Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.2.7.2

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.97786	0.823
27DAP/17DAP	0.9915	1
39DAP/27DAP	0.79491	0.425
41DAP/39DAP	0.94756	0.771
42DAP/41DAP	0.9781	1
43DAP/42DAP	1.11201	1
47DAP/43DAP	1.16585	0.584
52DAP/47DAP	0.72468	0.323
57DAP/52DAP	1.08253	0.977

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.10047	0.241
17DAP/reference	0.9941	0.858
27DAP/reference	1.00521	1
39DAP/reference	0.9063	0.267
41DAP/reference	0.72889	0.031
42DAP/reference	0.85312	0.006
43DAP/reference	0.88331	0.063
47DAP/reference	0.85896	0.015
52DAP/reference	0.96208	0.393
57DAP/reference	1.19653	0.136

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.07313	0.87
27DAP/17DAP	0.7466	0.312
39DAP/27DAP	0.86461	0.269
41DAP/39DAP	1.12736	0.603
42DAP/41DAP	0.99476	0.887
43DAP/42DAP	0.74857	0.023
47DAP/43DAP	1.01805	0.914
52DAP/47DAP	1.41568	0.334
57DAP/52DAP	1.43062	0.091
57DAP/7DAP	1.01985	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.83369	0.203
17DAP/reference	0.59259	0.018
27DAP/reference	0.64363	0.01
39DAP/reference	0.92831	0.354
41DAP/reference	0.85856	0.166
42DAP/reference	0.95632	0.641
43DAP/reference	0.77045	0.11
47DAP/reference	0.93301	0.383
52DAP/reference	1.05819	0.781
57DAP/reference	1.04208	0.966

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.10517	0.695
17DAP/reference	1.12174	0.236
27DAP/reference	0.87087	0.129
39DAP/reference	0.96163	0.442
41DAP/reference	0.99099	0.557
42DAP/reference	0.77523	0.032
43DAP/reference	0.62653	0.017
47DAP/reference	0.85302	0.022
52DAP/reference	0.90639	0.22
57DAP/reference	0.79657	0.058

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9495	0.526
17DAP/reference	1.02555	0.746
27DAP/reference	0.69559	0.218
39DAP/reference	1.07278	0.483
41DAP/reference	1.14929	1
42DAP/reference	1.49423	0.327
43DAP/reference	1.02259	0.712
47DAP/reference	0.77878	0.034
52DAP/reference	0.55562	0.119
57DAP/reference	0.9849	0.633

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.05356	1
26DAP/20DAP	1.1448	0.77
34DAP/26DAP	1.0904	1
51DAP/34DAP	0.75615	0.107
52DAP/51DAP	1.70961	0.035
53DAP/52DAP	0.88087	0.824
55DAP/53DAP	1.24547	0.271
57DAP/55DAP	0.5926	0.054
62DAP/57DAP	1.31069	0.098
68DAP/62DAP	1.13474	0.912
68DAP/14DAP	0.83759

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.50454	0.019

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	8.55004	0.058
Mature Green Tomato/Ripe Tomato	5.58069	0.016
Immature Eggplant/Mature Eggplant	0.58786	0.063
Ripe Pepper/Ripe Tomato	3.07609
Mature Eggplant/Ripe Tomato	26.0974	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	1.03756	1
12-2/M82	N/A	N/A
12-4/M82	0.75684	1
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	0.99925	1
4-3/M82	N/A	N/A
5-3/M82	0.86012	1
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	0.57561
7-2/M82	1.50604
9-3-2/M82	1.06299	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.92141	0.321
IL2-6/WTpooled	1.01798	1
IL7-5/WTpooled	0.7468	1
IL7-3/WTpooled	0.90649	0.418
IL12-4/WTpooled	0.76827	0.566
IL1-4/WTpooled	0.94901	0.699
WT/WTpooled	1.07243	0.999

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	1.06748	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.97244	1
DC3000/delta hrp 6h	1.1355	1
DC3000/delta hrp 12h	0.90157	1
DC3000/delta hrp 24h	0.41983	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.87207	0.048
DC3000 delta B/DC3000 delta AB	0.93827	0.543

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.95061	1
Exp 36h	0.73592	0.504
Exp 60h	0.59916	0.251

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

hybridization	ratio	FDR (corrected p value)
self-self	0.97999	1
Var 0h	0.89707	1
Var 12h I row2-row1	0.6978	0.338
Var 12h NI row2-row1	1.10138	0.649
Var 36h I row2-row1	0.905	1
Var 36h NI row2-row1	1.1919	0.482
Var 60h I row2-row1	0.82272	0.439
Var 60h NI row2-row1	1.05153	1
Time course 0hI-0hNI	0.93532	0.617
Time course 12hI-12hNI	0.96082	0.742
Time course 36hI-36hNI	0.83069	0.081
Time course 60hI-60hNI	0.2565	0.005

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)	0.8951	0.485
transgenic ySAMdc/azygous control (breaker)	1.25297	1
transgenic ySAMdc/azygous control (red)	1.61301	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.86458	0.057

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	2.97107	0.231

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	2.4841	0.086
Manapal/WT (break)	2.20595	1
Manapal/WT (red)	3.23582	0.164