Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.3.20.9

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.25324	0.615
27DAP/17DAP	1.15873	0.841
39DAP/27DAP	0.91725	0.529
41DAP/39DAP	1.20566	0.203
42DAP/41DAP	0.955	1
43DAP/42DAP	0.9407	0.877
47DAP/43DAP	1.30354	0.595
52DAP/47DAP	0.84967	0.607
57DAP/52DAP	0.97272	0.957

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90756	0.238
17DAP/reference	0.96478	0.567
27DAP/reference	0.87483	0.061
39DAP/reference	0.92672	0.412
41DAP/reference	1.09307	0.111
42DAP/reference	0.91121	0.078
43DAP/reference	0.96173	0.576
47DAP/reference	0.88971	0.071
52DAP/reference	0.97381	0.475
57DAP/reference	0.85722	0.038

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.48566	0.038
27DAP/17DAP	0.90605	0.537
39DAP/27DAP	0.98077	0.844
41DAP/39DAP	1.19729	0.603
42DAP/41DAP	0.87471	0.478
43DAP/42DAP	0.80732	0.143
47DAP/43DAP	0.93893	0.466
52DAP/47DAP	0.87205	0.29
57DAP/52DAP	0.80153	0.168
57DAP/7DAP	1.37127	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.14202	0.305
17DAP/reference	1.09668	0.754
27DAP/reference	0.88608	0.017
39DAP/reference	0.74524	0.073
41DAP/reference	0.82912	0.035
42DAP/reference	0.83271	0.13
43DAP/reference	0.93582	0.368
47DAP/reference	0.99781	1
52DAP/reference	0.94977	0.398
57DAP/reference	0.99086	0.569

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.09144	0.903
17DAP/reference	0.78413	0.005
27DAP/reference	0.78473	0.051
39DAP/reference	0.76574	0.048
41DAP/reference	0.79429	0.023
42DAP/reference	0.95347	0.392
43DAP/reference	0.80697	0.037
47DAP/reference	0.78141	0.012
52DAP/reference	0.94414	0.302
57DAP/reference	0.90431	0.068

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01763	1
17DAP/reference	1.08264	0.602
27DAP/reference	1.02308	1
39DAP/reference	1.06121	0.65
41DAP/reference	1.02977	1
42DAP/reference	0.90139	0.172
43DAP/reference	0.93186	0.305
47DAP/reference	0.87544	0.161
52DAP/reference	1.06068	1
57DAP/reference	1.00828	0.79

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.26128	0.966
26DAP/20DAP	0.82825	1
34DAP/26DAP	1.63356	1
51DAP/34DAP	1.08574	0.936
52DAP/51DAP	0.98222	1
53DAP/52DAP	1.05595	0.688
55DAP/53DAP	1.09194	0.782
57DAP/55DAP	1.47037	0.826
62DAP/57DAP	0.92464	0.871
68DAP/62DAP	1.77846	0.089
68DAP/14DAP	1.35477	0.236

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.36529	0.034

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.69701
Mature Green Tomato/Ripe Tomato	1.10755	0.69
Immature Eggplant/Mature Eggplant	1.4832	0.092
Ripe Pepper/Ripe Tomato	1.34075	1
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	1.07065
12-2/M82	N/A	N/A
12-4/M82	0.79461	0.282
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	1.0289	0.426
4-1-1/M82	N/A	N/A
4-1/M82	1.55429
4-3-2/M82	0.66655
4-3/M82	N/A	N/A
5-3/M82	1.22611	0.496
6-2/M82	1.02311	1
6-3/M82	1.34562
7-1/M82	0.954
7-2/M82	0.78948
9-3-2/M82	0.79607

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.63662	0.321
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	1.75896
IL7-3/WTpooled	2.03426
IL12-4/WTpooled	1.73707	0.546
IL1-4/WTpooled	0.87013	0.699
WT/WTpooled	0.93676	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	0.9826	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.0363	0.75
DC3000/delta hrp 6h	1.27225	1
DC3000/delta hrp 12h	1.11663	1
DC3000/delta hrp 24h	1.09904	0.69

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	2.44589
DC3000 delta B/DC3000 delta AB	2.20863	0.095

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.27591	1
Exp 36h	1.62201	1
Exp 60h	1.37539	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01429	1
Var 0h	N/A	N/A
Var 12h I row2-row1	1.12002	0.544
Var 12h NI row2-row1	1.24948	1
Var 36h I row2-row1	0.81711	0.805
Var 36h NI row2-row1	1.1181	1
Var 60h I row2-row1	0.90495	0.374
Var 60h NI row2-row1	0.95544	0.977
Time course 0hI-0hNI	1.13845	0.662
Time course 12hI-12hNI	0.88179	0.182
Time course 36hI-36hNI	1.19183	0.021
Time course 60hI-60hNI	3.15339	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)	0.87393	0.299
transgenic ySAMdc/azygous control (breaker)	1.60538	0.162
transgenic ySAMdc/azygous control (red)	1.15138	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.93929	0.231

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.72775	0.231

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.80173	1
Manapal/WT (break)	0.60635	0.333
Manapal/WT (red)	0.66953	0.187