Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.1.18.11

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.00892	0.839
27DAP/17DAP	1.30251	0.742
39DAP/27DAP	1.23183	0.579
41DAP/39DAP	1.09043	0.833
42DAP/41DAP	1.53573	0.159
43DAP/42DAP	0.75625	0.456
47DAP/43DAP	1.23613	0.502
52DAP/47DAP	0.60053	0.057
57DAP/52DAP	1.01314	0.988

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04682	0.71
17DAP/reference	1.01413	1
27DAP/reference	1.10041	0.696
39DAP/reference	0.99908	1
41DAP/reference	1.08964	0.552
42DAP/reference	1.17744	0.043
43DAP/reference	0.92036	0.103
47DAP/reference	0.93968	0.191
52DAP/reference	1.04181	0.766
57DAP/reference	1.079	0.109

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	2.42295	0.036
27DAP/17DAP	0.99132	0.943
39DAP/27DAP	3.01472	0.044
41DAP/39DAP	2.68934	0.009
42DAP/41DAP	1.19696	0.694
43DAP/42DAP	0.98183	0.774
47DAP/43DAP	4.91797	0.012
52DAP/47DAP	0.65808	0.372
57DAP/52DAP	2.82252	0.027
57DAP/7DAP	23.4862	0.207

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.25956	0.035
17DAP/reference	1.96803	0.006
27DAP/reference	1.52793	0.014
39DAP/reference	2.72424	0.006
41DAP/reference	1.8327	0.015
42DAP/reference	2.66248	0.006
43DAP/reference	2.92978	0.007
47DAP/reference	2.61326	0.014
52DAP/reference	2.65979	0.007
57DAP/reference	2.3455	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.78313	0.062
17DAP/reference	0.62448	0.005
27DAP/reference	0.89397	0.282
39DAP/reference	1.08637	0.571
41DAP/reference	1.17844	0.188
42DAP/reference	1.0306	1
43DAP/reference	1.35975	0.407
47DAP/reference	1.54986	0.025
52DAP/reference	0.85893	0.027
57DAP/reference	1.75118	0.057

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.66634	0.034
17DAP/reference	1.10757	1
27DAP/reference	1.64022	0.024
39DAP/reference	1.68556	0.017
41DAP/reference	1.55376	0.016
42DAP/reference	1.42391	0.099
43DAP/reference	1.74323	0.018
47DAP/reference	0.77674	0.034
52DAP/reference	1.70484	0.066
57DAP/reference	2.41178	0.009

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.00405	1
26DAP/20DAP	1.11529	1
34DAP/26DAP	0.82402	0.35
51DAP/34DAP	1.72529	0.565
52DAP/51DAP	1.44358	0.358
53DAP/52DAP	1.36458	0.565
55DAP/53DAP	1.40824	0.444
57DAP/55DAP	1.31966	0.643
62DAP/57DAP	0.4147	0.003
68DAP/62DAP	1.53119	0.174
68DAP/14DAP	1.39832	0.091

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	13.0866	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.15614	0.058
Mature Green Tomato/Ripe Tomato	0.82597	0.2
Immature Eggplant/Mature Eggplant	3.93153	0.05
Ripe Pepper/Ripe Tomato	0.08121	0.224
Mature Eggplant/Ripe Tomato	0.29096	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.80571	0.634
1-1-2/M82	1.03396	1
12-2/M82	1.87757
12-4/M82	1.18912	1
1-3/M82	1.79748
2-1-1/M82	0.58373
2-1/M82	0.83615	0.325
2-6/M82	0.69411
3-2/M82	1.01005
4-1-1/M82	0.7929	1
4-1/M82	0.92868
4-3-2/M82	0.91628	0.698
4-3/M82	0.94538	1
5-3/M82	1.05305	1
6-2/M82	2.81028	0.253
6-3/M82	0.94739	0.857
7-1/M82	0.84019	0.509
7-2/M82	0.77051	0.54
9-3-2/M82	0.87776

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	N/A	N/A
IL1-4/WTpooled	N/A	N/A
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	1.63203	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.01778	0.921
DC3000/delta hrp 6h	1.40105	0.978
DC3000/delta hrp 12h	1.02985	1
DC3000/delta hrp 24h	0.90236	0.387

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	2.29514	0.045
DC3000 delta B/DC3000 delta AB	2.18079	0.095

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.056	1
Exp 36h	2.46624	0.693
Exp 60h	2.03782	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	1.02728	1
Var 0h	1.5384	0.594
Var 12h I row2-row1	1.02851	0.795
Var 12h NI row2-row1	1.67267	0.34
Var 36h I row2-row1	0.67624	0.575
Var 36h NI row2-row1	0.84101	0.584
Var 60h I row2-row1	0.47407	0.285
Var 60h NI row2-row1	0.99125	1
Time course 0hI-0hNI	1.24283	0.537
Time course 12hI-12hNI	1.18932	0.647
Time course 36hI-36hNI	3.23999	0.005
Time course 60hI-60hNI	15.0706	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)	1.24956	0.321
transgenic ySAMdc/azygous control (breaker)	0.84115	0.251
transgenic ySAMdc/azygous control (red)	0.96257	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.94968	0.177

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.59512	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.76395	1
Manapal/WT (break)	0.86317	1
Manapal/WT (red)	0.38433	0.216