Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-6.3.20.4

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.19003	0.697
27DAP/17DAP	1.24291	0.778
39DAP/27DAP	0.96648	0.7
41DAP/39DAP	1.07665	0.96
42DAP/41DAP	1.22356	0.712
43DAP/42DAP	1.00661	0.937
47DAP/43DAP	1.12969	0.873
52DAP/47DAP	1.05965	0.943
57DAP/52DAP	0.73582	0.759

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.07877	0.9
17DAP/reference	0.82297	0.169
27DAP/reference	0.9108	0.339
39DAP/reference	0.68638	0.01
41DAP/reference	0.86219	0.341
42DAP/reference	1.09811	N/A
43DAP/reference	0.7182	0.016
47DAP/reference	0.7628	0.279
52DAP/reference	0.81537	0.183
57DAP/reference	0.42835	N/A

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.20223	0.91
27DAP/17DAP	1.10835	0.831
39DAP/27DAP	1.12645	0.596
41DAP/39DAP	1.55004	0.119
42DAP/41DAP	0.8224	0.416
43DAP/42DAP	4.88925	0.297
47DAP/43DAP	1.393	0.641
52DAP/47DAP	0.797	0.778
57DAP/52DAP	1.28207	0.282
57DAP/7DAP	N/A	N/A

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92053	0.138
17DAP/reference	0.96595	0.389
27DAP/reference	0.87017	0.109
39DAP/reference	0.95447	0.354
41DAP/reference	0.88369	0.103
42DAP/reference	0.78621	0.013
43DAP/reference	0.91392	0.279
47DAP/reference	0.79866	0.066
52DAP/reference	1.04665	0.732
57DAP/reference	0.97408	0.477

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.83656	0.157
17DAP/reference	0.84632	0.113
27DAP/reference	0.73836	0.104
39DAP/reference	0.76758	0.018
41DAP/reference	1.15874	1
42DAP/reference	N/A	N/A
43DAP/reference	1.25111	0.308
47DAP/reference	N/A	N/A
52DAP/reference	0.77385	0.072
57DAP/reference	0.73783	0.032

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.8714	0.049
17DAP/reference	0.99563	0.81
27DAP/reference	0.99996	0.843
39DAP/reference	1.05043	0.67
41DAP/reference	0.86045	0.077
42DAP/reference	0.82387	0.059
43DAP/reference	1.02978	0.744
47DAP/reference	0.71287	0.007
52DAP/reference	0.79893	0.153
57DAP/reference	0.97966	0.73

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.1824	0.966
26DAP/20DAP	0.93432	1
34DAP/26DAP	0.91781	0.874
51DAP/34DAP	0.98753	0.946
52DAP/51DAP	1.29544	0.676
53DAP/52DAP	1.6804	0.384
55DAP/53DAP	1.43891	0.693
57DAP/55DAP	0.62895	0.03
62DAP/57DAP	1.03005	1
68DAP/62DAP	1.12235	0.962
68DAP/14DAP	1.15781	0.436

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.82978	0.443

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.6028	0.256
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	N/A	N/A
1-1-2/M82	0.78643	0.958
12-2/M82	N/A	N/A
12-4/M82	0.97338	1
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	0.55396	N/A
4-1-1/M82	N/A	N/A
4-1/M82	0.79816	1
4-3-2/M82	0.86088	N/A
4-3/M82	N/A	N/A
5-3/M82	1.12321	0.572
6-2/M82	N/A	N/A
6-3/M82	0.90443	N/A
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	1.03267	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.26379	N/A
IL2-6/WTpooled	0.94697	0.348
IL7-5/WTpooled	0.90189	N/A
IL7-3/WTpooled	1.48718	1
IL12-4/WTpooled	1.19951	0.673
IL1-4/WTpooled	1.47892	1
WT/WTpooled	1.01229	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	1.28769	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.0107	0.921
DC3000/delta hrp 6h	1.58655	0.582
DC3000/delta hrp 12h	1.00533	1
DC3000/delta hrp 24h	1.89667	0.113

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.01199	N/A
DC3000 delta B/DC3000 delta AB	0.94785	0.657

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.58152	0.228
Exp 36h	1.19334	1
Exp 60h	1.74859	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	1.09968	1
Var 0h	N/A	N/A
Var 12h I row2-row1	0.99413	1
Var 12h NI row2-row1	1.15752	1
Var 36h I row2-row1	1.08317	1
Var 36h NI row2-row1	0.97928	0.852
Var 60h I row2-row1	1.07078	1
Var 60h NI row2-row1	0.47594	0.516
Time course 0hI-0hNI	1.02776	1
Time course 12hI-12hNI	1.282	0.746
Time course 36hI-36hNI	2.60875	0.005
Time course 60hI-60hNI	2.62171	0.047

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)	2.30803	0.571
transgenic ySAMdc/azygous control (breaker)	1.57697	0.248
transgenic ySAMdc/azygous control (red)	1.13671	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.06732	0.301

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	8.84918	0.087
Manapal/WT (break)	N/A	N/A
Manapal/WT (red)	0.88131	0.607