Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.3.17.2

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.97433	0.752
27DAP/17DAP	1.3903	0.642
39DAP/27DAP	1.15496	0.796
41DAP/39DAP	0.91729	0.645
42DAP/41DAP	1.09246	0.974
43DAP/42DAP	1.08837	1
47DAP/43DAP	1.34374	0.391
52DAP/47DAP	0.92945	0.724
57DAP/52DAP	1.21435	0.948

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96952	0.513
17DAP/reference	1.05426	0.764
27DAP/reference	1.32714	0.011
39DAP/reference	1.24516	0.066
41DAP/reference	1.00652	1
42DAP/reference	1.27512	0.007
43DAP/reference	1.22733	0.01
47DAP/reference	1.66057	0.001
52DAP/reference	1.74917	0.007
57DAP/reference	1.38732	0.012

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.1807	0.062
27DAP/17DAP	1.29516	0.084
39DAP/27DAP	1.09482	0.575
41DAP/39DAP	0.91322	0.781
42DAP/41DAP	1.46878	0.308
43DAP/42DAP	1.01837	1
47DAP/43DAP	0.99168	0.954
52DAP/47DAP	1.12153	0.703
57DAP/52DAP	1.16023	0.368
57DAP/7DAP	3.86676	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99559	0.758
17DAP/reference	0.90393	0.072
27DAP/reference	1.07151	0.371
39DAP/reference	1.29898	0.036
41DAP/reference	1.0836	0.363
42DAP/reference	1.24846	0.1
43DAP/reference	1.15433	0.035
47DAP/reference	1.26388	0.019
52DAP/reference	0.9964	0.74
57DAP/reference	1.07661	0.799

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.82757	0.022
17DAP/reference	0.96385	0.461
27DAP/reference	0.99034	0.642
39DAP/reference	1.12745	0.29
41DAP/reference	0.99517	0.601
42DAP/reference	1.09127	0.166
43DAP/reference	0.83735	0.132
47DAP/reference	0.98242	0.512
52DAP/reference	0.99129	0.619
57DAP/reference	0.76801	0.024

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91595	0.268
17DAP/reference	0.86539	0.103
27DAP/reference	0.87936	0.058
39DAP/reference	0.8929	0.015
41DAP/reference	0.79857	0.037
42DAP/reference	0.90662	0.287
43DAP/reference	1.18213	0.164
47DAP/reference	1.40851	0.017
52DAP/reference	1.40877	0.083
57DAP/reference	1.61635	0.01

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.97098	1
26DAP/20DAP	1.51998	0.197
34DAP/26DAP	0.96186	0.936
51DAP/34DAP	1.12395	0.339
52DAP/51DAP	0.87628	1
53DAP/52DAP	1.36489	0.055
55DAP/53DAP	0.8281	0.181
57DAP/55DAP	0.84037	0.375
62DAP/57DAP	0.85869	0.681
68DAP/62DAP	1.05932	0.936
68DAP/14DAP	1.16779	0.714

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	2.14085	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.26984	0.287
Mature Green Tomato/Ripe Tomato	0.49116	0.025
Immature Eggplant/Mature Eggplant	1.01314	1
Ripe Pepper/Ripe Tomato	0.445	0.224
Mature Eggplant/Ripe Tomato	0.64446	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.05232	1
1-1-2/M82	1.11008	0.977
12-2/M82	1.00574	1
12-4/M82	1.2604	1
1-3/M82	1.76081	0.277
2-1-1/M82	0.99038	1
2-1/M82	1.0816	1
2-6/M82	0.99532	1
3-2/M82	1.02203	1
4-1-1/M82	1.31632	0.966
4-1/M82	2.65247	0.853
4-3-2/M82	1.23267	0.508
4-3/M82	1.37543	1
5-3/M82	0.94211	0.642
6-2/M82	0.98329	1
6-3/M82	1.03134	1
7-1/M82	0.88902	0.476
7-2/M82	1.37169	0.302
9-3-2/M82	1.34655	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	N/A	N/A
IL12-4/WTpooled	0.77926
IL1-4/WTpooled	0.87193	0.834
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	0.98264	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.01751	1
DC3000/delta hrp 6h	1.05746	0.95
DC3000/delta hrp 12h	0.97733	1
DC3000/delta hrp 24h	1.20893	0.356

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.34482	0.045
DC3000 delta B/DC3000 delta AB	1.41363	0.089

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.02298	1
Exp 36h	1.02075	1
Exp 60h	1.00034	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98553	1
Var 0h	0.98973	1
Var 12h I row2-row1	0.87678	0.338
Var 12h NI row2-row1	1.07439	0.649
Var 36h I row2-row1	1.16139	0.309
Var 36h NI row2-row1	0.96293	0.852
Var 60h I row2-row1	0.79911	0.582
Var 60h NI row2-row1	0.85365	0.63
Time course 0hI-0hNI	1.01711	1
Time course 12hI-12hNI	1.06113	0.773
Time course 36hI-36hNI	1.17786	0.089
Time course 60hI-60hNI	1.93947	0.008

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)	0.97585	0.722
transgenic ySAMdc/azygous control (breaker)	0.95151	1
transgenic ySAMdc/azygous control (red)	1.0682	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.05013	0.854

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.65554	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.82661	1
Manapal/WT (break)	0.81137	1
Manapal/WT (red)	0.67414	0.181