Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-5.2.4.13

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.05307	0.838
27DAP/17DAP	1.08813	0.88
39DAP/27DAP	1.26678	0.332
41DAP/39DAP	1.01519	0.96
42DAP/41DAP	1.03611	0.962
43DAP/42DAP	1.05746	1
47DAP/43DAP	1.21544	0.261
52DAP/47DAP	1.0681	0.96
57DAP/52DAP	0.90041	0.666

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92056	0.07
17DAP/reference	1.0358	0.412
27DAP/reference	0.95219	0.275
39DAP/reference	0.97436	0.704
41DAP/reference	0.96412	0.667
42DAP/reference	0.89427	0.012
43DAP/reference	0.91454	0.061
47DAP/reference	0.91769	0.03
52DAP/reference	0.91623	0.152
57DAP/reference	0.85512	0.031

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.93829	0.388
27DAP/17DAP	1.01876	0.924
39DAP/27DAP	1.08331	0.478
41DAP/39DAP	1.09643	0.69
42DAP/41DAP	1.02204	0.947
43DAP/42DAP	0.96864	0.558
47DAP/43DAP	0.99602	0.99
52DAP/47DAP	1.08535	0.676
57DAP/52DAP	0.96827	0.591
57DAP/7DAP	1.0869	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04008	0.747
17DAP/reference	1.07069	0.162
27DAP/reference	1.42404	0.014
39DAP/reference	1.44883	0.006
41DAP/reference	1.35137	0.022
42DAP/reference	1.57146	0.009
43DAP/reference	1.50165	0.007
47DAP/reference	1.36188	0.145
52DAP/reference	1.87976	0.007
57DAP/reference	1.88452	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.06903	0.284
17DAP/reference	1.02622	0.806
27DAP/reference	1.14038	0.974
39DAP/reference	0.9742	0.428
41DAP/reference	0.93814	0.299
42DAP/reference	0.98439	0.534
43DAP/reference	0.94102	0.385
47DAP/reference	0.93315	0.159
52DAP/reference	0.96325	0.433
57DAP/reference	0.97962	0.581

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00837	1
17DAP/reference	0.99945	0.855
27DAP/reference	1.29055	0.017
39DAP/reference	1.33495	0.029
41DAP/reference	1.1808	0.257
42DAP/reference	1.43743	0.233
43DAP/reference	1.17672	0.524
47DAP/reference	0.9545	0.357
52DAP/reference	1.42982	0.167
57DAP/reference	0.78026	0.048

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.06666	0.945
26DAP/20DAP	0.93016	0.512
34DAP/26DAP	0.92045	0.419
51DAP/34DAP	1.03703	0.814
52DAP/51DAP	1.01989	0.888
53DAP/52DAP	1.03608	0.921
55DAP/53DAP	1.02995	0.964
57DAP/55DAP	1.04363	0.87
62DAP/57DAP	1.19085	0.004
68DAP/62DAP	0.92379	0.406
68DAP/14DAP	0.95444	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.05215	0.326

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.79648	0.268
Mature Green Tomato/Ripe Tomato	1.40539	0.048
Immature Eggplant/Mature Eggplant	0.81063	0.448
Ripe Pepper/Ripe Tomato	1.38423	1
Mature Eggplant/Ripe Tomato	0.8876	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.97889	0.961
1-1-2/M82	1.00703	N/A
12-2/M82	1.15203	N/A
12-4/M82	1.04931	1
1-3/M82	0.9248	1
2-1-1/M82	1.2918	N/A
2-1/M82	N/A	N/A
2-6/M82	1.13123	0.695
3-2/M82	0.9572	1
4-1-1/M82	0.88231	1
4-1/M82	0.72007	N/A
4-3-2/M82	1.08478	1
4-3/M82	0.8206	0.72
5-3/M82	0.99905	1
6-2/M82	N/A	N/A
6-3/M82	1.02774	N/A
7-1/M82	0.90016	1
7-2/M82	0.90175	0.434
9-3-2/M82	0.99426	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.69752	N/A
IL2-6/WTpooled	0.80152	0.348
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.8004	0.25
IL12-4/WTpooled	0.95689	1
IL1-4/WTpooled	0.79581	0.699
WT/WTpooled	1.19223	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	1.23918	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.03231	0.921
DC3000/delta hrp 6h	0.79457	0.95
DC3000/delta hrp 12h	1.05856	1
DC3000/delta hrp 24h	1.0729	0.483

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.91465	0.46
DC3000 delta B/DC3000 delta AB	0.81768	0.025

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.60415	1
Exp 36h	1.10505	1
Exp 60h	1.01618	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	N/A	N/A
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)	0.94034	0.246
transgenic ySAMdc/azygous control (breaker)	1.38183	0.172
transgenic ySAMdc/azygous control (red)	1.05141	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.99413	0.444

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.02935	0.239

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.8527	1
Manapal/WT (break)	0.98375	1
Manapal/WT (red)	1.18757	0.413