Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-3.2.18.1

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.95401	0.713
27DAP/17DAP	1.2399	0.845
39DAP/27DAP	0.92074	0.594
41DAP/39DAP	1.23621	0.85
42DAP/41DAP	1.07807	0.978
43DAP/42DAP	0.94013	0.877
47DAP/43DAP	1.20172	0.809
52DAP/47DAP	0.78222	0.488
57DAP/52DAP	1.0412	1

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.23658	0.009
17DAP/reference	1.06645	0.239
27DAP/reference	1.17501	0.045
39DAP/reference	1.08193	0.144
41DAP/reference	1.31738	0.018
42DAP/reference	1.40855	0.001
43DAP/reference	1.01832	1
47DAP/reference	1.24472	0.001
52DAP/reference	1.5339	0.128
57DAP/reference	1.035	0.901

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.94973	0.442
27DAP/17DAP	0.97753	0.508
39DAP/27DAP	0.97383	0.754
41DAP/39DAP	1.04276	0.641
42DAP/41DAP	0.99944	0.926
43DAP/42DAP	1.034	0.212
47DAP/43DAP	0.98311	0.861
52DAP/47DAP	1.00369	0.991
57DAP/52DAP	1.06856	0.533
57DAP/7DAP	0.9572	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90488	0.066
17DAP/reference	0.96778	0.338
27DAP/reference	0.99199	0.494
39DAP/reference	0.97231	0.354
41DAP/reference	1.07481	0.141
42DAP/reference	0.97238	0.554
43DAP/reference	1.10523	0.032
47DAP/reference	0.98643	0.671
52DAP/reference	0.99262	0.679
57DAP/reference	1.03254	0.158

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.17628	0.187
17DAP/reference	1.31567	0.023
27DAP/reference	1.3825	0.049
39DAP/reference	1.53955	0.023
41DAP/reference	1.51963	0.021
42DAP/reference	1.37437	0.035
43DAP/reference	1.37395	0.164
47DAP/reference	1.32579	0.012
52DAP/reference	1.37497	0.006
57DAP/reference	1.43123	0.009

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95135	0.061
17DAP/reference	1.0408	0.685
27DAP/reference	1.02742	0.596
39DAP/reference	1.07423	0.563
41DAP/reference	1.05668	0.486
42DAP/reference	1.23039	0.327
43DAP/reference	1.31632	0.16
47DAP/reference	1.29093	0.046
52DAP/reference	1.08608	0.491
57DAP/reference	1.82861	0.01

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.97314	1
26DAP/20DAP	0.98758	1
34DAP/26DAP	1.04304	0.542
51DAP/34DAP	0.99432	0.937
52DAP/51DAP	1.01145	0.888
53DAP/52DAP	0.98092	0.924
55DAP/53DAP	1.01199	1
57DAP/55DAP	1.04544	0.915
62DAP/57DAP	1.06596	0.833
68DAP/62DAP	0.78539	0.429
68DAP/14DAP	0.77271	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.94406	0.211

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.86489	0.058
Mature Green Tomato/Ripe Tomato	0.64591	0.055
Immature Eggplant/Mature Eggplant	0.54884	0.125
Ripe Pepper/Ripe Tomato	0.3311	0.224
Mature Eggplant/Ripe Tomato	0.33661	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.98497	0.944
1-1-2/M82	0.95529	1
12-2/M82	0.85529	0.721
12-4/M82	0.99087	1
1-3/M82	0.83811	0.441
2-1-1/M82	0.96859	1
2-1/M82	N/A	N/A
2-6/M82	0.9844	1
3-2/M82	0.89712	1
4-1-1/M82	0.96351	1
4-1/M82	0.87021	N/A
4-3-2/M82	0.86186	0.698
4-3/M82	0.94436	1
5-3/M82	1.02663	1
6-2/M82	0.99399	1
6-3/M82	0.97697	0.916
7-1/M82	1.01892	N/A
7-2/M82	0.97402	1
9-3-2/M82	0.76564	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.88407	N/A
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	0.83453	N/A
IL7-3/WTpooled	0.90206	0.294
IL12-4/WTpooled	0.8706	0.71
IL1-4/WTpooled	0.99612	1
WT/WTpooled	0.89847	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	0.80608	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.99881	1
DC3000/delta hrp 6h	1.32001	1
DC3000/delta hrp 12h	1.18038	1
DC3000/delta hrp 24h	1.05127	0.673

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.01531	0.515
DC3000 delta B/DC3000 delta AB	1.05901	0.457

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.11331	1
Exp 36h	0.66569	0.449
Exp 60h	0.59816	0.259

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98406	1
Var 0h	0.97288	1
Var 12h I row2-row1	1.10208	0.201
Var 12h NI row2-row1	0.91047	0.546
Var 36h I row2-row1	0.99011	1
Var 36h NI row2-row1	0.9912	0.743
Var 60h I row2-row1	1.18646	1
Var 60h NI row2-row1	1.08111	1
Time course 0hI-0hNI	0.98942	1
Time course 12hI-12hNI	0.98241	0.909
Time course 36hI-36hNI	0.92395	0.139
Time course 60hI-60hNI	0.89778	0.026

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)	2.03361	0.25
transgenic ySAMdc/azygous control (breaker)	0.4834	0.139
transgenic ySAMdc/azygous control (red)	2.25884	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.90989	0.074

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.89819	0.255

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.414	0.172
Manapal/WT (break)	1.12041	1
Manapal/WT (red)	0.6438	0.181