Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.2.7.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.06673	0.912
27DAP/17DAP	1.13596	0.859
39DAP/27DAP	0.7992	0.462
41DAP/39DAP	1.49582	0.224
42DAP/41DAP	1.7774	0.051
43DAP/42DAP	1.1366	0.875
47DAP/43DAP	0.93988	0.779
52DAP/47DAP	1.14622	0.718
57DAP/52DAP	1.06084	0.962

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95549	0.352
17DAP/reference	0.94442	0.298
27DAP/reference	1.07837	0.498
39DAP/reference	1.1171	0.368
41DAP/reference	0.97682	0.667
42DAP/reference	0.9495	0.134
43DAP/reference	0.90206	0.143
47DAP/reference	1.03155	0.862
52DAP/reference	1.23077	0.022
57DAP/reference	1.11747	0.114

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.06342	0.445
27DAP/17DAP	1.08543	0.909
39DAP/27DAP	1.77072	0.046
41DAP/39DAP	0.57525	0.026
42DAP/41DAP	2.19779	0.002
43DAP/42DAP	3.44218	0.013
47DAP/43DAP	1.09791	0.827
52DAP/47DAP	1.10791	0.851
57DAP/52DAP	0.73385	0.245
57DAP/7DAP	1.09416	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.78584	0.076
17DAP/reference	0.79619	0.012
27DAP/reference	0.88195	0.094
39DAP/reference	0.75841	0.012
41DAP/reference	0.74018	0.018
42DAP/reference	0.80097	0.012
43DAP/reference	0.73907	0.031
47DAP/reference	0.84584	0.222
52DAP/reference	0.77223	0.028
57DAP/reference	0.76445	0.012

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.77995	0.017
17DAP/reference	0.83622	0.019
27DAP/reference	1.0326	0.974
39DAP/reference	1.06137	0.502
41DAP/reference	1.08423	0.502
42DAP/reference	0.99544	0.655
43DAP/reference	1.10636	0.785
47DAP/reference	0.9192	0.159
52DAP/reference	1.04404	0.629
57DAP/reference	0.94001	0.318

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.80965	0.054
17DAP/reference	0.91791	0.3
27DAP/reference	0.73128	0.028
39DAP/reference	0.82919	0.035
41DAP/reference	0.84981	0.023
42DAP/reference	0.83088	0.108
43DAP/reference	1.04448	0.755
47DAP/reference	0.95913	0.296
52DAP/reference	0.78919	0.197
57DAP/reference	0.98866	0.623

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.82922	1
26DAP/20DAP	0.90896	1
34DAP/26DAP	1.25	0.819
51DAP/34DAP	1.31224	0.281
52DAP/51DAP	1.71526
53DAP/52DAP	2.03041	0.029
55DAP/53DAP	1.56679	0.039
57DAP/55DAP	1.05213	1
62DAP/57DAP	0.75	0.871
68DAP/62DAP	2.52111	0.206
68DAP/14DAP	1.80793	0.048

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	5.50986	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.38875
Mature Green Tomato/Ripe Tomato	0.32634	0.019
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.52775	1
Mature Eggplant/Ripe Tomato	0.07694	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.38297	0.877
1-1-2/M82	1.29125	0.977
12-2/M82	0.98402	1
12-4/M82	1.34566	1
1-3/M82	2.3235	0.248
2-1-1/M82	0.97288	1
2-1/M82	0.8062	0.74
2-6/M82	0.98688	1
3-2/M82	0.1193
4-1-1/M82	1.19817	1
4-1/M82	1.13387	1
4-3-2/M82	1.31453	1
4-3/M82	1.01556	1
5-3/M82	0.96731	1
6-2/M82	1.21739	1
6-3/M82	1.02039	1
7-1/M82	1.03526	1
7-2/M82	1.27885	1
9-3-2/M82	1.49693	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.77918	0.243
IL2-6/WTpooled	0.99664	1
IL7-5/WTpooled	1.6822	1
IL7-3/WTpooled	1.10872	0.362
IL12-4/WTpooled	1.09895	0.646
IL1-4/WTpooled	1.07143	1
WT/WTpooled	0.96479	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	0.83435	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.0404	0.921
DC3000/delta hrp 6h	1.1625	0.978
DC3000/delta hrp 12h	1.03553	1
DC3000/delta hrp 24h	0.62941	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.05583	0.25
DC3000 delta B/DC3000 delta AB	1.08819	0.498

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.78946	1
Exp 36h	1.08519	1
Exp 60h	1.20114	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98732	1
Var 0h	0.89188	1
Var 12h I row2-row1	0.9756	0.948
Var 12h NI row2-row1	1.04777	1
Var 36h I row2-row1	1.21089	0.742
Var 36h NI row2-row1	1.24599	0.253
Var 60h I row2-row1	0.7453	0.293
Var 60h NI row2-row1	1.19052	0.904
Time course 0hI-0hNI	0.91924	0.399
Time course 12hI-12hNI	0.92596	0.497
Time course 36hI-36hNI	1.00193	0.811
Time course 60hI-60hNI	0.87733	0.161

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)	0.96903	0.454
transgenic ySAMdc/azygous control (breaker)	1.06471	1
transgenic ySAMdc/azygous control (red)	1.11186	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.03761	0.059

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.88833	0.35

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.20726	0.105
Manapal/WT (break)	1.104	0.381
Manapal/WT (red)	1.3345	0.164