Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-5.3.4.1

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	49.1393	0.008
27DAP/17DAP	1.26852	0.761
39DAP/27DAP	1.22075	0.61
41DAP/39DAP	0.4896	0.042
42DAP/41DAP	0.53219	0.397
43DAP/42DAP	0.65551	0.454
47DAP/43DAP	1.14897	0.689
52DAP/47DAP	0.89457	0.681
57DAP/52DAP	1.93906	0.55

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.38834	0.026
17DAP/reference	8.52258	0.013
27DAP/reference	11.5982	0.007
39DAP/reference	4.0492	0.017
41DAP/reference	4.09331	0.012
42DAP/reference	1.9466	0.001
43DAP/reference	0.82201	0.222
47DAP/reference	1.0593	0.72
52DAP/reference	2.08842	0.088
57DAP/reference	2.4296	0.013

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	7.78369	0.038
27DAP/17DAP	1.40777	0.045
39DAP/27DAP	0.5365	0.028
41DAP/39DAP	1.13381	0.98
42DAP/41DAP	1.20044	0.961
43DAP/42DAP	0.35351	0.02
47DAP/43DAP	0.63581	0.008
52DAP/47DAP	1.786	0.06
57DAP/52DAP	0.90988	0.564
57DAP/7DAP	1.21478	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.937	0.495
17DAP/reference	6.31023	0.006
27DAP/reference	5.80132	0.008
39DAP/reference	3.19753	0.007
41DAP/reference	2.83576	0.008
42DAP/reference	1.67839	0.174
43DAP/reference	0.49921	0.011
47DAP/reference	1.29739	0.133
52DAP/reference	0.61463	0.013
57DAP/reference	0.62811	0.017

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.27837	0.007
17DAP/reference	7.72398	0.007
27DAP/reference	8.49863	0.012
39DAP/reference	6.08984	0.011
41DAP/reference	2.59458	0.005
42DAP/reference	5.30202	0.007
43DAP/reference	1.62578	0.097
47DAP/reference	3.30549	0.011
52DAP/reference	4.74625	0.006
57DAP/reference	1.11185	0.754

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.36282	0.048
17DAP/reference	1.8588	0.013
27DAP/reference	4.66666	0.012
39DAP/reference	2.1635	0.004
41DAP/reference	1.32157	0.024
42DAP/reference	0.87597	0.287
43DAP/reference	0.71905	0.092
47DAP/reference	0.25523	0.004
52DAP/reference	0.40672	0.052
57DAP/reference	3.43696	0.013

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.9879	1
26DAP/20DAP	0.93056	1
34DAP/26DAP	1.24357	0.304
51DAP/34DAP	1.79498	0.032
52DAP/51DAP	0.54201	0.151
53DAP/52DAP	4.54374	0.026
55DAP/53DAP	0.97384	0.784
57DAP/55DAP	1.19599	0.906
62DAP/57DAP	0.63473	0.003
68DAP/62DAP	0.83595	0.609
68DAP/14DAP	1.86472	0.034

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	7.67618	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.03797	0.908
Mature Green Tomato/Ripe Tomato	6.14071	0.015
Immature Eggplant/Mature Eggplant	26.3891	0.05
Ripe Pepper/Ripe Tomato	0.15387	0.224
Mature Eggplant/Ripe Tomato	0.22141	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.59233	0.651
1-1-2/M82	0.99468	1
12-2/M82	1.13628	1
12-4/M82	0.76289	1
1-3/M82	2.22044	0.479
2-1-1/M82	0.95569	0.784
2-1/M82	0.9751	1
2-6/M82	0.94617	0.327
3-2/M82	1.26424	0.463
4-1-1/M82	1.62872	1
4-1/M82	1.50267	0.397
4-3-2/M82	0.72098	0.698
4-3/M82	0.90304	0.72
5-3/M82	1.13677	1
6-2/M82	0.97994	1
6-3/M82	0.99036	1
7-1/M82	1.33027	0.598
7-2/M82	1.01464	1
9-3-2/M82	0.73846	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.81158	0.473
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.43407	0.362
IL12-4/WTpooled	1.17623	0.695
IL1-4/WTpooled	1.06463	N/A
WT/WTpooled	0.98167	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	1.33153	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.9994	1
DC3000/delta hrp 6h	1.00402	0.95
DC3000/delta hrp 12h	1.16923	1
DC3000/delta hrp 24h	0.44455	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.67924	0.024
DC3000 delta B/DC3000 delta AB	0.73687	0.08

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.89359	1
Exp 36h	0.34245	0.434
Exp 60h	0.2699	0.258

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

hybridization	ratio	FDR (corrected p value)
self-self	0.97031	1
Var 0h	1.16993	0.98
Var 12h I row2-row1	0.90564	0.39
Var 12h NI row2-row1	0.97765	0.906
Var 36h I row2-row1	1.05033	1
Var 36h NI row2-row1	1.2312	0.482
Var 60h I row2-row1	1.23008	0.562
Var 60h NI row2-row1	1.11377	0.904
Time course 0hI-0hNI	0.94416	0.659
Time course 12hI-12hNI	0.95664	0.682
Time course 36hI-36hNI	0.98602	0.621
Time course 60hI-60hNI	0.17353	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)	0.80133	0.297
transgenic ySAMdc/azygous control (breaker)	1.09257	1
transgenic ySAMdc/azygous control (red)	0.88106	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.45235	0.046

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.02384	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.53778	1
Manapal/WT (break)	0.29582	0.299
Manapal/WT (red)	0.81747	0.36