Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.2.1.9

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.48925	0.138
27DAP/17DAP	1.11327	0.859
39DAP/27DAP	0.87675	0.573
41DAP/39DAP	1.18594	0.701
42DAP/41DAP	0.95523	1
43DAP/42DAP	0.94581	0.89
47DAP/43DAP	1.23216	0.538
52DAP/47DAP	1.02117	0.984
57DAP/52DAP	0.97028	0.957

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.72352	0.025
17DAP/reference	0.66227	0.007
27DAP/reference	0.89399	0.304
39DAP/reference	0.70277	0.012
41DAP/reference	0.59758	0.009
42DAP/reference	0.90246	0.111
43DAP/reference	0.83106	0.018
47DAP/reference	1.05119	0.989
52DAP/reference	1.4198	0.088
57DAP/reference	1.30076	0.012

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.23071	0.536
27DAP/17DAP	0.83613	0.508
39DAP/27DAP	1.05559	0.698
41DAP/39DAP	0.95069	0.893
42DAP/41DAP	1.03864	1
43DAP/42DAP	1.21874	0.627
47DAP/43DAP	1.20383	0.245
52DAP/47DAP	1.11186	0.656
57DAP/52DAP	1.00674	0.905
57DAP/7DAP	0.70165	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96914	0.495
17DAP/reference	1.03131	0.599
27DAP/reference	0.98943	0.614
39DAP/reference	0.81133	0.018
41DAP/reference	0.74067	0.047
42DAP/reference	0.70831	0.01
43DAP/reference	0.87858	0.132
47DAP/reference	0.87187	0.293
52DAP/reference	0.77421	0.026
57DAP/reference	0.96905	0.477

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.71618	0.02
17DAP/reference	0.60042	0.003
27DAP/reference	0.97517	0.519
39DAP/reference	1.12791	0.746
41DAP/reference	1.14063	0.318
42DAP/reference	1.01774	1
43DAP/reference	0.66035	0.027
47DAP/reference	0.72366	0.01
52DAP/reference	1.15007	0.838
57DAP/reference	0.66856	0.013

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91446	0.335
17DAP/reference	0.90352	0.398
27DAP/reference	0.91548	0.319
39DAP/reference	0.89045	0.101
41DAP/reference	0.99679	0.826
42DAP/reference	1.59103	0.052
43DAP/reference	1.17882	0.465
47DAP/reference	0.96505	0.465
52DAP/reference	1.26975	0.724
57DAP/reference	2.10887	0.026

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.94877	1
26DAP/20DAP	0.96981	1
34DAP/26DAP	1.10492	1
51DAP/34DAP	0.85323	0.513
52DAP/51DAP	1.2151	0.077
53DAP/52DAP	0.94518	0.811
55DAP/53DAP	1.12123	0.784
57DAP/55DAP	0.77061	0.106
62DAP/57DAP	1.30931	0.003
68DAP/62DAP	2.40954	0.081
68DAP/14DAP	2.91107	0.025

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.73155	0.052

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	2.49169	0.022
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	1.09332
12-2/M82	N/A	N/A
12-4/M82	N/A	N/A
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	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	0.96636
4-3/M82	N/A	N/A
5-3/M82	N/A	N/A
6-2/M82	N/A	N/A
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	0.68692

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.19421
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	2.43119
IL12-4/WTpooled	0.85023
IL1-4/WTpooled	1.17161	1
WT/WTpooled	0.80867

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	1.00626	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.91071	1
DC3000/delta hrp 6h	0.92562	0.95
DC3000/delta hrp 12h	1.18004	1
DC3000/delta hrp 24h	1.2563	0.821

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.55008	0.25
DC3000 delta B/DC3000 delta AB	1.04414	0.748

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.05672	1
Exp 36h	0.65723	0.504
Exp 60h	0.6837	0.386

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

hybridization	ratio	FDR (corrected p value)
self-self	0.86907	1
Var 0h	1.09345	1
Var 12h I row2-row1	0.86998	0.39
Var 12h NI row2-row1	0.94154	0.906
Var 36h I row2-row1	0.88717	1
Var 36h NI row2-row1	1.29461	1
Var 60h I row2-row1	0.85011	0.374
Var 60h NI row2-row1	1.28996	0.904
Time course 0hI-0hNI	0.97605	0.906
Time course 12hI-12hNI	0.96736	0.79
Time course 36hI-36hNI	0.93027	0.194
Time course 60hI-60hNI	0.82148	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)	0.95749	0.348
transgenic ySAMdc/azygous control (breaker)	1.54218	0.178
transgenic ySAMdc/azygous control (red)	1.03863	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.97353	0.27

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.68217	0.233

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	2.15965	0.105
Manapal/WT (break)	1.84163	0.126
Manapal/WT (red)	1.76512	0.164