Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.3.3.10

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	3.27384	0.067
27DAP/17DAP	2.23419	0.134
39DAP/27DAP	1.66574	0.489
41DAP/39DAP	1.61763	0.483
42DAP/41DAP	0.74065	0.774
43DAP/42DAP	0.74395	0.495
47DAP/43DAP	0.59443	0.07
52DAP/47DAP	1.02132	0.88
57DAP/52DAP	1.04321	0.98

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.75956	0.027
17DAP/reference	0.94694	0.129
27DAP/reference	0.99563	0.867
39DAP/reference	1.42783	0.301
41DAP/reference	1.09871	0.365
42DAP/reference	0.92003	0.182
43DAP/reference	0.95661	0.429
47DAP/reference	1.04205	0.764
52DAP/reference	0.82555	0.143
57DAP/reference	N/A	N/A

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	3.39841	0.036
27DAP/17DAP	0.93958	0.748
39DAP/27DAP	1.06968	0.751
41DAP/39DAP	1.40577	0.08
42DAP/41DAP	0.88441	0.343
43DAP/42DAP	0.48229	0.022
47DAP/43DAP	0.85404	0.09
52DAP/47DAP	1.09881	0.819
57DAP/52DAP	1.19464	0.434
57DAP/7DAP	0.64399	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92738	0.402
17DAP/reference	1.01838	1
27DAP/reference	0.92618	0.231
39DAP/reference	1.12774	0.371
41DAP/reference	0.97814	0.512
42DAP/reference	0.89078	0.16
43DAP/reference	1.04471	0.974
47DAP/reference	1.12503	0.604
52DAP/reference	0.65102	0.017
57DAP/reference	0.98846	0.61

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90049	0.176
17DAP/reference	0.9931	0.728
27DAP/reference	1.02711	0.948
39DAP/reference	1.00068	0.642
41DAP/reference	0.92504	0.25
42DAP/reference	0.92309	0.237
43DAP/reference	0.99233	0.657
47DAP/reference	0.94687	0.253
52DAP/reference	1.10288	0.471
57DAP/reference	0.9786	0.519

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.0018	0.804
17DAP/reference	0.89128	0.249
27DAP/reference	1.04557	0.575
39DAP/reference	0.94022	0.328
41DAP/reference	0.95271	0.459
42DAP/reference	0.91384	0.172
43DAP/reference	0.83298	0.102
47DAP/reference	0.81569	0.03
52DAP/reference	1.23613	0.965
57DAP/reference	0.85929	0.122

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.62181	1
26DAP/20DAP	1.76977	0.14
34DAP/26DAP	0.85314	0.682
51DAP/34DAP	1.21259	0.241
52DAP/51DAP	0.85073	1
53DAP/52DAP	0.65779	0.307
55DAP/53DAP	0.6411	0.13
57DAP/55DAP	0.51197	0.103
62DAP/57DAP	1.51176	0.8
68DAP/62DAP	1.72394	0.821
68DAP/14DAP	3.19282	0.146

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.88079	0.211

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.71363	0.193
Mature Green Tomato/Ripe Tomato	13.8601	0.015
Immature Eggplant/Mature Eggplant	3.97028	0.3
Ripe Pepper/Ripe Tomato	13.462	1
Mature Eggplant/Ripe Tomato	13.2047	0.26

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	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	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	N/A	N/A
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.89976
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	1.01895
IL7-3/WTpooled	0.59264
IL12-4/WTpooled	0.96231	0.581
IL1-4/WTpooled	1.02566	1
WT/WTpooled	0.99901	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	0.81594	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.07493	0.921
DC3000/delta hrp 6h	2.13577	1
DC3000/delta hrp 12h	1.09759	1
DC3000/delta hrp 24h	1.13505	0.422

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.97429	1
DC3000 delta B/DC3000 delta AB	0.88663	0.381

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	2.07062	1
Exp 36h	1.82354	1
Exp 60h	1.80683	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	1.07819	1
Var 0h	0.62679	0.933
Var 12h I row2-row1	0.79792	0.705
Var 12h NI row2-row1	0.93301
Var 36h I row2-row1	1.1758	1
Var 36h NI row2-row1	N/A	N/A
Var 60h I row2-row1	0.70559	0.306
Var 60h NI row2-row1	1.06631	0.904
Time course 0hI-0hNI	0.96343	0.812
Time course 12hI-12hNI	0.94134	0.65
Time course 36hI-36hNI	1.18239	0.28
Time course 60hI-60hNI	2.55055	0.008

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)	0.94597	0.529
transgenic ySAMdc/azygous control (breaker)	0.79708	0.251
transgenic ySAMdc/azygous control (red)	1.00512	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.01827	0.587

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.99286	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.6625	0.172
Manapal/WT (break)	0.65133	0.299
Manapal/WT (red)	1.73254	0.413