Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.2.2.1

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.14683	0.498
27DAP/17DAP	1.10674	0.859
39DAP/27DAP	0.86456	0.397
41DAP/39DAP	1.28259	0.27
42DAP/41DAP	0.90119	1
43DAP/42DAP	0.92003	0.787
47DAP/43DAP	1.0042	0.926
52DAP/47DAP	1.14688	0.665
57DAP/52DAP	1.14473	0.918

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.07315	0.154
17DAP/reference	0.98447	0.503
27DAP/reference	0.99889	0.904
39DAP/reference	0.98078	0.663
41DAP/reference	0.95025	0.542
42DAP/reference	1.10485	0.002
43DAP/reference	1.01563	0.73
47DAP/reference	1.07037	0.105
52DAP/reference	1.10381	0.388
57DAP/reference	1.10577	0.141

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.006	1
27DAP/17DAP	0.99865	0.969
39DAP/27DAP	1.0927	0.505
41DAP/39DAP	1.08133	0.484
42DAP/41DAP	0.99948	0.936
43DAP/42DAP	0.99183	0.854
47DAP/43DAP	0.99289	0.971
52DAP/47DAP	0.97481	0.9
57DAP/52DAP	1.04213	0.708
57DAP/7DAP	0.98307	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92078	0.246
17DAP/reference	0.8	0.011
27DAP/reference	0.75294	0.01
39DAP/reference	0.86579	0.064
41DAP/reference	0.86572	0.098
42DAP/reference	0.74901	0.015
43DAP/reference	0.83156	0.026
47DAP/reference	0.87542	0.222
52DAP/reference	0.93067	0.137
57DAP/reference	0.83428	0.043

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04682	0.463
17DAP/reference	1.10317	0.027
27DAP/reference	1.09397	0.338
39DAP/reference	1.104	0.29
41DAP/reference	1.06092	0.614
42DAP/reference	0.99286	0.655
43DAP/reference	1.05312	0.509
47DAP/reference	0.97929	0.328
52DAP/reference	1.08789	0.057
57DAP/reference	1.04409	0.538

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84063	0.052
17DAP/reference	0.98809	0.751
27DAP/reference	0.78962	0.031
39DAP/reference	0.84207	0.076
41DAP/reference	0.86326	0.107
42DAP/reference	0.78838	0.134
43DAP/reference	0.90451	0.246
47DAP/reference	1.00106	0.754
52DAP/reference	0.71575	0.204
57DAP/reference	1.08311	0.625

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.06164	0.966
26DAP/20DAP	0.99341	1
34DAP/26DAP	1.00042	1
51DAP/34DAP	0.97954	0.873
52DAP/51DAP	1.02359	0.776
53DAP/52DAP	1.00104	0.983
55DAP/53DAP	0.98705	0.807
57DAP/55DAP	0.97824	0.859
62DAP/57DAP	0.96573	0.994
68DAP/62DAP	1.07846	0.878
68DAP/14DAP	1.00484	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.00508	1

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.12094	0.666
Mature Green Tomato/Ripe Tomato	0.89878	0.287
Immature Eggplant/Mature Eggplant	1.73134	0.13
Ripe Pepper/Ripe Tomato	1.23408	1
Mature Eggplant/Ripe Tomato	0.77896	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.98475	0.961
1-1-2/M82	1.04311	1
12-2/M82	1.02047	1
12-4/M82	0.99865	1
1-3/M82	0.91176	1
2-1-1/M82	0.92496
2-1/M82	N/A	N/A
2-6/M82	0.87713	1
3-2/M82	1.03424
4-1-1/M82	0.86799	1
4-1/M82	0.89135
4-3-2/M82	1.17096
4-3/M82	0.91544	1
5-3/M82	1.07928	1
6-2/M82	0.88351	1
6-3/M82	0.84797
7-1/M82	1.22
7-2/M82	1.01299	1
9-3-2/M82	0.69027

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.26756	0.277
IL2-6/WTpooled	0.72505	0.337
IL7-5/WTpooled	0.76304	1
IL7-3/WTpooled	1.63856	1
IL12-4/WTpooled	1.07117	0.516
IL1-4/WTpooled	0.97694	0.699
WT/WTpooled	1.02812	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	1.2198	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.05733	0.894
DC3000/delta hrp 6h	1.2133	1
DC3000/delta hrp 12h	1.07024	1
DC3000/delta hrp 24h	0.95321	0.654

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.32924	0.042
DC3000 delta B/DC3000 delta AB	1.2605	0.124

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.78043	0.328
Exp 36h	1.10104	1
Exp 60h	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01884	1
Var 0h	1.67479	0.936
Var 12h I row2-row1	1.35581	0.506
Var 12h NI row2-row1	1.07693	1
Var 36h I row2-row1	0.94333	1
Var 36h NI row2-row1	0.96261	0.791
Var 60h I row2-row1	1.28112	0.562
Var 60h NI row2-row1	1.09185	1
Time course 0hI-0hNI	0.97242	0.881
Time course 12hI-12hNI	1.05812	0.526
Time course 36hI-36hNI	1.01855	1
Time course 60hI-60hNI	1.193	0.022

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)	1.02272	0.654
transgenic ySAMdc/azygous control (breaker)	1.13659	0.248
transgenic ySAMdc/azygous control (red)	1.06647	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.0045	0.811

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.03211	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.10406	1
Manapal/WT (break)	1.04392	1
Manapal/WT (red)	1.1267	0.413