Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.4.15.11

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.98254	0.811
27DAP/17DAP	1.36463	0.873
39DAP/27DAP	1.14438	0.745
41DAP/39DAP	1.09165	0.914
42DAP/41DAP	1.40139	0.18
43DAP/42DAP	1.02379	0.937
47DAP/43DAP	1.17932	0.702
52DAP/47DAP	1.62179	0.269
57DAP/52DAP	0.78367	0.503

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02963	0.788
17DAP/reference	1.0979	0.025
27DAP/reference	1.06437	0.156
39DAP/reference	1.06587	0.098
41DAP/reference	1.14463	0.019
42DAP/reference	0.9081	0.026
43DAP/reference	1.05272	0.495
47DAP/reference	0.92944	0.023
52DAP/reference	0.82154	0.102
57DAP/reference	0.87255	0.138

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.26265	0.176
27DAP/17DAP	0.7348	0.144
39DAP/27DAP	2.05277	0.044
41DAP/39DAP	0.61324	0.013
42DAP/41DAP	1.10868	0.947
43DAP/42DAP	2.56073	0.013
47DAP/43DAP	1.02991	0.901
52DAP/47DAP	1.01148	0.969
57DAP/52DAP	1.63822	0.188
57DAP/7DAP	1.48257	0.23

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94744	0.402
17DAP/reference	0.99465	0.599
27DAP/reference	0.90793	0.117
39DAP/reference	1.11931	0.157
41DAP/reference	1.11427	0.28
42DAP/reference	1.22483	0.233
43DAP/reference	1.41234	0.011
47DAP/reference	1.03862	0.885
52DAP/reference	1.15107	0.328
57DAP/reference	1.46462	0.027

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99855	0.97
17DAP/reference	1.01267	0.873
27DAP/reference	0.92655	0.304
39DAP/reference	0.84971	0.136
41DAP/reference	0.83978	0.108
42DAP/reference	0.87664	0.05
43DAP/reference	1.12225	0.532
47DAP/reference	1.00843	1
52DAP/reference	0.94286	0.066
57DAP/reference	1.08356	0.409

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99455	0.653
17DAP/reference	0.96198	0.592
27DAP/reference	1.08823	0.575
39DAP/reference	0.9075	0.122
41DAP/reference	0.80377	0.077
42DAP/reference	0.78744	0.172
43DAP/reference	0.91656	0.348
47DAP/reference	0.95326	0.421
52DAP/reference	1.35986	0.483
57DAP/reference	0.57624	0.019

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.98631	1
26DAP/20DAP	1.00183	1
34DAP/26DAP	1.05923	1
51DAP/34DAP	1.54553	0.038
52DAP/51DAP	0.95262	1
53DAP/52DAP	1.1514	0.565
55DAP/53DAP	0.71397	0.031
57DAP/55DAP	1.14783	0.826
62DAP/57DAP	1.22988	0.133
68DAP/62DAP	0.95345	0.747
68DAP/14DAP	0.9706	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.46299	0.068

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.46812	0.14
Mature Green Tomato/Ripe Tomato	0.21538	0.02
Immature Eggplant/Mature Eggplant	3.04382
Ripe Pepper/Ripe Tomato	0.46546	0.224
Mature Eggplant/Ripe Tomato	0.07036	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.73098
1-1-2/M82	0.52133
12-2/M82	1.37347
12-4/M82	0.76983	0.298
1-3/M82	N/A	N/A
2-1-1/M82	0.98811	1
2-1/M82	1.19443	0.345
2-6/M82	0.97162
3-2/M82	0.74961	0.455
4-1-1/M82	1.03162	1
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	1.14848	1
5-3/M82	0.82241	0.642
6-2/M82	1.73853
6-3/M82	0.62701
7-1/M82	0.97376	1
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	0.98595	1
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	1.03121	0.792
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	1.2214	1
WT/WTpooled	1.17092	0.874

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	1.22988	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.91211	1
DC3000/delta hrp 6h	1.0372	1
DC3000/delta hrp 12h	1.16011	1
DC3000/delta hrp 24h	1.07302	0.595

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.78754
DC3000 delta B/DC3000 delta AB	0.94274	0.805

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.80854	1
Exp 36h	1.06144	1
Exp 60h	1.10799	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	0.96613	1
Var 0h	0.9084	1
Var 12h I row2-row1	2.73604	0.506
Var 12h NI row2-row1	1.1554	0.235
Var 36h I row2-row1	1.0044	1
Var 36h NI row2-row1	0.77447	0.549
Var 60h I row2-row1	0.73476	1
Var 60h NI row2-row1	0.64867	0.932
Time course 0hI-0hNI	0.93502	0.711
Time course 12hI-12hNI	1.25417	0.201
Time course 36hI-36hNI	1.45766	0.005
Time course 60hI-60hNI	2.71532	0.011

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)	1.01658	0.921
transgenic ySAMdc/azygous control (breaker)	0.79373	0.139
transgenic ySAMdc/azygous control (red)	1.09749	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.97526	0.27

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.80507	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.65774	0.172
Manapal/WT (break)	0.68586	0.285
Manapal/WT (red)	1.02506	1