Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.2.4.10

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.83103	0.413
27DAP/17DAP	0.70146	0.377
39DAP/27DAP	0.60233	0.326
41DAP/39DAP	0.77922	0.245
42DAP/41DAP	0.85573	0.774
43DAP/42DAP	0.76433	0.709
47DAP/43DAP	0.80592	0.416
52DAP/47DAP	1.01397	0.973
57DAP/52DAP	0.92185	0.926

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.32053	0.022
17DAP/reference	1.11656	0.201
27DAP/reference	0.99095	0.741
39DAP/reference	0.98867	0.816
41DAP/reference	0.96726	0.667
42DAP/reference	0.86956	0.013
43DAP/reference	0.96966	0.576
47DAP/reference	0.9039	0.025
52DAP/reference	0.86789	0.025
57DAP/reference	0.90085	0.131

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.74014	0.141
27DAP/17DAP	1.19153	0.681
39DAP/27DAP	0.53762	0.029
41DAP/39DAP	0.91112	0.747
42DAP/41DAP	0.79985	0.047
43DAP/42DAP	1.23702	0.015
47DAP/43DAP	0.91392	0.476
52DAP/47DAP	0.88446	0.528
57DAP/52DAP	0.93718	0.587
57DAP/7DAP	0.3625	0.181

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.77685	0.024
17DAP/reference	1.81558	0.032
27DAP/reference	1.09769	0.301
39DAP/reference	1.2057	0.086
41DAP/reference	1.43439	0.019
42DAP/reference	1.28976	0.01
43DAP/reference	1.30111	0.074
47DAP/reference	0.96334	0.504
52DAP/reference	1.07086	1
57DAP/reference	1.09381	0.571

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.41598	0.032
17DAP/reference	1.386	0.049
27DAP/reference	1.06972	0.497
39DAP/reference	0.93403	0.14
41DAP/reference	0.97311	0.519
42DAP/reference	0.9858	0.594
43DAP/reference	1.06669	0.704
47DAP/reference	0.87088	0.045
52DAP/reference	0.90589	0.047
57DAP/reference	1.02656	0.908

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.73918	0.017
17DAP/reference	1.6389	0.091
27DAP/reference	1.35937	0.027
39DAP/reference	1.00738	0.819
41DAP/reference	1.03701	0.692
42DAP/reference	1.00436	1
43DAP/reference	0.91221	0.267
47DAP/reference	0.90035	0.174
52DAP/reference	0.91581	0.327
57DAP/reference	0.78147	0.016

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.87552	0.89
26DAP/20DAP	3.37669	0.097
34DAP/26DAP	1.00302	1
51DAP/34DAP	0.95925	0.758
52DAP/51DAP	1.10146	0.51
53DAP/52DAP	0.49718	0.049
55DAP/53DAP	0.46412	0.037
57DAP/55DAP	0.84436	0.433
62DAP/57DAP	1.6258	0.158
68DAP/62DAP	1.0883	0.914
68DAP/14DAP	0.79582	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.373	0.021

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	4.45756	0.058
Mature Green Tomato/Ripe Tomato	4.78508	0.015
Immature Eggplant/Mature Eggplant	0.6005	0.063
Ripe Pepper/Ripe Tomato	11.8562	0.256
Mature Eggplant/Ripe Tomato	42.4838	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.97551
12-2/M82	N/A	N/A
12-4/M82	N/A	N/A
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	N/A	N/A
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	1.1936
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
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	1.06888	0.395
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.86562	1
IL12-4/WTpooled	0.92236	0.71
IL1-4/WTpooled	1.10089
WT/WTpooled	1.01092	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	0.75647	0.341

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.9336	1
DC3000/delta hrp 6h	0.98294	0.95
DC3000/delta hrp 12h	0.93607	1
DC3000/delta hrp 24h	0.50629	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.92041	0.882
DC3000 delta B/DC3000 delta AB	0.66611	0.034

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.12485	1
Exp 36h	1.17321	0.409
Exp 60h	1.00299	1

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

hybridization	ratio	FDR (corrected p value)
self-self	N/A	N/A
Var 0h	0.91905	1
Var 12h I row2-row1	N/A	N/A
Var 12h NI row2-row1	N/A	N/A
Var 36h I row2-row1	N/A	N/A
Var 36h NI row2-row1	N/A	N/A
Var 60h I row2-row1	N/A	N/A
Var 60h NI row2-row1	N/A	N/A
Time course 0hI-0hNI	N/A	N/A
Time course 12hI-12hNI	N/A	N/A
Time course 36hI-36hNI	N/A	N/A
Time course 60hI-60hNI	N/A	N/A

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)	1.15411	0.286
transgenic ySAMdc/azygous control (breaker)	1.45335	0.248
transgenic ySAMdc/azygous control (red)	1.03805	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.02668	0.142

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.07389	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.10835	0.14
Manapal/WT (break)	1.36161	1
Manapal/WT (red)	1.36829	0.164