Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.4.16.1

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.43158	0.365
27DAP/17DAP	1.42049	0.761
39DAP/27DAP	1.31641	0.643
41DAP/39DAP	1.26821	0.416
42DAP/41DAP	1.16145	0.82
43DAP/42DAP	1.17838	0.793
47DAP/43DAP	1.09884	0.926
52DAP/47DAP	1.2978	0.832
57DAP/52DAP	1.01747	0.983

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99428	0.526
17DAP/reference	0.69612	0.007
27DAP/reference	0.92662	0.349
39DAP/reference	0.75626	0.018
41DAP/reference	0.64037	0.008
42DAP/reference	1.14144	0.869
43DAP/reference	0.84522	0.107
47DAP/reference	1.18257	0.541
52DAP/reference	1.8296	0.02
57DAP/reference	1.7221	0.016

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.13064	0.482
27DAP/17DAP	0.99907	0.969
39DAP/27DAP	1.33968	0.249
41DAP/39DAP	0.78786	0.209
42DAP/41DAP	1.10406	0.241
43DAP/42DAP	1.63361	0.015
47DAP/43DAP	1.03927	0.88
52DAP/47DAP	1.27564	0.315
57DAP/52DAP	1.39413	0.153
57DAP/7DAP	1.16086	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.07513	0.676
17DAP/reference	1.29533	0.077
27DAP/reference	0.97482	0.494
39DAP/reference	1.08092	0.237
41DAP/reference	0.83941	0.064
42DAP/reference	0.91865	0.235
43DAP/reference	1.31875	0.013
47DAP/reference	1.47063	0.071
52DAP/reference	1.17199	0.781
57DAP/reference	1.2821	0.125

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.88143	0.238
17DAP/reference	1.04593	0.979
27DAP/reference	1.22097	0.31
39DAP/reference	1.44926	0.194
41DAP/reference	1.70845	0.012
42DAP/reference	1.28525	0.066
43DAP/reference	0.83828	0.17
47DAP/reference	1.05282	0.712
52DAP/reference	1.26553	0.013
57DAP/reference	0.85667	0.18

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.23572	0.19
17DAP/reference	1.07678	0.854
27DAP/reference	1.16218	0.111
39DAP/reference	1.20052	0.275
41DAP/reference	1.14649	0.265
42DAP/reference	1.67002	0.065
43DAP/reference	1.83553	0.06
47DAP/reference	1.06382	1
52DAP/reference	1.06243	0.779
57DAP/reference	3.22849	0.023

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.83225	0.65
26DAP/20DAP	0.92961	1
34DAP/26DAP	1.2829	0.819
51DAP/34DAP	0.99809	0.844
52DAP/51DAP	1.82699	0.041
53DAP/52DAP	0.79785	0.124
55DAP/53DAP	1.14127	0.562
57DAP/55DAP	0.64195	0.043
62DAP/57DAP	1.09346	1
68DAP/62DAP	1.93062	0.057
68DAP/14DAP	2.26025	0.087

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.82481	0.137

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.94425	0.058
Mature Green Tomato/Ripe Tomato	0.21261	0.017
Immature Eggplant/Mature Eggplant	2.64818	0.05
Ripe Pepper/Ripe Tomato	2.01834	1
Mature Eggplant/Ripe Tomato	1.1433	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.85953
12-2/M82	N/A	N/A
12-4/M82	0.81275
1-3/M82	N/A	N/A
2-1-1/M82	0.91723
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	0.78385
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	0.86601
4-3/M82	N/A	N/A
5-3/M82	N/A	N/A
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	0.67887
7-2/M82	N/A	N/A
9-3-2/M82	1.17106	0.196

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.06702	1
IL2-6/WTpooled	1.76106	0.441
IL7-5/WTpooled	0.97786	1
IL7-3/WTpooled	1.14775	0.362
IL12-4/WTpooled	1.04544	1
IL1-4/WTpooled	1.15136	1
WT/WTpooled	1.01185	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	1.68191	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.88388	1
DC3000/delta hrp 6h	1.1361	1
DC3000/delta hrp 12h	1.30643	1
DC3000/delta hrp 24h	0.61719	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.42328	0.208
DC3000 delta B/DC3000 delta AB	1.04553	0.625

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.14244	1
Exp 36h	1.25695	1
Exp 60h	1.22197	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	0.97052	1
Var 0h	1.0948	0.782
Var 12h I row2-row1	0.96733	0.705
Var 12h NI row2-row1	0.98142	0.82
Var 36h I row2-row1	1.17696	0.742
Var 36h NI row2-row1	1.39139	0.482
Var 60h I row2-row1	1.21226	1
Var 60h NI row2-row1	1.0069	1
Time course 0hI-0hNI	0.97744	0.849
Time course 12hI-12hNI	1.02474	0.786
Time course 36hI-36hNI	0.94079	0.153
Time course 60hI-60hNI	0.68179	0.006

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)	0.95042	0.32
transgenic ySAMdc/azygous control (breaker)	0.50542	0.134
transgenic ySAMdc/azygous control (red)	1.25713	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.95922	0.371

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.74465	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.9328	0.105
Manapal/WT (break)	1.19374	1
Manapal/WT (red)	1.53511	0.413