Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.3.13.16

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.86431	0.405
27DAP/17DAP	1.02219	1
39DAP/27DAP	1.3453	0.546
41DAP/39DAP	0.99343	0.954
42DAP/41DAP	1.33418	0.743
43DAP/42DAP	0.71247	0.709
47DAP/43DAP	1.35538	0.306
52DAP/47DAP	0.9457	0.702
57DAP/52DAP	1.35458	0.977

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97093	0.465
17DAP/reference	1	0.957
27DAP/reference	1.05185	0.623
39DAP/reference	1.01447	0.842
41DAP/reference	0.89824	0.201
42DAP/reference	0.81554	0.005
43DAP/reference	1.0154	0.957
47DAP/reference	0.85305	0.006
52DAP/reference	0.92966	0.172
57DAP/reference	0.99298	0.671

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.88908	0.299
27DAP/17DAP	0.93341	0.748
39DAP/27DAP	1.06684	0.643
41DAP/39DAP	1.27479	0.65
42DAP/41DAP	1.09799	0.999
43DAP/42DAP	1.10713	0.134
47DAP/43DAP	1.08482	0.641
52DAP/47DAP	0.92262	0.797
57DAP/52DAP	0.91135	0.545
57DAP/7DAP	0.99629	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.79996	0.086
17DAP/reference	0.78538	0.013
27DAP/reference	0.76335	0.01
39DAP/reference	0.89454	0.198
41DAP/reference	0.90907	0.16
42DAP/reference	0.88547	0.048
43DAP/reference	0.82211	0.054
47DAP/reference	0.93202	0.383
52DAP/reference	0.80058	0.033
57DAP/reference	0.82849	0.043

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90231	0.248
17DAP/reference	0.81539	0.05
27DAP/reference	0.92366	0.282
39DAP/reference	0.8807	0.195
41DAP/reference	0.84476	0.11
42DAP/reference	0.96128	0.392
43DAP/reference	0.98838	0.646
47DAP/reference	0.90369	0.032
52DAP/reference	0.87674	0.047
57DAP/reference	1.03735	1

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.81927	0.092
17DAP/reference	0.94512	0.308
27DAP/reference	0.82529	0.045
39DAP/reference	0.86435	0.018
41DAP/reference	0.9308	0.293
42DAP/reference	0.91036	0.22
43DAP/reference	0.7353	0.033
47DAP/reference	0.99254	0.646
52DAP/reference	0.9266	0.551
57DAP/reference	0.84217	0.02

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.04581	1
26DAP/20DAP	N/A	N/A
34DAP/26DAP	2.00197
51DAP/34DAP	1.18845
52DAP/51DAP	1.05585
53DAP/52DAP	0.9027	0.587
55DAP/53DAP	1.01322	1
57DAP/55DAP	1.12735	0.969
62DAP/57DAP	1.12489	0.569
68DAP/62DAP	0.82804	0.641
68DAP/14DAP	0.86277	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.21315	0.7

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	N/A	N/A
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	0.75589

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.31743
1-1-2/M82	0.94216	1
12-2/M82	1.06121
12-4/M82	0.9173	1
1-3/M82	N/A	N/A
2-1-1/M82	0.75136	0.465
2-1/M82	N/A	N/A
2-6/M82	1.14668
3-2/M82	0.76367	0.455
4-1-1/M82	1.03592	1
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	0.86687	0.72
5-3/M82	0.97101	1
6-2/M82	N/A	N/A
6-3/M82	1.08892
7-1/M82	N/A	N/A
7-2/M82	0.85366	0.881
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	0.84162	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.94777
IL12-4/WTpooled	0.82314	0.581
IL1-4/WTpooled	0.96102	0.834
WT/WTpooled	1.02084	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	1.12219	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.03824	0.921
DC3000/delta hrp 6h	0.76259
DC3000/delta hrp 12h	0.841	1
DC3000/delta hrp 24h	1.49228	0.036

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	N/A
DC3000 delta B/DC3000 delta AB	4.7458	0.105

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	N/A	N/A
Exp 60h	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
self-self	0.96994	1
Var 0h	1.00896	1
Var 12h I row2-row1	N/A	N/A
Var 12h NI row2-row1	0.79908	0.33
Var 36h I row2-row1	0.68818	1
Var 36h NI row2-row1	1.10443
Var 60h I row2-row1	1.04991
Var 60h NI row2-row1	1.21431	0.904
Time course 0hI-0hNI	0.95699	0.715
Time course 12hI-12hNI	1.03809	0.803
Time course 36hI-36hNI	0.84332	0.139
Time course 60hI-60hNI	0.99142	1

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)	1.1612	0.253
transgenic ySAMdc/azygous control (breaker)	1.00514	1
transgenic ySAMdc/azygous control (red)	1.23112	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.92073	0.05

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.88236	0.59

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.96308	1
Manapal/WT (break)	0.91547	1
Manapal/WT (red)	0.78607	0.181