Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.2.4.17

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.27343	0.561
27DAP/17DAP	0.87218	0.746
39DAP/27DAP	0.90202	0.62
41DAP/39DAP	1.38284	0.398
42DAP/41DAP	0.92383	1
43DAP/42DAP	0.94723	0.887
47DAP/43DAP	0.86993	0.522
52DAP/47DAP	1.55583	0.468
57DAP/52DAP	0.899	0.89

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.10391	0.241
17DAP/reference	1.00514	1
27DAP/reference	1.07294	0.227
39DAP/reference	1.06202	0.393
41DAP/reference	1.14518	0.067
42DAP/reference	0.95937	0.157
43DAP/reference	1.01816	0.928
47DAP/reference	0.97079	0.366
52DAP/reference	0.96004	0.382
57DAP/reference	1.01472	1

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.91104	0.442
27DAP/17DAP	1.11428	0.632
39DAP/27DAP	1.17515	0.151
41DAP/39DAP	0.91303	0.696
42DAP/41DAP	1.0085	0.892
43DAP/42DAP	0.94597	0.576
47DAP/43DAP	0.97324	0.823
52DAP/47DAP	1.04645	0.862
57DAP/52DAP	0.98156	0.773
57DAP/7DAP	1.20374

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.51481	0.066
17DAP/reference	0.66934	0.044
27DAP/reference	0.99206	0.462
39DAP/reference	0.5412	0.011
41DAP/reference	1.14062	0.27
42DAP/reference	2.35814	0.03
43DAP/reference	2.10908	0.011
47DAP/reference	1.12105	0.45
52DAP/reference	0.58914	0.015
57DAP/reference	0.42529	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01242	0.831
17DAP/reference	1.07903	0.367
27DAP/reference	1.14486	0.359
39DAP/reference	0.85122	0.147
41DAP/reference	1.13877	0.459
42DAP/reference	1.19211	0.038
43DAP/reference	1.09636	0.801
47DAP/reference	1.10096	0.413
52DAP/reference	0.95386	0.5
57DAP/reference	1.18225	0.538

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.5652	0.031
17DAP/reference	0.8477	0.305
27DAP/reference	0.62079	0.058
39DAP/reference	0.57841	0.016
41DAP/reference	0.61168	0.046
42DAP/reference	2.87438	0.012
43DAP/reference	1.82824	0.157
47DAP/reference	0.99028	0.593
52DAP/reference	1.48918	0.09
57DAP/reference	1.19721	0.339

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.03513	1
26DAP/20DAP	1.07463	0.778
34DAP/26DAP	1.02743	1
51DAP/34DAP	1.08959	0.597
52DAP/51DAP	0.8544	0.151
53DAP/52DAP	1.05665	0.882
55DAP/53DAP	0.95929	0.725
57DAP/55DAP	1.13299	0.854
62DAP/57DAP	1.12796	0.902
68DAP/62DAP	1.00257	0.914
68DAP/14DAP	1.07271	0.87

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.94052	0.378

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.94084	0.523
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.17729	0.293
Mature Eggplant/Ripe Tomato	0.55803	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.06838	0.877
1-1-2/M82	0.77363
12-2/M82	N/A	N/A
12-4/M82	0.8416	1
1-3/M82	0.78769
2-1-1/M82	N/A	N/A
2-1/M82	1.20876
2-6/M82	0.91866	1
3-2/M82	1.3803
4-1-1/M82	0.96477	1
4-1/M82	0.9833	1
4-3-2/M82	N/A	N/A
4-3/M82	1.0753
5-3/M82	0.97113	1
6-2/M82	0.87941
6-3/M82	N/A	N/A
7-1/M82	0.87387
7-2/M82	0.97283	0.881
9-3-2/M82	0.87232	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.98258	0.247
IL2-6/WTpooled	0.97909	1
IL7-5/WTpooled	1.64789	0.722
IL7-3/WTpooled	0.89696	1
IL12-4/WTpooled	0.9001	0.554
IL1-4/WTpooled	1.10615	0.426
WT/WTpooled	0.88732	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	0.77655	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.97031	1
DC3000/delta hrp 6h	1.09452	1
DC3000/delta hrp 12h	1.1133	1
DC3000/delta hrp 24h	1.05718	0.604

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.91389	0.691
DC3000 delta B/DC3000 delta AB	1.05902	0.544

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.9034	0.328
Exp 36h	1.15469	0.693
Exp 60h	0.92621	0.855

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

hybridization	ratio	FDR (corrected p value)
self-self	1.07614	1
Var 0h	0.90713	0.933
Var 12h I row2-row1	0.96335	0.627
Var 12h NI row2-row1	1.16637	0.649
Var 36h I row2-row1	0.98675	1
Var 36h NI row2-row1	1.11406	1
Var 60h I row2-row1	0.80797	0.285
Var 60h NI row2-row1	0.98264	1
Time course 0hI-0hNI	0.92322	0.411
Time course 12hI-12hNI	1.08716	0.512
Time course 36hI-36hNI	1.07006	0.218
Time course 60hI-60hNI	1.89876	0.011

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)	0.95552	0.348
transgenic ySAMdc/azygous control (breaker)	1.03658	1
transgenic ySAMdc/azygous control (red)	0.96474	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.00072	1

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.10204	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.139	1
Manapal/WT (break)	0.99961	1
Manapal/WT (red)	1.28585	0.164