Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.3.13.16

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.61197	0.083
27DAP/17DAP	1.00745	1
39DAP/27DAP	1.67199	0.107
41DAP/39DAP	0.88138	0.52
42DAP/41DAP	0.82389	0.774
43DAP/42DAP	0.83636	0.741
47DAP/43DAP	0.80925	0.424
52DAP/47DAP	0.91027	0.716
57DAP/52DAP	1.00435	0.983

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.20529	0.126
17DAP/reference	0.98093	0.63
27DAP/reference	0.9157	0.134
39DAP/reference	0.97133	0.565
41DAP/reference	0.96305	0.542
42DAP/reference	0.86411	0.003
43DAP/reference	0.98832	0.763
47DAP/reference	0.84129	0.004
52DAP/reference	0.76367	0.015
57DAP/reference	0.84378	0.049

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.52773	0.034
27DAP/17DAP	1.16014	0.557
39DAP/27DAP	1.29683	0.102
41DAP/39DAP	1.05884	0.817
42DAP/41DAP	1.01746	1
43DAP/42DAP	0.90263	0.101
47DAP/43DAP	1.10946	0.24
52DAP/47DAP	0.80195	0.389
57DAP/52DAP	0.84312	0.403
57DAP/7DAP	0.81815	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.41874	0.035
17DAP/reference	1.07528	0.896
27DAP/reference	1.07604	0.664
39DAP/reference	0.98334	0.552
41DAP/reference	0.90307	0.326
42DAP/reference	1.02321	1
43DAP/reference	0.94741	0.22
47DAP/reference	0.96777	0.671
52DAP/reference	1.11527	0.491
57DAP/reference	0.75359	0.012

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.4661	0.114
17DAP/reference	0.80953	0.036
27DAP/reference	0.87045	0.155
39DAP/reference	0.87994	0.119
41DAP/reference	0.88715	0.124
42DAP/reference	0.80114	0.016
43DAP/reference	1.01149	0.831
47DAP/reference	0.87654	0.083
52DAP/reference	0.85769	0.066
57DAP/reference	1.07234	0.64

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.7051	0.028
17DAP/reference	0.94669	0.407
27DAP/reference	1.00288	1
39DAP/reference	1.00902	0.935
41DAP/reference	0.91769	0.096
42DAP/reference	0.90387	0.172
43DAP/reference	0.85441	0.143
47DAP/reference	0.79888	0.045
52DAP/reference	0.8081	0.131
57DAP/reference	0.70963	0.016

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.0282	1
26DAP/20DAP	1.61075	0.099
34DAP/26DAP	0.74679	0.18
51DAP/34DAP	0.64163	0.077
52DAP/51DAP	0.98908	1
53DAP/52DAP	1.02604	0.944
55DAP/53DAP	1.11569	0.806
57DAP/55DAP	1.21785	0.171
62DAP/57DAP	1.04312	0.902
68DAP/62DAP	0.97144	0.787
68DAP/14DAP	0.95351	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.7401	0.02

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.26218
Mature Green Tomato/Ripe Tomato	1.67978	0.038
Immature Eggplant/Mature Eggplant	2.93997	0.05
Ripe Pepper/Ripe Tomato	0.98737	1
Mature Eggplant/Ripe Tomato	1.54809	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.92168	0.883
1-1-2/M82	0.88433	1
12-2/M82	0.75576
12-4/M82	0.80416	1
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	1.26053
2-6/M82	1.34619
3-2/M82	0.9385
4-1-1/M82	1.00265
4-1/M82	N/A	N/A
4-3-2/M82	0.81814
4-3/M82	N/A	N/A
5-3/M82	1.55331	0.496
6-2/M82	2.43659
6-3/M82	N/A	N/A
7-1/M82	1.72683
7-2/M82	N/A	N/A
9-3-2/M82	1.01524	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.37604	0.659
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.77826	0.362
IL12-4/WTpooled	1.38151	0.522
IL1-4/WTpooled	0.97201	0.834
WT/WTpooled	0.95227	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	1.57733	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.02796	0.921
DC3000/delta hrp 6h	0.90193	0.95
DC3000/delta hrp 12h	1.05965	1
DC3000/delta hrp 24h	3.32515	0.024

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.3979
DC3000 delta B/DC3000 delta AB	1.18287	0.243

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.16724	1
Exp 36h	1.93749	0.489
Exp 60h	2.37976	0.283

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

hybridization	ratio	FDR (corrected p value)
self-self	0.93387
Var 0h	1.02707	1
Var 12h I row2-row1	1.50312	0.196
Var 12h NI row2-row1	1.36799	0.266
Var 36h I row2-row1	0.82335	1
Var 36h NI row2-row1	0.88151	0.645
Var 60h I row2-row1	0.74601	0.285
Var 60h NI row2-row1	0.85574	0.313
Time course 0hI-0hNI	1.09314	0.764
Time course 12hI-12hNI	2.30911	0.004
Time course 36hI-36hNI	3.6393	0.004
Time course 60hI-60hNI	11.9498	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)	1.22116	0.297
transgenic ySAMdc/azygous control (breaker)	1.16619	0.248
transgenic ySAMdc/azygous control (red)	1.00383	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.94544	0.117

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.66817	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.10488	0.307
Manapal/WT (break)	0.87371	1
Manapal/WT (red)	0.98565	0.863