Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.3.6.11

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.84054	0.211
27DAP/17DAP	0.88877	0.73
39DAP/27DAP	1.0841	1
41DAP/39DAP	0.99726	0.789
42DAP/41DAP	1.0512	1
43DAP/42DAP	1.18582	0.993
47DAP/43DAP	1.01729	0.979
52DAP/47DAP	1.01442	0.837
57DAP/52DAP	0.96112	0.869

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.89716	0.149
17DAP/reference	0.98254	0.701
27DAP/reference	1.04115	0.721
39DAP/reference	1.09283	0.191
41DAP/reference	1.14713	0.102
42DAP/reference	0.96742	0.268
43DAP/reference	1.00335	0.904
47DAP/reference	0.91564	0.055
52DAP/reference	0.93037	0.244
57DAP/reference	1.05172	0.355

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.4869	0.062
27DAP/17DAP	0.93739	0.878
39DAP/27DAP	0.89877	0.579
41DAP/39DAP	0.99042	1
42DAP/41DAP	1.32004	0.675
43DAP/42DAP	1.35248	0.045
47DAP/43DAP	0.70214	0.012
52DAP/47DAP	1.03261	0.9
57DAP/52DAP	1.14134	0.798
57DAP/7DAP	N/A	N/A

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.1725	0.197
17DAP/reference	0.93231	0.295
27DAP/reference	1.04141	0.371
39DAP/reference	1.14984	0.411
41DAP/reference	1.23284	0.184
42DAP/reference	1.05665	0.889
43DAP/reference	0.89412	0.086
47DAP/reference	1.03074	1
52DAP/reference	1.15223	0.13
57DAP/reference	1.151	0.076

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04286	0.62
17DAP/reference	1.0392	0.739
27DAP/reference	0.96231	0.501
39DAP/reference	0.9738	0.497
41DAP/reference	1.13844	0.629
42DAP/reference	1.00157	1
43DAP/reference	1.12984	0.532
47DAP/reference	1.18503	0.029
52DAP/reference	1.22389	0.036
57DAP/reference	1.16842	0.172

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01685	1
17DAP/reference	0.97499	0.647
27DAP/reference	1.19911	0.357
39DAP/reference	0.99749	0.755
41DAP/reference	1.3469	0.213
42DAP/reference	1.12458	0.589
43DAP/reference	0.89235	0.246
47DAP/reference	1.11314	0.14
52DAP/reference	0.84907	0.163
57DAP/reference	1.04469	0.878

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.1417	0.966
26DAP/20DAP	0.91646	1
34DAP/26DAP	1.01732	1
51DAP/34DAP	0.99669	0.946
52DAP/51DAP	1.04313	0.842
53DAP/52DAP	0.67786	0.235
55DAP/53DAP	0.77404	0.273
57DAP/55DAP	1.01241	1
62DAP/57DAP	1.02565	0.902
68DAP/62DAP	0.92568	0.7
68DAP/14DAP	0.80987	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.631	0.558

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.14663	1
Mature Green Tomato/Ripe Tomato	0.95472	0.569
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.4493
Mature Eggplant/Ripe Tomato	N/A	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	1.42436
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	0.83075
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	N/A	N/A
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	0.83668
7-2/M82	N/A	N/A
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	1.50602
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	0.83604	0.71
IL1-4/WTpooled	1.15729	1
WT/WTpooled	0.91699	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	1.01705

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.08294	0.914
DC3000/delta hrp 6h	0.91917	0.95
DC3000/delta hrp 12h	1.03151	1
DC3000/delta hrp 24h	0.75511	0.1

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	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.81988	0.245
Exp 36h	1.38649	0.693
Exp 60h	1.14838	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	0.91612	1
Var 0h	0.95298	1
Var 12h I row2-row1	0.84915	0.627
Var 12h NI row2-row1	0.91475	0.713
Var 36h I row2-row1	0.90083	1
Var 36h NI row2-row1	1.77512	1
Var 60h I row2-row1	0.91407	0.952
Var 60h NI row2-row1	1.11851	1
Time course 0hI-0hNI	0.864	0.438
Time course 12hI-12hNI	1.03396	0.914
Time course 36hI-36hNI	0.85233	0.206
Time course 60hI-60hNI	0.8348	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)	0.87569	0.286
transgenic ySAMdc/azygous control (breaker)	1.11951	1
transgenic ySAMdc/azygous control (red)	1.40366	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.99075	0.651

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.01388	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.99076	1
Manapal/WT (break)	0.92662	1
Manapal/WT (red)	1.29957	1