Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.2.6.8

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.85794	0.427
27DAP/17DAP	0.56512	0.05
39DAP/27DAP	1.01651	0.82
41DAP/39DAP	0.81794	0.283
42DAP/41DAP	1.03463	1
43DAP/42DAP	1.14607	0.985
47DAP/43DAP	0.99035	0.943
52DAP/47DAP	0.76376	0.498
57DAP/52DAP	1.4807	0.87

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04016	0.872
17DAP/reference	0.97108	0.597
27DAP/reference	0.97719	0.654
39DAP/reference	0.96237	0.35
41DAP/reference	1.03122	0.855
42DAP/reference	0.92086	0.103
43DAP/reference	1.00692	1
47DAP/reference	1.02429	1
52DAP/reference	1.01218	1
57DAP/reference	1.18632	0.044

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.11111	0.871
27DAP/17DAP	1.01019	0.969
39DAP/27DAP	0.85564	0.344
41DAP/39DAP	0.79337	0.645
42DAP/41DAP	0.87552	0.552
43DAP/42DAP	1.00198	1
47DAP/43DAP	0.91088	0.796
52DAP/47DAP	0.83561	0.77
57DAP/52DAP	0.9815	0.81
57DAP/7DAP	N/A	N/A

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.12003	0.292
17DAP/reference	1.12359	0.269
27DAP/reference	0.94729	0.348
39DAP/reference	0.92463	0.264
41DAP/reference	1.06031	0.577
42DAP/reference	0.85171	0.169
43DAP/reference	1.09466	0.637
47DAP/reference	1.07184	0.504
52DAP/reference	1.09945	0.732
57DAP/reference	1.06717	0.746

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.10079	0.241
17DAP/reference	0.95282	0.422
27DAP/reference	0.98715	0.598
39DAP/reference	0.92264	0.202
41DAP/reference	0.92324	0.169
42DAP/reference	0.94811	0.355
43DAP/reference	0.97349	0.561
47DAP/reference	1.35841	0.332
52DAP/reference	0.98585	0.576
57DAP/reference	1.06771	0.672

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.24107	0.076
17DAP/reference	1.0503	0.824
27DAP/reference	1.08965	0.777
39DAP/reference	1.06245	0.39
41DAP/reference	1.34676	0.125
42DAP/reference	1.05855	0.658
43DAP/reference	1.18196	0.28
47DAP/reference	1.09708	0.187
52DAP/reference	1.44558	0.138
57DAP/reference	1.19375	0.025

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.22297	1
26DAP/20DAP	0.64858	0.244
34DAP/26DAP	1.3632	0.819
51DAP/34DAP	0.82012	0.41
52DAP/51DAP	1.95333	0.082
53DAP/52DAP	1.07814	0.895
55DAP/53DAP	0.85904	0.417
57DAP/55DAP	1.21938	0.997
62DAP/57DAP	5.74768
68DAP/62DAP	0.66525	0.7
68DAP/14DAP	0.38124

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.90799	0.399

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.12688	0.666
Mature Green Tomato/Ripe Tomato	0.28913
Immature Eggplant/Mature Eggplant	0.86784
Ripe Pepper/Ripe Tomato	1.22552
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	1.19895	1
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	1.20841
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	1.02323
7-2/M82	N/A	N/A
9-3-2/M82	1.37919	0.196

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.74598	0.243
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	1.22117	0.792
IL7-3/WTpooled	1.13494	0.362
IL12-4/WTpooled	1.1158	0.785
IL1-4/WTpooled	0.8591	0.699
WT/WTpooled	1.04544	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	0.88212

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.97783
DC3000/delta hrp 6h	0.97918	0.95
DC3000/delta hrp 12h	1.02709	1
DC3000/delta hrp 24h	N/A	N/A

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	2.319
DC3000 delta B/DC3000 delta AB	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.88966	1
Exp 36h	1.02562	1
Exp 60h	0.95286	0.994

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

hybridization	ratio	FDR (corrected p value)
self-self	1.14914	1
Var 0h	0.95897	1
Var 12h I row2-row1	0.87636	0.31
Var 12h NI row2-row1	1.21826	0.228
Var 36h I row2-row1	0.967	1
Var 36h NI row2-row1	0.8974	0.413
Var 60h I row2-row1	1.3448	0.562
Var 60h NI row2-row1	1.25524	0.904
Time course 0hI-0hNI	0.82461	0.329
Time course 12hI-12hNI	0.93357	0.279
Time course 36hI-36hNI	0.7764	0.023
Time course 60hI-60hNI	0.42853	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)	0.97736	0.529
transgenic ySAMdc/azygous control (breaker)	0.98399	1
transgenic ySAMdc/azygous control (red)	1.14272	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.03097	0.08

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.89888	0.241

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.08233	0.307
Manapal/WT (break)	1.21754	0.381
Manapal/WT (red)	1.54516	0.222