Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.3.2.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	7.04197	0.016
27DAP/17DAP	1.05541	0.93
39DAP/27DAP	1.42599	0.17
41DAP/39DAP	0.70002	0.121
42DAP/41DAP	1.2176	0.888
43DAP/42DAP	1.19083	0.974
47DAP/43DAP	1.15623	0.542
52DAP/47DAP	0.84312	0.579
57DAP/52DAP	1.73829	0.969

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.49058	0.025
17DAP/reference	1.65462	0.089
27DAP/reference	3.73479	0.008
39DAP/reference	3.75781	0.012
41DAP/reference	2.17561	0.019
42DAP/reference	5.58926	0.001
43DAP/reference	5.17181	0.006
47DAP/reference	7.21775	0.001
52DAP/reference	3.51659	0.011
57DAP/reference	2.72321	0.008

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	N/A	N/A
27DAP/17DAP	N/A	N/A
39DAP/27DAP	N/A	N/A
41DAP/39DAP	1.0467	0.817
42DAP/41DAP	0.95463	0.77
43DAP/42DAP	N/A	N/A
47DAP/43DAP	1.02086	0.88
52DAP/47DAP	N/A	N/A
57DAP/52DAP	0.81911
57DAP/7DAP	3.24542	0.249

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.89348	0.326
17DAP/reference	1.51851	0.006
27DAP/reference	1.59053	0.008
39DAP/reference	1.21936	0.333
41DAP/reference	1.75203	0.199
42DAP/reference	1.3806	0.009
43DAP/reference	1.37231	0.011
47DAP/reference	4.178	0.014
52DAP/reference	2.42898	0.012
57DAP/reference	1.35681	0.027

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.29291	0.006
17DAP/reference	2.77046	0.008
27DAP/reference	3.94068	0.013
39DAP/reference	2.74945	0.013
41DAP/reference	4.67969	0.005
42DAP/reference	4.76468	0.007
43DAP/reference	1.3817	0.503
47DAP/reference	3.47449	0.008
52DAP/reference	3.41607	0.006
57DAP/reference	1.63113	0.688

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.39102	0.043
17DAP/reference	1.45177	0.436
27DAP/reference	1.53605	0.034
39DAP/reference	1.9667	0.006
41DAP/reference	1.40071	0.104
42DAP/reference	4.31867	0.028
43DAP/reference	3.04799	0.031
47DAP/reference	3.89594	0.004
52DAP/reference	2.26006	0.027
57DAP/reference	5.66935	0.009

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.86584	0.997
26DAP/20DAP	1.3641	0.165
34DAP/26DAP	0.60062	0.098
51DAP/34DAP	0.44754	0.049
52DAP/51DAP	0.70366	0.151
53DAP/52DAP	2.47937	0.027
55DAP/53DAP	0.66701	0.02
57DAP/55DAP	0.99853	0.875
62DAP/57DAP	0.68386	0.162
68DAP/62DAP	1.47268	0.657
68DAP/14DAP	0.50358	0.121

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	58.484	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.32758	0.058
Mature Green Tomato/Ripe Tomato	1.20292	0.948
Immature Eggplant/Mature Eggplant	0.54072	0.063
Ripe Pepper/Ripe Tomato	0.29129	0.224
Mature Eggplant/Ripe Tomato	0.19316	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.95119	0.944
1-1-2/M82	1.09508	1
12-2/M82	0.92595	0.955
12-4/M82	1.02655	1
1-3/M82	1.06509	1
2-1-1/M82	0.85037	0.565
2-1/M82	1.0182	1
2-6/M82	0.96084	1
3-2/M82	1.00751	0.967
4-1-1/M82	0.98532	1
4-1/M82	1.38122	1
4-3-2/M82	0.90089	1
4-3/M82	0.88488	0.72
5-3/M82	0.99191	1
6-2/M82	0.95132	1
6-3/M82	1.01349	1
7-1/M82	1.05031	0.925
7-2/M82	0.92007	0.796
9-3-2/M82	0.89076

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.12082	0.365
IL2-6/WTpooled	0.71024	0.473
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.864	1
IL12-4/WTpooled	1.39781	0.785
IL1-4/WTpooled	1.04668	1
WT/WTpooled	0.84269	0.764

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	0.96522	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.97358	1
DC3000/delta hrp 6h	1.06858	1
DC3000/delta hrp 12h	1.13405	1
DC3000/delta hrp 24h	0.70383	0.038

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	0.59399

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.1094	1
Exp 36h	1.39912	1
Exp 60h	0.91748	0.855

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

hybridization	ratio	FDR (corrected p value)
self-self	0.96645	1
Var 0h	1.23207	0.98
Var 12h I row2-row1	1.18221	0.654
Var 12h NI row2-row1	1.1006	1
Var 36h I row2-row1	0.91732	1
Var 36h NI row2-row1	0.97785	0.706
Var 60h I row2-row1	0.96234	0.285
Var 60h NI row2-row1	1.03452	1
Time course 0hI-0hNI	1.03009	1
Time course 12hI-12hNI	0.87167	0.246
Time course 36hI-36hNI	0.74738	0.045
Time course 60hI-60hNI	0.38703	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)	1.04792	0.748
transgenic ySAMdc/azygous control (breaker)	1.04031	1
transgenic ySAMdc/azygous control (red)	0.98943	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.31945	0.035

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.72435	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.05213	1
Manapal/WT (break)	0.93323	1
Manapal/WT (red)	0.96787	0.728