Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.4.18.21

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.93051	0.652
27DAP/17DAP	1.07325	0.926
39DAP/27DAP	0.80194	0.443
41DAP/39DAP	1.13122	0.575
42DAP/41DAP	1.14602	0.786
43DAP/42DAP	0.91169	0.705
47DAP/43DAP	0.99714	0.92
52DAP/47DAP	1.25627	0.641
57DAP/52DAP	0.94314	0.92

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03231	0.71
17DAP/reference	0.9907	0.777
27DAP/reference	0.96989	0.581
39DAP/reference	0.98676	0.72
41DAP/reference	1.01283	0.963
42DAP/reference	0.97374	0.287
43DAP/reference	1.02518	0.547
47DAP/reference	0.91659	0.023
52DAP/reference	0.93983	0.172
57DAP/reference	0.8187	0.014

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.98237	0.75
27DAP/17DAP	0.98871	0.943
39DAP/27DAP	1.01437	0.751
41DAP/39DAP	0.96962	0.959
42DAP/41DAP	0.99226	0.876
43DAP/42DAP	1.07827	0.23
47DAP/43DAP	0.97621	0.909
52DAP/47DAP	0.99958	0.969
57DAP/52DAP	0.96731	0.612
57DAP/7DAP	1.00498	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.45761	0.104
17DAP/reference	1.39932	0.123
27DAP/reference	0.80506	0.101
39DAP/reference	0.887	0.307
41DAP/reference	0.90879	0.298
42DAP/reference	0.92014	0.211
43DAP/reference	1.22224	0.148
47DAP/reference	0.9904	0.671
52DAP/reference	1.01564	0.74
57DAP/reference	1.10033	1

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00263	0.97
17DAP/reference	1.00747	1
27DAP/reference	1.38756	0.552
39DAP/reference	0.92024	0.029
41DAP/reference	0.90533	0.096
42DAP/reference	0.88241	0.022
43DAP/reference	0.95951	0.486
47DAP/reference	0.88902	0.026
52DAP/reference	0.9213	0.023
57DAP/reference	0.98057	0.61

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.11388	0.347
17DAP/reference	0.95957	0.537
27DAP/reference	1.15402
39DAP/reference	0.93467	0.643
41DAP/reference	0.74465	0.018
42DAP/reference	0.74202	0.049
43DAP/reference	0.80019	0.188
47DAP/reference	0.94967	0.335
52DAP/reference	0.93522	0.277
57DAP/reference	0.77911	0.031

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.04903	0.966
26DAP/20DAP	0.97059	1
34DAP/26DAP	0.91317	0.394
51DAP/34DAP	0.92427	0.504
52DAP/51DAP	0.93129	1
53DAP/52DAP	1.04001	0.83
55DAP/53DAP	0.9955	0.908
57DAP/55DAP	1.06034	0.898
62DAP/57DAP	1.11838	0.833
68DAP/62DAP	0.85193	0.464
68DAP/14DAP	1.20753	0.469

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.84886	0.092

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.85984	0.371
Mature Green Tomato/Ripe Tomato	0.89988	0.165
Immature Eggplant/Mature Eggplant	1.36231	0.05
Ripe Pepper/Ripe Tomato	2.08084	0.258
Mature Eggplant/Ripe Tomato	1.48951	0.268

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.00754	1
1-1-2/M82	0.92578	1
12-2/M82	1.11168	1
12-4/M82	0.99152	1
1-3/M82	0.96316	1
2-1-1/M82	1.28096
2-1/M82	0.76761	0.519
2-6/M82	0.88103	0.421
3-2/M82	0.90248	0.451
4-1-1/M82	0.97251	1
4-1/M82	0.92797	1
4-3-2/M82	1.01746	1
4-3/M82	0.87967	1
5-3/M82	0.99021	1
6-2/M82	0.97434	1
6-3/M82	1.00566	1
7-1/M82	0.9429
7-2/M82	1.14189
9-3-2/M82	1.01611	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.94711	1
IL2-6/WTpooled	1.21492	0.584
IL7-5/WTpooled	0.84531	1
IL7-3/WTpooled	0.74461	1
IL12-4/WTpooled	1.07164	0.891
IL1-4/WTpooled	1.02493	1
WT/WTpooled	1.14328	0.87

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	1.06862	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.09185	0.875
DC3000/delta hrp 6h	1.05053	1
DC3000/delta hrp 12h	1.09412	1
DC3000/delta hrp 24h	0.96677	0.769

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.06328	0.355
DC3000 delta B/DC3000 delta AB	1.04724	0.586

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.06511	1
Exp 36h	0.94987	0.879
Exp 60h	1.05943	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.97492	1
Var 0h	0.92153	1
Var 12h I row2-row1	1.12921	0.209
Var 12h NI row2-row1	1.01575	1
Var 36h I row2-row1	0.94193	1
Var 36h NI row2-row1	0.77038	0.522
Var 60h I row2-row1	1.18609	0.562
Var 60h NI row2-row1	1.07182	1
Time course 0hI-0hNI	1.02948	0.867
Time course 12hI-12hNI	1.01951	0.836
Time course 36hI-36hNI	1.02646	0.355
Time course 60hI-60hNI	1.98736	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)	0.99778	0.931
transgenic ySAMdc/azygous control (breaker)	0.79146	0.142
transgenic ySAMdc/azygous control (red)	0.95399	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.13177	0.038

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.96614	0.789

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.83891	1
Manapal/WT (break)	0.80044	0.299
Manapal/WT (red)	0.80809	0.181