Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-6.3.1.1

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.91371	0.543
27DAP/17DAP	1.38941	0.646
39DAP/27DAP	0.83146	0.537
41DAP/39DAP	1.5771	0.423
42DAP/41DAP	0.99202	1
43DAP/42DAP	1.01236	0.937
47DAP/43DAP	1.19448	0.689
52DAP/47DAP	0.90409	0.646
57DAP/52DAP	1.181	0.969

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90286	0.182
17DAP/reference	0.95776	0.393
27DAP/reference	1.02366	0.82
39DAP/reference	1.1522	0.108
41DAP/reference	0.99514	1
42DAP/reference	1.16484	0.13
43DAP/reference	1.2167	0.569
47DAP/reference	0.94055	0.258
52DAP/reference	1.26009	0.158
57DAP/reference	1.05079	0.548

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.19979	0.271
27DAP/17DAP	1.08699	0.805
39DAP/27DAP	0.70718	0.311
41DAP/39DAP	1.64323	0.827
42DAP/41DAP	1.40017	0.005
43DAP/42DAP	0.68772	0.165
47DAP/43DAP	0.85241	0.637
52DAP/47DAP	2.74848	0.048
57DAP/52DAP	2.05753	0.152
57DAP/7DAP	3.17415	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.7893	0.129
17DAP/reference	0.87916	0.094
27DAP/reference	1.23638	0.017
39DAP/reference	0.76928	0.011
41DAP/reference	0.94744	0.375
42DAP/reference	0.98045	0.531
43DAP/reference	0.71973	0.011
47DAP/reference	0.75756	0.101
52DAP/reference	0.66716	0.014
57DAP/reference	0.66859	0.008

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.33877	0.108
17DAP/reference	1.39304	0.077
27DAP/reference	1.52303	0.019
39DAP/reference	1.19506	0.164
41DAP/reference	1.34215	0.02
42DAP/reference	1.49784	0.018
43DAP/reference	2.17297	0.009
47DAP/reference	1.56128	0.008
52DAP/reference	1.44825	0.006
57DAP/reference	1.1377	0.538

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.75097	0.032
17DAP/reference	1.11261	0.65
27DAP/reference	0.79947	0.113
39DAP/reference	0.72218	0.021
41DAP/reference	1.19576	0.521
42DAP/reference	1.25685	0.251
43DAP/reference	0.84333	0.131
47DAP/reference	1.18485	0.073
52DAP/reference	1.03977	0.79
57DAP/reference	1.08146	0.892

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.95541	1
26DAP/20DAP	5.04035	0.931
34DAP/26DAP	3.74648	1
51DAP/34DAP	3.29462	0.692
52DAP/51DAP	7.67873	0.034
53DAP/52DAP	0.5589	0.049
55DAP/53DAP	1.68422	0.022
57DAP/55DAP	0.49132	0.045
62DAP/57DAP	0.90741	0.871
68DAP/62DAP	1.00471	0.81
68DAP/14DAP	1.84115	0.146

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.10193	0.019

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	69.6006	0.075
Mature Green Tomato/Ripe Tomato	1.0807	N/A
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	N/A	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.91656	0.841
1-1-2/M82	1.0411	N/A
12-2/M82	N/A	N/A
12-4/M82	1.32089	N/A
1-3/M82	N/A	N/A
2-1-1/M82	0.76096	0.465
2-1/M82	N/A	N/A
2-6/M82	1.03444	1
3-2/M82	N/A	N/A
4-1-1/M82	1.03019	1
4-1/M82	1.6402	N/A
4-3-2/M82	0.93359	N/A
4-3/M82	0.89916	0.72
5-3/M82	0.91537	1
6-2/M82	0.76757	0.497
6-3/M82	1.21418	N/A
7-1/M82	N/A	N/A
7-2/M82	0.87249	0.881
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.33601	0.277
IL2-6/WTpooled	1.06983	1
IL7-5/WTpooled	2.63138	0.792
IL7-3/WTpooled	1.06396	1
IL12-4/WTpooled	1.21466	0.839
IL1-4/WTpooled	1.45269	0.426
WT/WTpooled	1.05997	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	1.22916	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.02042	0.921
DC3000/delta hrp 6h	1.04758	1
DC3000/delta hrp 12h	0.88993	1
DC3000/delta hrp 24h	0.97379	0.988

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.03378	0.384
DC3000 delta B/DC3000 delta AB	0.97576	1

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.90866	0.328
Exp 36h	0.85671	0.623
Exp 60h	0.76342	0.386

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

hybridization	ratio	FDR (corrected p value)
self-self	1.02444	1
Var 0h	0.96289	0.339
Var 12h I row2-row1	0.7079	0.514
Var 12h NI row2-row1	1.17559	0.649
Var 36h I row2-row1	1.33532	1
Var 36h NI row2-row1	1.30928	1
Var 60h I row2-row1	0.6525	N/A
Var 60h NI row2-row1	1.01345	1
Time course 0hI-0hNI	0.805	0.219
Time course 12hI-12hNI	1.10833	1
Time course 36hI-36hNI	1.06486	0.484
Time course 60hI-60hNI	0.80219	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)	1.23365	0.798
transgenic ySAMdc/azygous control (breaker)	1.72169	0.178
transgenic ySAMdc/azygous control (red)	0.97195	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.01861	0.35

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.39538	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.02216	1
Manapal/WT (break)	0.74532	0.333
Manapal/WT (red)	0.908	0.728