Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.1.3.6

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.8202	0.26
27DAP/17DAP	1.02798	0.982
39DAP/27DAP	2.00571	0.132
41DAP/39DAP	0.85187	0.416
42DAP/41DAP	1.37643	0.797
43DAP/42DAP	1.80266	0.899
47DAP/43DAP	0.47179	0.05
52DAP/47DAP	1.21986	0.806
57DAP/52DAP	1.3931	0.849

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.19695	0.008
17DAP/reference	1.4323	0.014
27DAP/reference	1.53691	0.008
39DAP/reference	0.39281	0.009
41DAP/reference	0.48446	0.039
42DAP/reference	0.72976	0.035
43DAP/reference	0.37587
47DAP/reference	0.38952	0.001
52DAP/reference	0.43214	0.012
57DAP/reference	N/A	N/A

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.68978	0.036
27DAP/17DAP	0.94833	0.887
39DAP/27DAP	0.86631	0.668
41DAP/39DAP	1.07448	0.773
42DAP/41DAP	1.25742	0.694
43DAP/42DAP	1.41463	0.035
47DAP/43DAP	0.96045	0.923
52DAP/47DAP	0.85041	0.433
57DAP/52DAP	1.07036	0.838
57DAP/7DAP	0.74473	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.40205	0.024
17DAP/reference	1.75932	0.008
27DAP/reference	1.24999	0.011
39DAP/reference	1.39938	0.012
41DAP/reference	1.36215	0.075
42DAP/reference	2.34216	0.006
43DAP/reference	2.90443	0.007
47DAP/reference	2.57237	0.43
52DAP/reference	2.53887	0.007
57DAP/reference	2.36775	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.59561	0.39
17DAP/reference	1.90533	0.021
27DAP/reference	1.73781	0.244
39DAP/reference	0.78986	0.113
41DAP/reference	0.97022	0.422
42DAP/reference	1.21881	0.455
43DAP/reference	0.58084	0.017
47DAP/reference	0.56691	0.01
52DAP/reference	0.63935	0.004
57DAP/reference	0.41591	0.002

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.08053	0.602
17DAP/reference	1.51244	0.13
27DAP/reference	1.16863	0.125
39DAP/reference	1.2297	0.053
41DAP/reference	1.10547	0.112
42DAP/reference	1.8851	0.011
43DAP/reference	1.6483	0.029
47DAP/reference	0.54672	0.007
52DAP/reference	1.00684	0.675
57DAP/reference	1.37003	0.138

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.91263	1
26DAP/20DAP	1.42521	0.212
34DAP/26DAP	0.9187	0.763
51DAP/34DAP	1.30231	0.352
52DAP/51DAP	0.87668	0.151
53DAP/52DAP	1.00898	1
55DAP/53DAP	0.67904	0.017
57DAP/55DAP	1.30189	0.898
62DAP/57DAP	1.15716	0.002
68DAP/62DAP	1.58661	0.139
68DAP/14DAP	0.68325	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	4.8274	0.015

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.70423	0.058
Mature Green Tomato/Ripe Tomato	1.22067	0.299
Immature Eggplant/Mature Eggplant	0.4924	0.066
Ripe Pepper/Ripe Tomato	27.8269	1
Mature Eggplant/Ripe Tomato	16.2148	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	1.82091	1
12-2/M82	N/A	N/A
12-4/M82	0.91394	0.282
1-3/M82	N/A	N/A
2-1-1/M82	0.58379
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	0.99055	1
4-1-1/M82	N/A	N/A
4-1/M82	11.3774
4-3-2/M82	2.58991	1
4-3/M82	N/A	N/A
5-3/M82	0.95344	1
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	2.31814
9-3-2/M82	2.39035	0.196

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.96922	1
IL2-6/WTpooled	0.95652	0.383
IL7-5/WTpooled	1.20917	0.792
IL7-3/WTpooled	0.71766	0.418
IL12-4/WTpooled	1.00096	1
IL1-4/WTpooled	0.94147	0.444
WT/WTpooled	1.054	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	1.18217	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.97651	0.941
DC3000/delta hrp 6h	0.9789	0.95
DC3000/delta hrp 12h	0.86712	1
DC3000/delta hrp 24h	0.90765	0.598

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.53419	0.046
DC3000 delta B/DC3000 delta AB	0.54711	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.92841	1
Exp 36h	0.95502	0.589
Exp 60h	0.78242	0.257

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99138	1
Var 0h	N/A	N/A
Var 12h I row2-row1	0.79511
Var 12h NI row2-row1	1.00955
Var 36h I row2-row1	0.9711	1
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	1.11595	0.63
Time course 12hI-12hNI	0.9183	0.368
Time course 36hI-36hNI	0.72361	0.023
Time course 60hI-60hNI	0.30118	0.005

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)	0.73838	0.314
transgenic ySAMdc/azygous control (breaker)	2.39722	1
transgenic ySAMdc/azygous control (red)	1.30764	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.46048	0.066

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	4.40806	0.233

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.21456	0.307
Manapal/WT (break)	2.61265	0.381
Manapal/WT (red)	1.83324	0.413