Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.1.20.1

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.20397	0.947
27DAP/17DAP	1.05039	0.905
39DAP/27DAP	1.05304	1
41DAP/39DAP	1.05412	0.765
42DAP/41DAP	1.42813	0.632
43DAP/42DAP	1.17138	0.993
47DAP/43DAP	1.09156	0.965
52DAP/47DAP	1.20122	0.91
57DAP/52DAP	0.89899	0.926

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90015
17DAP/reference	0.31406
27DAP/reference	1.48249
39DAP/reference	N/A	N/A
41DAP/reference	0.1983
42DAP/reference	0.71766	0.046
43DAP/reference	1.02316
47DAP/reference	0.73222	0.055
52DAP/reference	0.98516	0.689
57DAP/reference	N/A	N/A

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.83624	0.311
27DAP/17DAP	1.01678	0.969
39DAP/27DAP	1.15169	0.603
41DAP/39DAP	1.23238	0.284
42DAP/41DAP	1.00578	0.865
43DAP/42DAP	1.18129	0.554
47DAP/43DAP	1.01239	1
52DAP/47DAP	1.11689	0.666
57DAP/52DAP	1.16188	0.858
57DAP/7DAP	1.30193	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01654	1
17DAP/reference	1.28002	0.018
27DAP/reference	1.32359	0.012
39DAP/reference	N/A	N/A
41DAP/reference	1.00507	0.811
42DAP/reference	N/A	N/A
43DAP/reference	1.0376	0.637
47DAP/reference	1.20749	0.247
52DAP/reference	1.27036	0.247
57DAP/reference	0.93737	0.458

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.4365	0.007
17DAP/reference	0.44518	0.004
27DAP/reference	1.60821	0.283
39DAP/reference	0.79132	0.119
41DAP/reference	0.81062	0.237
42DAP/reference	1.01062	1
43DAP/reference	0.50877	0.036
47DAP/reference	0.8226	0.053
52DAP/reference	0.77015	0.005
57DAP/reference	0.32615	0.003

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96663	0.653
17DAP/reference	1.22818	0.699
27DAP/reference	2.61552	0.198
39DAP/reference	2.15718	0.466
41DAP/reference	1.59961	0.031
42DAP/reference	N/A	N/A
43DAP/reference	1.27704	0.58
47DAP/reference	0.85629	0.249
52DAP/reference	1.1206	0.99
57DAP/reference	5.41299	0.039

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.78487	0.966
26DAP/20DAP	0.79593	0.317
34DAP/26DAP	1.10402	1
51DAP/34DAP	0.99385	0.893
52DAP/51DAP	0.97733	1
53DAP/52DAP	1.09061	0.753
55DAP/53DAP	1.41844	0.113
57DAP/55DAP	1.78922	0.044
62DAP/57DAP	2.17671	0.115
68DAP/62DAP	5.23264	0.068
68DAP/14DAP	9.59756	0.017

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.98613	0.665

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.06224	0.863
Mature Green Tomato/Ripe Tomato	0.19552	0.014
Immature Eggplant/Mature Eggplant	1.39672	0.072
Ripe Pepper/Ripe Tomato	1.72528	0.256
Mature Eggplant/Ripe Tomato	1.34896

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.16451
1-1-2/M82	0.99251	0.958
12-2/M82	1.08126	0.448
12-4/M82	1.0147	1
1-3/M82	0.77928	0.378
2-1-1/M82	1.18368	0.764
2-1/M82	N/A	N/A
2-6/M82	0.9353	1
3-2/M82	0.93047
4-1-1/M82	0.74134
4-1/M82	1.55504
4-3-2/M82	0.7902
4-3/M82	1.02529	1
5-3/M82	0.99299	1
6-2/M82	0.82775	0.497
6-3/M82	1.02114	1
7-1/M82	N/A	N/A
7-2/M82	0.94849	0.599
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	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	N/A	N/A
WT/WTpooled	N/A	N/A

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	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.91025	0.875
DC3000/delta hrp 6h	1.22063	1
DC3000/delta hrp 12h	1.33166	1
DC3000/delta hrp 24h	1.14636	0.422

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	2.51697	0.042
DC3000 delta B/DC3000 delta AB	5.53896	0.085

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.09135	1
Exp 36h	1.07884	1
Exp 60h	0.90686	0.586

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

hybridization	ratio	FDR (corrected p value)
self-self	1.04297	1
Var 0h	N/A	N/A
Var 12h I row2-row1	1.06189	0.379
Var 12h NI row2-row1	0.7539	0.438
Var 36h I row2-row1	1.52243	0.489
Var 36h NI row2-row1	1.05124	1
Var 60h I row2-row1	1.06373	0.562
Var 60h NI row2-row1	0.76352	0.516
Time course 0hI-0hNI	1.02313	0.867
Time course 12hI-12hNI	1.2837	0.367
Time course 36hI-36hNI	1.45534	0.039
Time course 60hI-60hNI	1.29904	0.359

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)	1.03559	0.798
transgenic ySAMdc/azygous control (breaker)	1.22689	0.248
transgenic ySAMdc/azygous control (red)	1.03494	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.87809	0.308

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.98167	0.096
Manapal/WT (break)	1.5556	0.381
Manapal/WT (red)	2.0081	0.164