Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.4.4.8

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.6869	0.128
27DAP/17DAP	0.64707	0.102
39DAP/27DAP	0.76913	0.392
41DAP/39DAP	0.85712	0.512
42DAP/41DAP	0.84378	0.774
43DAP/42DAP	1.21068	1
47DAP/43DAP	0.45643	0.05
52DAP/47DAP	0.86304	0.646
57DAP/52DAP	1.29711	0.969

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.23022	0.028
17DAP/reference	1.07165	0.014
27DAP/reference	1.12245	0.221
39DAP/reference	1.0551	0.191
41DAP/reference	0.96462	0.542
42DAP/reference	1.0715	0.113
43DAP/reference	1.01703	0.787
47DAP/reference	0.94645	0.191
52DAP/reference	0.87706	0.177
57DAP/reference	0.95954	0.221

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.89726	0.454
27DAP/17DAP	1.28126	0.311
39DAP/27DAP	0.48399	0.075
41DAP/39DAP	1.76957	0.382
42DAP/41DAP	0.81377	0.162
43DAP/42DAP	1.4223	0.554
47DAP/43DAP	0.77841	0.219
52DAP/47DAP	1.65977	0.115
57DAP/52DAP	0.88383	0.356
57DAP/7DAP	0.55243	0.219

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.71552	0.032
17DAP/reference	1.07796	0.244
27DAP/reference	0.86396	0.076
39DAP/reference	0.93028	0.307
41DAP/reference	0.77148	0.021
42DAP/reference	0.77432	0.058
43DAP/reference	0.74183	0.014
47DAP/reference	0.85453	0.05
52DAP/reference	0.81602	0.021
57DAP/reference	0.82789	0.037

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.29905	0.122
17DAP/reference	0.91627	0.357
27DAP/reference	0.99936	0.765
39DAP/reference	0.96071	0.183
41DAP/reference	1.08362	0.737
42DAP/reference	0.91646	0.098
43DAP/reference	0.93337	0.423
47DAP/reference	0.83667	0.025
52DAP/reference	0.89491	0.01
57DAP/reference	0.96348	0.433

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	3.36159	0.015
17DAP/reference	1.82501	0.064
27DAP/reference	1.57823	0.025
39DAP/reference	1.24988	0.052
41DAP/reference	1.12133	0.383
42DAP/reference	1.71943	0.08
43DAP/reference	1.60989	0.008
47DAP/reference	1.71374	0.005
52DAP/reference	1.31235	0.067
57DAP/reference	1.06971	0.501

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.21509	0.966
26DAP/20DAP	0.90887	1
34DAP/26DAP	1.00563	1
51DAP/34DAP	0.94111	0.727
52DAP/51DAP	1.0229	0.836
53DAP/52DAP	0.93601	0.772
55DAP/53DAP	1.127	0.951
57DAP/55DAP	1.21197	0.935
62DAP/57DAP	1.01265	1
68DAP/62DAP	1.37008	0.105
68DAP/14DAP	1.06813	0.958

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.0237	0.696

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	4.44017	0.058
Mature Green Tomato/Ripe Tomato	39.9739	0.015
Immature Eggplant/Mature Eggplant	0.71337	0.176
Ripe Pepper/Ripe Tomato	9.15519	1
Mature Eggplant/Ripe Tomato	6.10868

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	N/A	N/A
12-4/M82	1.25854	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	0.57177
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
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	0.72037
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.18015	0.584
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.10912	1
IL12-4/WTpooled	1.16148	0.695
IL1-4/WTpooled	0.79103
WT/WTpooled	0.97537	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	0.72803	0.497

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.89319
DC3000/delta hrp 6h	1.01635	1
DC3000/delta hrp 12h	0.97165	1
DC3000/delta hrp 24h	0.42318	0.034

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	0.88694	0.619

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.95762	1
Exp 36h	0.79159	0.471
Exp 60h	0.90746	0.754

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

hybridization	ratio	FDR (corrected p value)
self-self	N/A	N/A
Var 0h	0.98009	0.261
Var 12h I row2-row1	N/A	N/A
Var 12h NI row2-row1	N/A	N/A
Var 36h I row2-row1	N/A	N/A
Var 36h NI row2-row1	N/A	N/A
Var 60h I row2-row1	N/A	N/A
Var 60h NI row2-row1	N/A	N/A
Time course 0hI-0hNI	N/A	N/A
Time course 12hI-12hNI	N/A	N/A
Time course 36hI-36hNI	N/A	N/A
Time course 60hI-60hNI	N/A	N/A

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)	1.4288	0.221
transgenic ySAMdc/azygous control (breaker)	1.97704	0.248
transgenic ySAMdc/azygous control (red)	2.23454	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.89275	0.067

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	2.84445	0.237

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	7.53529	0.083
Manapal/WT (break)	8.53742	0.13
Manapal/WT (red)	15.6484	0.15