0.05
Ripe Pepper/Ripe Tomato	2.33772	1
Mature Eggplant/Ripe Tomato	0.51571	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.87005	0.638
1-1-2/M82	1.38378	1
12-2/M82	1.04662	1
12-4/M82	1.17165	1
1-3/M82	5.36814	0.479
2-1-1/M82	1.02762	1
2-1/M82	1.0721	1
2-6/M82	1.31459	0.364
3-2/M82	1.21913	0.717
4-1-1/M82	2.18122	1
4-1/M82	1.24311	1
4-3-2/M82	2.37464	0.262
4-3/M82	1.07631	1
5-3/M82	0.54886	0.49
6-2/M82	0.6337	0.481
6-3/M82	1.01277	1
7-1/M82	0.94609	0.803
7-2/M82	2.55821	0.385
9-3-2/M82	2.40767	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	N/A	N/A
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	1.61009	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	N/A	N/A
DC3000/delta hrp 6h	0.83757	0.95
DC3000/delta hrp 12h	1.03391	1
DC3000/delta hrp 24h	0.73607	0.143

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	N/A
DC3000 delta B/DC3000 delta AB	2.98807	0.079

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.04967	1
Exp 36h	1.15995	1
Exp 60h	1.0323	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99408	1
Var 0h	0.85533	0.933
Var 12h I row2-row1	0.86314	0.77
Var 12h NI row2-row1	1.96994	0.649
Var 36h I row2-row1	1.09331	1
Var 36h NI row2-row1	0.92276	0.791
Var 60h I row2-row1	0.50376	0.285
Var 60h NI row2-row1	0.56889	0.292
Time course 0hI-0hNI	1.06087	0.852
Time course 12hI-12hNI	1.66808	0.04
Time course 36hI-36hNI	3.9531	0.005
Time course 60hI-60hNI	20.4778	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)	0.62925	0.314
transgenic ySAMdc/azygous control (breaker)	0.89369	0.15
transgenic ySAMdc/azygous control (red)	1.26322	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.68313	0.061

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.66549	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	5.77323	0.105
Manapal/WT (break)	6.54448	0.14
Manapal/WT (red)	1.80174	0.15