Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.1.4.16

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.81464	0.389
27DAP/17DAP	1.11458	0.852
39DAP/27DAP	1.44603	0.61
41DAP/39DAP	0.97094	0.789
42DAP/41DAP	0.79426	0.774
43DAP/42DAP	0.99392	0.937
47DAP/43DAP	1.57289	0.173
52DAP/47DAP	0.89303	0.678
57DAP/52DAP	1.04618	0.996

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.17233	0.049
17DAP/reference	0.97981	0.701
27DAP/reference	1.31425	0.01
39DAP/reference	1.0134	0.8
41DAP/reference	1.09191	0.265
42DAP/reference	1.01407	0.731
43DAP/reference	1.16969	0.035
47DAP/reference	1.10972	0.101
52DAP/reference	0.99745	0.689
57DAP/reference	0.92111	0.118

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.34409	0.326
27DAP/17DAP	0.89343	0.724
39DAP/27DAP	1.08892	0.707
41DAP/39DAP	0.84404	0.384
42DAP/41DAP	1.04046	0.893
43DAP/42DAP	0.81427	0.034
47DAP/43DAP	1.04188	0.848
52DAP/47DAP	1.317	0.432
57DAP/52DAP	1.17235	0.574
57DAP/7DAP	0.80597	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96573	0.138
17DAP/reference	0.91564	0.024
27DAP/reference	0.83961	0.016
39DAP/reference	0.86976	0.015
41DAP/reference	0.83348	0.042
42DAP/reference	0.86168	0.014
43DAP/reference	0.81891	0.013
47DAP/reference	0.93568	0.383
52DAP/reference	0.83	0.026
57DAP/reference	0.85259	0.026

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.21859	0.226
17DAP/reference	1.27352	0.723
27DAP/reference	1.02698	0.745
39DAP/reference	1.09905	0.188
41DAP/reference	1.03693	1
42DAP/reference	0.88533	0.108
43DAP/reference	0.99449	0.801
47DAP/reference	0.90029	0.141
52DAP/reference	0.81611	0.06
57DAP/reference	1.02057	1

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01411	0.882
17DAP/reference	0.9488	0.243
27DAP/reference	0.90238	0.058
39DAP/reference	0.90636	0.04
41DAP/reference	0.98137	0.56
42DAP/reference	0.85939	0.019
43DAP/reference	0.95306	0.294
47DAP/reference	1.09571	0.196
52DAP/reference	0.68095	0.071
57DAP/reference	0.96067	0.394

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.05292	0.966
26DAP/20DAP	2.6421	0.21
34DAP/26DAP	0.89825	0.741
51DAP/34DAP	1.73229	0.033
52DAP/51DAP	0.68423	0.151
53DAP/52DAP	1.566	0.045
55DAP/53DAP	0.83657	0.188
57DAP/55DAP	0.74359	0.154
62DAP/57DAP	0.81693
68DAP/62DAP	1.03305	0.977
68DAP/14DAP	0.97456	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.29731	0.019

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.32831	0.058
Mature Green Tomato/Ripe Tomato	3.2454	0.038
Immature Eggplant/Mature Eggplant	1.90248	0.05
Ripe Pepper/Ripe Tomato	2.01695	1
Mature Eggplant/Ripe Tomato	2.95899	0.268

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.26005	0.877
1-1-2/M82	1.10902	1
12-2/M82	0.91872	0.955
12-4/M82	1.26519	1
1-3/M82	1.67562	0.277
2-1-1/M82	0.84255	0.565
2-1/M82	0.99499	1
2-6/M82	0.9742	1
3-2/M82	1.54802
4-1-1/M82	1.02908	1
4-1/M82	0.97408	1
4-3-2/M82	1.16593	0.246
4-3/M82	1.37262	1
5-3/M82	1.08998	1
6-2/M82	0.89507	1
6-3/M82	1.32478	1
7-1/M82	0.90963	0.803
7-2/M82	1.31911	0.385
9-3-2/M82	0.87831	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.88191	0.247
IL2-6/WTpooled	1.16573
IL7-5/WTpooled	1.09587	0.67
IL7-3/WTpooled	0.84589	1
IL12-4/WTpooled	1.22264
IL1-4/WTpooled	0.81074	0.699
WT/WTpooled	1.3123	0.785

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	0.87601	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.97165	1
DC3000/delta hrp 6h	0.96151	0.95
DC3000/delta hrp 12h	0.91921	1
DC3000/delta hrp 24h	0.80677	0.216

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.98483	1
DC3000 delta B/DC3000 delta AB	1.03752	0.694

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.07508	1
Exp 36h	1.10349	1
Exp 60h	1.24199	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	N/A	N/A
Var 0h	1.00665	1
Var 12h I row2-row1	N/A	N/A
Var 12h NI row2-row1	N/A	N/A
Var 36h I row2-row1	N/A	N/A
Var 36h NI row2-row1	N/A	N/A
Var 60h I row2-row1	N/A	N/A
Var 60h NI row2-row1	N/A	N/A
Time course 0hI-0hNI	N/A	N/A
Time course 12hI-12hNI	N/A	N/A
Time course 36hI-36hNI	N/A	N/A
Time course 60hI-60hNI	N/A	N/A

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)	0.98658	0.789
transgenic ySAMdc/azygous control (breaker)	0.43469	0.119
transgenic ySAMdc/azygous control (red)	1.91855	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.07467	0.317

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	2.61715	0.229

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.22626	0.14
Manapal/WT (break)	1.27086	1
Manapal/WT (red)	1.35499	0.222