Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.4.6.17

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.84385	0.364
27DAP/17DAP	0.98201	1
39DAP/27DAP	1.02341	1
41DAP/39DAP	0.98325	0.852
42DAP/41DAP	0.9241	1
43DAP/42DAP	0.94327	0.694
47DAP/43DAP	1.05485	0.943
52DAP/47DAP	1.17884	0.683
57DAP/52DAP	0.97655	0.966

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.05172	0.32
17DAP/reference	0.96141	0.208
27DAP/reference	0.99648	0.847
39DAP/reference	1.02287	0.842
41DAP/reference	1.02619	0.587
42DAP/reference	1.06445	0.048
43DAP/reference	1.0056	0.928
47DAP/reference	0.97996	0.258
52DAP/reference	1.07213	0.607
57DAP/reference	1.09188	0.031

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.63107	0.055
27DAP/17DAP	1.1942	0.3
39DAP/27DAP	0.93393	0.579
41DAP/39DAP	1.02688	0.895
42DAP/41DAP	0.96772	0.717
43DAP/42DAP	1.03469	0.585
47DAP/43DAP	0.90371	0.188
52DAP/47DAP	0.86051	0.507
57DAP/52DAP	0.88036	0.322
57DAP/7DAP	0.62276	0.186

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.10717	0.351
17DAP/reference	0.90334	0.22
27DAP/reference	0.94135	0.231
39DAP/reference	0.95626	0.354
41DAP/reference	0.87936	0.09
42DAP/reference	0.88865	0.169
43DAP/reference	0.75095	0.013
47DAP/reference	0.89059	0.293
52DAP/reference	0.86193	0.15
57DAP/reference	0.83438	0.028

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98896	0.786
17DAP/reference	1.1033	0.12
27DAP/reference	1.09759	0.239
39DAP/reference	0.9961	0.661
41DAP/reference	1.00045	0.718
42DAP/reference	1.01686	0.934
43DAP/reference	1.0801	0.575
47DAP/reference	0.99686	0.714
52DAP/reference	1.0002	1
57DAP/reference	0.98899	0.68

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01246	1
17DAP/reference	1.031	0.689
27DAP/reference	0.76178	0.051
39DAP/reference	0.97773	0.544
41DAP/reference	0.97536	0.56
42DAP/reference	0.91477	0.22
43DAP/reference	1.06534	0.388
47DAP/reference	1.0105	1
52DAP/reference	0.81623	0.197
57DAP/reference	1.03588	0.531

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.96965	1
26DAP/20DAP	1.72454	0.097
34DAP/26DAP	0.92618	0.811
51DAP/34DAP	0.99686	0.924
52DAP/51DAP	0.96559	1
53DAP/52DAP	1.07983	0.517
55DAP/53DAP	0.96323	0.735
57DAP/55DAP	0.78825	0.132
62DAP/57DAP	0.89509	0.466
68DAP/62DAP	0.92661	0.668
68DAP/14DAP	1.03287	0.802

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.75731	0.045

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.2953	0.089
Mature Green Tomato/Ripe Tomato	2.42056	0.015
Immature Eggplant/Mature Eggplant	1.2421	0.065
Ripe Pepper/Ripe Tomato	2.10391	1
Mature Eggplant/Ripe Tomato	3.28311	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.00726	1
1-1-2/M82	1.13965	1
12-2/M82	1.10217	1
12-4/M82	1.08749
1-3/M82	0.82264	0.501
2-1-1/M82	1.01855	1
2-1/M82	N/A	N/A
2-6/M82	1.19333	0.695
3-2/M82	0.86586	0.451
4-1-1/M82	1.18708	0.977
4-1/M82	1.19658
4-3-2/M82	1.16407	0.253
4-3/M82	0.92967	0.72
5-3/M82	0.85414	0.363
6-2/M82	0.79534
6-3/M82	0.79803
7-1/M82	1.115
7-2/M82	0.95066	1
9-3-2/M82	1.04466	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	0.70791
IL12-4/WTpooled	1.04753
IL1-4/WTpooled	0.96741	1
WT/WTpooled	N/A	N/A

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	1.04163	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.12238	0.921
DC3000/delta hrp 6h	1.02796	0.95
DC3000/delta hrp 12h	1.05356	1
DC3000/delta hrp 24h	0.96012	0.736

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.68474	0.026
DC3000 delta B/DC3000 delta AB	0.78836	0.037

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.83787	1
Exp 36h	1.09773	1
Exp 60h	0.99673	0.994

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99337	1
Var 0h	1.92271	0.936
Var 12h I row2-row1	1.22794	0.209
Var 12h NI row2-row1	0.86394	0.394
Var 36h I row2-row1	0.99913	1
Var 36h NI row2-row1	1.25789	0.276
Var 60h I row2-row1	1.38566	0.562
Var 60h NI row2-row1	1.20628	0.5
Time course 0hI-0hNI	0.9221	0.458
Time course 12hI-12hNI	0.91464	0.225
Time course 36hI-36hNI	0.68232	0.023
Time course 60hI-60hNI	0.38447	0.009

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)	0.93329	0.485
transgenic ySAMdc/azygous control (breaker)	1.28927	0.248
transgenic ySAMdc/azygous control (red)	1.20177	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.06883	0.059

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.55138	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.84393	1
Manapal/WT (break)	1.09934	0.381
Manapal/WT (red)	1.49282	0.164