Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.3.10.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.91776	0.578
27DAP/17DAP	1.18595	0.845
39DAP/27DAP	1.09334	0.789
41DAP/39DAP	1.39262	0.356
42DAP/41DAP	0.97896	1
43DAP/42DAP	0.9277	0.841
47DAP/43DAP	1.32634	0.384
52DAP/47DAP	1.22122	0.674
57DAP/52DAP	0.91637	0.796

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.16691	0.097
17DAP/reference	0.69588	0.008
27DAP/reference	0.87753	0.286
39DAP/reference	0.84856	0.17
41DAP/reference	0.64829	0.014
42DAP/reference	0.86567	0.014
43DAP/reference	0.95948	0.5
47DAP/reference	0.95286	0.258
52DAP/reference	1.04787	0.951
57DAP/reference	1.20242	0.013

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.99126	0.801
27DAP/17DAP	0.88772	0.39
39DAP/27DAP	0.92871	0.622
41DAP/39DAP	1.00094	1
42DAP/41DAP	0.98241	0.801
43DAP/42DAP	1.07399	0.382
47DAP/43DAP	0.99387	0.983
52DAP/47DAP	0.95211	0.814
57DAP/52DAP	1.08873	0.547
57DAP/7DAP	0.85401	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.98617	0.038
17DAP/reference	3.57179	0.006
27DAP/reference	3.8648	0.006
39DAP/reference	4.85631	0.005
41DAP/reference	4.95571	0.01
42DAP/reference	6.12999	0.006
43DAP/reference	6.63704	0.006
47DAP/reference	2.93215	0.158
52DAP/reference	4.96761	0.007
57DAP/reference	3.79652	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.05041	0.577
17DAP/reference	0.76859	0.028
27DAP/reference	0.87638	0.09
39DAP/reference	0.85466	0.119
41DAP/reference	1.017	0.666
42DAP/reference	0.84166	0.039
43DAP/reference	0.74871	0.034
47DAP/reference	0.76976	0.018
52DAP/reference	0.77975	0.013
57DAP/reference	0.69777	0.058

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.95328	0.031
17DAP/reference	1.7704	0.467
27DAP/reference	3.41625	0.022
39DAP/reference	3.5968	0.014
41DAP/reference	3.40077	0.011
42DAP/reference	3.03377	0.01
43DAP/reference	3.44111	0.011
47DAP/reference	0.88154	0.153
52DAP/reference	3.32957	0.091
57DAP/reference	2.00181	0.157

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.96348	1
26DAP/20DAP	0.98304	1
34DAP/26DAP	0.91444	0.712
51DAP/34DAP	1.02411	0.98
52DAP/51DAP	1.02201	0.808
53DAP/52DAP	1.02251	0.858
55DAP/53DAP	1.29375	0.348
57DAP/55DAP	0.80963	0.3
62DAP/57DAP	0.87952	0.466
68DAP/62DAP	1.30804	0.091
68DAP/14DAP	1.33208	0.453

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.25496	0.212

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.81761	0.274
Mature Green Tomato/Ripe Tomato	0.81275	0.2
Immature Eggplant/Mature Eggplant	1.92002	0.05
Ripe Pepper/Ripe Tomato	1.62448	1
Mature Eggplant/Ripe Tomato	1.63234	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	N/A	N/A
12-2/M82	0.77736	0.955
12-4/M82	0.92203	0.619
1-3/M82	2.94277
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	1.45611
3-2/M82	1.58839
4-1-1/M82	1.30742	1
4-1/M82	0.84774
4-3-2/M82	0.87736
4-3/M82	2.21714	0.268
5-3/M82	0.89311	1
6-2/M82	2.52675	0.253
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	0.84728	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.98101	1
IL2-6/WTpooled	1.04971	1
IL7-5/WTpooled	0.91536
IL7-3/WTpooled	1.07058	1
IL12-4/WTpooled	1.27096	0.553
IL1-4/WTpooled	1.11568	1
WT/WTpooled	0.94985	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	1.40712	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.03901	0.921
DC3000/delta hrp 6h	1.08107	1
DC3000/delta hrp 12h	0.63187	1
DC3000/delta hrp 24h	1.2205	0.054

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.66783	0.033
DC3000 delta B/DC3000 delta AB	0.58846	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.95024	1
Exp 36h	0.8581	0.749
Exp 60h	0.68612	0.32

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

hybridization	ratio	FDR (corrected p value)
self-self	1.03135	1
Var 0h	1.0814	0.98
Var 12h I row2-row1	0.58092	0.338
Var 12h NI row2-row1	1.066	0.649
Var 36h I row2-row1	0.79109	0.575
Var 36h NI row2-row1	1.17823	0.482
Var 60h I row2-row1	1.2244	0.543
Var 60h NI row2-row1	1.08057	0.904
Time course 0hI-0hNI	1.00706	1
Time course 12hI-12hNI	0.9248	0.147
Time course 36hI-36hNI	0.82606	0.044
Time course 60hI-60hNI	0.16162	0.005

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)	0.90413	0.362
transgenic ySAMdc/azygous control (breaker)	0.70633	0.134
transgenic ySAMdc/azygous control (red)	0.97387	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.97633	0.208

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.24745	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.15159	1
Manapal/WT (break)	0.72389	0.333
Manapal/WT (red)	1.24761	0.134