Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.1.10.19

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.69718	0.238
27DAP/17DAP	0.47768	0.045
39DAP/27DAP	0.94524	0.682
41DAP/39DAP	1.04886	0.949
42DAP/41DAP	1.18463	0.691
43DAP/42DAP	1.09353	0.993
47DAP/43DAP	1.16354	0.793
52DAP/47DAP	0.79853	0.54
57DAP/52DAP	1.05529	0.992

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.68459	0.038
17DAP/reference	0.61934	0.018
27DAP/reference	0.4931	0.012
39DAP/reference	0.64746	0.04
41DAP/reference	0.63388	0.031
42DAP/reference	0.59367	0.001
43DAP/reference	0.80851	0.103
47DAP/reference	0.59289	0.001
52DAP/reference	0.42732	0.013
57DAP/reference	0.70928	0.014

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.46288	0.036
27DAP/17DAP	1.1777	0.403
39DAP/27DAP	1.31952	0.236
41DAP/39DAP	1.10536	0.417
42DAP/41DAP	1.24911	0.129
43DAP/42DAP	2.20154	0.016
47DAP/43DAP	0.91425	0.597
52DAP/47DAP	1.75766	0.123
57DAP/52DAP	1.04727	1
57DAP/7DAP	1.2817	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.80936	0.091
17DAP/reference	0.75694	0.021
27DAP/reference	0.65765	0.011
39DAP/reference	0.65954	0.02
41DAP/reference	0.62373	0.034
42DAP/reference	0.44487	0.01
43DAP/reference	0.43563	0.01
47DAP/reference	0.45839	0.03
52DAP/reference	0.52268	0.014
57DAP/reference	0.52245	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.82829	0.1
17DAP/reference	0.62276	0.007
27DAP/reference	0.50675	0.007
39DAP/reference	0.5041	0.008
41DAP/reference	0.716	0.018
42DAP/reference	0.54726	0.011
43DAP/reference	0.51429	0.022
47DAP/reference	0.71372	0.011
52DAP/reference	0.50948	0.003
57DAP/reference	0.53773	0.002

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.88249	0.098
17DAP/reference	0.7661	0.182
27DAP/reference	0.64849	0.021
39DAP/reference	0.56644	0.008
41DAP/reference	0.6792	0.018
42DAP/reference	0.59876	0.019
43DAP/reference	0.52728	0.03
47DAP/reference	0.47945	0.005
52DAP/reference	0.58503	0.059
57DAP/reference	0.41991	0.016

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.0825	0.966
26DAP/20DAP	0.91943	0.512
34DAP/26DAP	0.91904	0.848
51DAP/34DAP	1.15405	0.241
52DAP/51DAP	1.27095	0.288
53DAP/52DAP	1.1825	0.688
55DAP/53DAP	1.11233	0.656
57DAP/55DAP	0.6526	0.08
62DAP/57DAP	0.80024	0.681
68DAP/62DAP	0.77432	0.245
68DAP/14DAP	0.67758	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.27997	0.015

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.7694	0.377
Immature Eggplant/Mature Eggplant	0.0392
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	0.72125
1-1-2/M82	1.33486
12-2/M82	N/A	N/A
12-4/M82	0.94705	1
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	0.65028	0.698
4-3/M82	N/A	N/A
5-3/M82	1.03149	1
6-2/M82	0.97693
6-3/M82	0.92713
7-1/M82	N/A	N/A
7-2/M82	1.04232
9-3-2/M82	1.08139

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.60183	0.277
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	1.16545	0.722
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	1.10989	1
WT/WTpooled	N/A	N/A

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	0.39443	0.201

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.6093	0.571
DC3000/delta hrp 6h	1.41713	0.978
DC3000/delta hrp 12h	0.79747	1
DC3000/delta hrp 24h	1.19333	0.535

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.34678	0.06
DC3000 delta B/DC3000 delta AB	1.11402	0.412

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.27383	1
Exp 36h	0.85816	0.749
Exp 60h	0.66509	0.454

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01341	1
Var 0h	1.43555	0.782
Var 12h I row2-row1	0.80931	0.627
Var 12h NI row2-row1	0.68848	0.627
Var 36h I row2-row1	1.10723	0.742
Var 36h NI row2-row1	0.7921	0.61
Var 60h I row2-row1	0.99717	1
Var 60h NI row2-row1	1.20228	0.904
Time course 0hI-0hNI	0.81163	0.118
Time course 12hI-12hNI	0.77549	0.284
Time course 36hI-36hNI	0.69689	0.023
Time course 60hI-60hNI	0.34433	0.007

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)	0.90911	0.391
transgenic ySAMdc/azygous control (breaker)	1.48206	1
transgenic ySAMdc/azygous control (red)	1.49991	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.95871	0.16

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	2.00215	0.233

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.95076	1
Manapal/WT (break)	1.04279	1
Manapal/WT (red)	0.89164	0.229