Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.4.19.16

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.08854	0.932
27DAP/17DAP	1.87062	0.341
39DAP/27DAP	1.48301	0.548
41DAP/39DAP	1.0723	0.708
42DAP/41DAP	1.14465	0.877
43DAP/42DAP	0.88336	0.699
47DAP/43DAP	0.99002	0.876
52DAP/47DAP	0.77851	0.459
57DAP/52DAP	0.96519	0.957

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.76566	0.031
17DAP/reference	0.95166	0.393
27DAP/reference	1.01536	0.782
39DAP/reference	0.9819	0.762
41DAP/reference	0.71495	0.008
42DAP/reference	0.85689	0.006
43DAP/reference	0.94718	0.346
47DAP/reference	0.9147	0.077
52DAP/reference	1.02792	0.951
57DAP/reference	1.05407	0.433

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.90929	0.038
27DAP/17DAP	0.66827	0.121
39DAP/27DAP	2.20401	0.04
41DAP/39DAP	0.34526	0.013
42DAP/41DAP	1.34289	0.028
43DAP/42DAP	1.18885	0.162
47DAP/43DAP	0.86353	0.138
52DAP/47DAP	1.67816	0.053
57DAP/52DAP	0.83244	0.229
57DAP/7DAP	1.26783	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.34769	0.046
17DAP/reference	1.84585	0.007
27DAP/reference	1.9247	0.006
39DAP/reference	2.06355	0.005
41DAP/reference	2.09991	0.013
42DAP/reference	2.12516	0.006
43DAP/reference	2.44449	0.006
47DAP/reference	1.49545	0.059
52DAP/reference	2.12339	0.007
57DAP/reference	2.02922	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.79981	0.067
17DAP/reference	0.77813	0.035
27DAP/reference	0.74395	0.006
39DAP/reference	0.83293	0.038
41DAP/reference	0.86161	0.026
42DAP/reference	0.75155	0.037
43DAP/reference	0.94424	0.385
47DAP/reference	0.91055	0.019
52DAP/reference	0.80887	0.009
57DAP/reference	0.88711	0.085

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.38083	0.034
17DAP/reference	1.08683	0.956
27DAP/reference	1.45907	0.037
39DAP/reference	1.26389	0.104
41DAP/reference	1.40147	0.031
42DAP/reference	1.24459	0.251
43DAP/reference	1.39912	0.114
47DAP/reference	0.93813	0.215
52DAP/reference	1.64925	0.103
57DAP/reference	1.02127	0.742

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.89845	1
26DAP/20DAP	1.1727	1
34DAP/26DAP	1.08527	1
51DAP/34DAP	2.82139	0.029
52DAP/51DAP	1.0291	0.776
53DAP/52DAP	3.33352	0.021
55DAP/53DAP	0.82306	0.125
57DAP/55DAP	0.28682	0.01
62DAP/57DAP	0.56765	0.003
68DAP/62DAP	1.49654	0.021
68DAP/14DAP	1.83769	0.021

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.52928	0.02

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.70321	0.188
Mature Green Tomato/Ripe Tomato	1.98197	0.166
Immature Eggplant/Mature Eggplant	7.75916	0.05
Ripe Pepper/Ripe Tomato	4.95261	0.256
Mature Eggplant/Ripe Tomato	2.12104	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.81291	0.605
1-1-2/M82	1.15817	1
12-2/M82	1.84361
12-4/M82	1.05683
1-3/M82	1.1162
2-1-1/M82	0.79231	0.683
2-1/M82	0.74998
2-6/M82	0.66024	1
3-2/M82	1.32275	0.463
4-1-1/M82	0.58267	1
4-1/M82	N/A	N/A
4-3-2/M82	1.00214
4-3/M82	0.66056	0.509
5-3/M82	1.24249	0.447
6-2/M82	0.69676
6-3/M82	1.36463
7-1/M82	0.9386	1
7-2/M82	0.61671
9-3-2/M82	0.55006

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.5894	0.277
IL2-6/WTpooled	0.64062	1
IL7-5/WTpooled	1.37309	0.792
IL7-3/WTpooled	1.40427	1
IL12-4/WTpooled	1.10579	0.785
IL1-4/WTpooled	1.06726	0.426
WT/WTpooled	0.99626	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	1.51005	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.83041	0.868
DC3000/delta hrp 6h	1.36989	1
DC3000/delta hrp 12h	1.48949	1
DC3000/delta hrp 24h	0.75079	0.05

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	2.57752

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	1.29597	0.693
Exp 60h	1.0586	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.94832	1
Var 0h	0.83354	0.457
Var 12h I row2-row1	1.10987	0.348
Var 12h NI row2-row1	0.86422	0.627
Var 36h I row2-row1	0.90553	1
Var 36h NI row2-row1	0.77167	0.584
Var 60h I row2-row1	1.91904	1
Var 60h NI row2-row1	1.02829	0.904
Time course 0hI-0hNI	0.94879	0.758
Time course 12hI-12hNI	0.9898	0.968
Time course 36hI-36hNI	1.13294	0.147
Time course 60hI-60hNI	1.45741	0.009

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)	0.82959	0.229
transgenic ySAMdc/azygous control (breaker)	0.8326	0.173
transgenic ySAMdc/azygous control (red)	1.01586	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.38208	0.069

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.84101	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.53892	1
Manapal/WT (break)	0.61856	0.333
Manapal/WT (red)	0.52975	0.181