Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.4.13.19

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.34725	0.951
27DAP/17DAP	2.24196	0.096
39DAP/27DAP	2.12201	0.094
41DAP/39DAP	0.89118	0.545
42DAP/41DAP	0.70966	0.397
43DAP/42DAP	0.82727	0.547
47DAP/43DAP	0.70429	0.2
52DAP/47DAP	1.08108	0.906
57DAP/52DAP	0.95334	0.949

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87581	0.064
17DAP/reference	0.83793	0.012
27DAP/reference	0.97773	0.642
39DAP/reference	0.88944	0.097
41DAP/reference	0.83969	0.014
42DAP/reference	0.84533	0.005
43DAP/reference	0.95251	0.331
47DAP/reference	0.848	0.005
52DAP/reference	0.83462	0.082
57DAP/reference	1.00651	0.927

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.06358	0.87
27DAP/17DAP	1.38136	0.045
39DAP/27DAP	1.03934	0.643
41DAP/39DAP	0.74983	0.069
42DAP/41DAP	1.31233	0.028
43DAP/42DAP	0.79377	0.029
47DAP/43DAP	0.84306	0.024
52DAP/47DAP	1.02157	0.97
57DAP/52DAP	0.84587	0.321
57DAP/7DAP	1.2348	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.09942	0.843
17DAP/reference	1.03885	1
27DAP/reference	0.96441	0.43
39DAP/reference	1.11826	0.21
41DAP/reference	1.15762	0.402
42DAP/reference	1.23733	0.233
43DAP/reference	0.98704	0.58
47DAP/reference	1.20519	0.377
52DAP/reference	0.91158	0.278
57DAP/reference	0.70854	0.043

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04641	0.993
17DAP/reference	0.8588	0.049
27DAP/reference	1.05913	0.834
39DAP/reference	0.91849	0.129
41DAP/reference	0.89893	0.212
42DAP/reference	0.92146	0.15
43DAP/reference	0.90992	0.243
47DAP/reference	0.88112	0.075
52DAP/reference	0.90638	0.121
57DAP/reference	1.00016	0.834

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93348	0.362
17DAP/reference	0.9175	0.292
27DAP/reference	0.97629	0.566
39DAP/reference	1.04486	0.773
41DAP/reference	1.0617	0.537
42DAP/reference	0.77485	0.023
43DAP/reference	0.69485	0.018
47DAP/reference	0.77087	0.009
52DAP/reference	0.80532	0.193
57DAP/reference	0.71865	0.024

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.85665	0.611
26DAP/20DAP	1.18122	0.338
34DAP/26DAP	0.99453	1
51DAP/34DAP	1.68021	0.035
52DAP/51DAP	0.84195	0.151
53DAP/52DAP	1.96069	0.025
55DAP/53DAP	0.81183	0.07
57DAP/55DAP	0.96474	0.795
62DAP/57DAP	1.04968	0.935
68DAP/62DAP	0.84702	0.406
68DAP/14DAP	0.89209	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.91148	0.304

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.423
Mature Green Tomato/Ripe Tomato	6.08518	0.015
Immature Eggplant/Mature Eggplant	7.50128	0.05
Ripe Pepper/Ripe Tomato	0.63948	1
Mature Eggplant/Ripe Tomato	3.60078	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.97946
1-1-2/M82	0.80215	0.804
12-2/M82	1.16608
12-4/M82	1.21774
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	0.67748
6-3/M82	1.50161
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	N/A	N/A
IL2-6/WTpooled	0.84739	0.348
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.11065	1
IL12-4/WTpooled	0.64333	0.205
IL1-4/WTpooled	0.72715
WT/WTpooled	1.04159	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	0.84756

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.96618	1
DC3000/delta hrp 6h	1.62494	0.978
DC3000/delta hrp 12h	1.01586	1
DC3000/delta hrp 24h	0.67489	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.87111	0.765
DC3000 delta B/DC3000 delta AB	1.08018	0.579

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.16386	1
Exp 36h	0.83463	0.661
Exp 60h	1.05586	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98523	1
Var 0h	0.97997	1
Var 12h I row2-row1	1.05903	0.654
Var 12h NI row2-row1	0.95141	0.82
Var 36h I row2-row1	1.11695	1
Var 36h NI row2-row1	1.299	1
Var 60h I row2-row1	1.18892	1
Var 60h NI row2-row1	1.19549	0.904
Time course 0hI-0hNI	1.11858	0.719
Time course 12hI-12hNI	0.74963	0.063
Time course 36hI-36hNI	0.82679	0.187
Time course 60hI-60hNI	1.54128	0.009

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)	0.89902	0.485
transgenic ySAMdc/azygous control (breaker)	0.86493	0.49
transgenic ySAMdc/azygous control (red)	0.73695	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.13976	0.035

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.99784	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.40284	0.172
Manapal/WT (break)	0.94201	1
Manapal/WT (red)	0.77988	0.424