Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.3.18.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.4205	0.124
27DAP/17DAP	1.36888	0.742
39DAP/27DAP	1.96096	0.11
41DAP/39DAP	0.96933	0.769
42DAP/41DAP	1.25162	0.644
43DAP/42DAP	0.73723	0.454
47DAP/43DAP	0.91156	0.696
52DAP/47DAP	0.83471	0.559
57DAP/52DAP	1.374	0.873

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91359	0.284
17DAP/reference	1.00009	0.904
27DAP/reference	1.05608	0.435
39DAP/reference	0.94265	0.284
41DAP/reference	1.0435	0.624
42DAP/reference	0.93174	0.069
43DAP/reference	1.03942	0.73
47DAP/reference	1.12777	0.154
52DAP/reference	0.77585	0.034
57DAP/reference	0.80524	0.028

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.55281	0.047
27DAP/17DAP	0.87497	0.614
39DAP/27DAP	1.03416	0.854
41DAP/39DAP	1.28955	0.382
42DAP/41DAP	0.91542	0.466
43DAP/42DAP	0.75087	0.022
47DAP/43DAP	1.06979	0.837
52DAP/47DAP	1.02822	0.973
57DAP/52DAP	1.01699	1
57DAP/7DAP	1.37775

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90117	0.122
17DAP/reference	1.02921	1
27DAP/reference	0.95648	0.43
39DAP/reference	1.42759	0.013
41DAP/reference	1.06132	0.745
42DAP/reference	1.19554	0.076
43DAP/reference	1.17293	0.408
47DAP/reference	1.59228	0.019
52DAP/reference	1.10252	0.308
57DAP/reference	1.19489	0.117

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.15045	0.41
17DAP/reference	1.1525	0.979
27DAP/reference	0.92009	0.22
39DAP/reference	1.03936	0.67
41DAP/reference	0.87109	0.148
42DAP/reference	0.87344	0.039
43DAP/reference	0.99974	0.761
47DAP/reference	1.11262	0.527
52DAP/reference	0.943	0.28
57DAP/reference	0.98303	0.61

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92901	0.335
17DAP/reference	0.94717	0.444
27DAP/reference	1.03093	0.834
39DAP/reference	1.00703	1
41DAP/reference	0.90282	0.293
42DAP/reference	0.99948	0.816
43DAP/reference	1.05456	0.721
47DAP/reference	1.19573	0.05
52DAP/reference	1.58747	0.053
57DAP/reference	1.09155	0.511

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.1817	0.966
26DAP/20DAP	1.25761	0.477
34DAP/26DAP	1.23958	0.819
51DAP/34DAP	1.61605	0.032
52DAP/51DAP	0.73617	0.151
53DAP/52DAP	1.18239	0.47
55DAP/53DAP	0.6914	0.12
57DAP/55DAP	1.2661	0.324
62DAP/57DAP	1.44338	0.185
68DAP/62DAP	0.93964	0.769
68DAP/14DAP	1.26164	0.676

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.80044	0.122

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.41485	0.078
Mature Green Tomato/Ripe Tomato	1.02694	1
Immature Eggplant/Mature Eggplant	1.43624	0.054
Ripe Pepper/Ripe Tomato	1.38114	0.256
Mature Eggplant/Ripe Tomato	0.68418	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.3064	0.591
1-1-2/M82	1.09116	1
12-2/M82	0.99373	1
12-4/M82	1.15771	1
1-3/M82	4.03819
2-1-1/M82	1.11608	1
2-1/M82	0.80264	0.74
2-6/M82	0.84648	1
3-2/M82	1.31042	0.967
4-1-1/M82	0.89044	1
4-1/M82	N/A	N/A
4-3-2/M82	1.37792	1
4-3/M82	1.47544	0.268
5-3/M82	1.10899	1
6-2/M82	1.86613	1
6-3/M82	1.09076	1
7-1/M82	1.11029	0.925
7-2/M82	1.38559	0.385
9-3-2/M82	1.40157	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	0.79929	0.71
IL1-4/WTpooled	1.14149	1
WT/WTpooled	1.04037	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	1.33144	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.96065	1
DC3000/delta hrp 6h	1.33258	0.582
DC3000/delta hrp 12h	1.1776	1
DC3000/delta hrp 24h	1.07408	0.553

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	2.2465
DC3000 delta B/DC3000 delta AB	1.46338	0.091

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.28266	1
Exp 36h	1.56569	0.326
Exp 60h	1.9898	0.237

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

hybridization	ratio	FDR (corrected p value)
self-self	0.96612	1
Var 0h	0.34677	1
Var 12h I row2-row1	1.09472	0.506
Var 12h NI row2-row1	1.3489	0.34
Var 36h I row2-row1	1.2031	0.742
Var 36h NI row2-row1	1.24832	1
Var 60h I row2-row1	0.72618	0.292
Var 60h NI row2-row1	0.75191	0.69
Time course 0hI-0hNI	0.95574	0.758
Time course 12hI-12hNI	1.44483	0.029
Time course 36hI-36hNI	2.71896	0.004
Time course 60hI-60hNI	8.92008	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)	0.98665	0.722
transgenic ySAMdc/azygous control (breaker)	0.86734	0.49
transgenic ySAMdc/azygous control (red)	0.88667	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.13219	0.055

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.83485	0.255

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.98447	1
Manapal/WT (break)	0.92873	1
Manapal/WT (red)	0.94706	0.863