Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.4.16.5

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.93898	0.617
27DAP/17DAP	1.05878	0.9
39DAP/27DAP	1.33683	0.2
41DAP/39DAP	1.15268	0.642
42DAP/41DAP	1.11741	0.871
43DAP/42DAP	1.05733	1
47DAP/43DAP	1.25688	0.355
52DAP/47DAP	0.64905	0.174
57DAP/52DAP	1.13098	0.98

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.89075	0.246
17DAP/reference	0.84617	0.069
27DAP/reference	0.7724	0.041
39DAP/reference	1.0744	0.706
41DAP/reference	0.99702	0.814
42DAP/reference	1.06925	0.324
43DAP/reference	1.43387	0.01
47DAP/reference	1.4256	0.004
52DAP/reference	1.10042	0.766
57DAP/reference	1.3133	0.059

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.27723	0.047
27DAP/17DAP	0.94584	0.782
39DAP/27DAP	1.18073	0.505
41DAP/39DAP	1.01125	1
42DAP/41DAP	1.01766	0.939
43DAP/42DAP	1.0756	0.273
47DAP/43DAP	0.99615	0.989
52DAP/47DAP	1.31679	0.232
57DAP/52DAP	1.16111	0.547
57DAP/7DAP	1.04661	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00537	0.758
17DAP/reference	0.89368	0.124
27DAP/reference	0.87012	0.076
39DAP/reference	0.95462	0.411
41DAP/reference	0.9121	0.247
42DAP/reference	1.12372	0.534
43DAP/reference	1.06624	0.746
47DAP/reference	1.12718	0.272
52DAP/reference	0.90699	0.137
57DAP/reference	0.80889	0.032

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97654	0.669
17DAP/reference	0.73114	0.028
27DAP/reference	0.80304	0.1
39DAP/reference	0.77271	0.032
41DAP/reference	0.68164	0.022
42DAP/reference	0.84107	0.042
43DAP/reference	0.9022	0.277
47DAP/reference	1.17369	0.343
52DAP/reference	0.72985	0.017
57DAP/reference	0.90619	0.073

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.81684	0.087
17DAP/reference	0.85888	0.069
27DAP/reference	0.89963	0.14
39DAP/reference	1.12427	0.318
41DAP/reference	0.92894	0.293
42DAP/reference	1.02194	0.816
43DAP/reference	1.31506	0.229
47DAP/reference	1.02386	1
52DAP/reference	1.09535	0.42
57DAP/reference	1.02812	0.954

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.97131	1
26DAP/20DAP	0.85349	1
34DAP/26DAP	1.39748	0.542
51DAP/34DAP	1.47601	0.192
52DAP/51DAP	0.90753	1
53DAP/52DAP	0.7021	0.323
55DAP/53DAP	0.80136	0.04
57DAP/55DAP	1.06104	1
62DAP/57DAP	0.87925	0.681
68DAP/62DAP	1.43806	0.827
68DAP/14DAP	1.39777	0.366

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	2.03113	0.017

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.60791	0.017
Immature Eggplant/Mature Eggplant	6.92312	0.05
Ripe Pepper/Ripe Tomato	0.25955	0.293
Mature Eggplant/Ripe Tomato	0.16647	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.72197	0.742
1-1-2/M82	0.9706	1
12-2/M82	1.41379	1
12-4/M82	1.40059	1
1-3/M82	1.48279	0.479
2-1-1/M82	1.21327	0.689
2-1/M82	1.35895	1
2-6/M82	0.70357	0.501
3-2/M82	1.71812	0.463
4-1-1/M82	0.847	1
4-1/M82	N/A	N/A
4-3-2/M82	0.82311	0.698
4-3/M82	1.1624	1
5-3/M82	1.21744	0.496
6-2/M82	0.96876	1
6-3/M82	0.98496	1
7-1/M82	0.84501	1
7-2/M82	0.86922	0.881
9-3-2/M82	0.80917	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.66411
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	1.5529
WT/WTpooled	0.53099

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	0.9308	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.27217	0.921
DC3000/delta hrp 6h	1.11921	1
DC3000/delta hrp 12h	0.8633	1
DC3000/delta hrp 24h	0.90991	0.523

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	N/A
DC3000 delta B/DC3000 delta AB	2.1086

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.86822	1
Exp 36h	2.50672	0.693
Exp 60h	1.40981	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99422	1
Var 0h	0.83152	0.933
Var 12h I row2-row1	0.98441	0.948
Var 12h NI row2-row1	1.12701	0.649
Var 36h I row2-row1	1.24097	0.489
Var 36h NI row2-row1	0.86541	0.61
Var 60h I row2-row1	0.9127	0.832
Var 60h NI row2-row1	0.90861	0.756
Time course 0hI-0hNI	1.0383	0.63
Time course 12hI-12hNI	1.03948	0.615
Time course 36hI-36hNI	1.02966	0.722
Time course 60hI-60hNI	1.08848	0.115

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)	0.79931	0.234
transgenic ySAMdc/azygous control (breaker)	0.94801	1
transgenic ySAMdc/azygous control (red)	1.28505	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.14525	0.083

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.14742	0.237

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.60245	1
Manapal/WT (break)	0.92776	1
Manapal/WT (red)	1.66502	0.134