Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.2.16.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.8906	0.445
27DAP/17DAP	1.11282	0.873
39DAP/27DAP	1.12184	0.938
41DAP/39DAP	1.16611	0.96
42DAP/41DAP	1.06538	0.999
43DAP/42DAP	0.87948	0.744
47DAP/43DAP	1.0877	0.999
52DAP/47DAP	1.15405	0.89
57DAP/52DAP	0.89309	0.86

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.0721	0.662
17DAP/reference	0.9452	0.26
27DAP/reference	0.97414	0.457
39DAP/reference	1.0082	0.786
41DAP/reference	0.88123	0.085
42DAP/reference	0.99816	0.628
43DAP/reference	0.9622	0.394
47DAP/reference	0.98413	0.445
52DAP/reference	1.00165	0.768
57DAP/reference	1.03344	0.31

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.07807	0.271
27DAP/17DAP	1.04339	0.909
39DAP/27DAP	0.9587	0.536
41DAP/39DAP	0.95737	0.63
42DAP/41DAP	1.01011	0.999
43DAP/42DAP	1.0059	0.699
47DAP/43DAP	1.00002	1
52DAP/47DAP	0.95331	0.824
57DAP/52DAP	0.97502	0.716
57DAP/7DAP	1.03124	0.204

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90075	0.1
17DAP/reference	0.88857	0.012
27DAP/reference	0.90075	0.016
39DAP/reference	1.00389	1
41DAP/reference	1.05055	0.375
42DAP/reference	1.03487	0.534
43DAP/reference	0.97622	0.115
47DAP/reference	0.95198	0.383
52DAP/reference	1.00032	1
57DAP/reference	0.97545	0.477

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.0182	0.842
17DAP/reference	1.00208	1
27DAP/reference	0.93007	0.188
39DAP/reference	0.98442	0.509
41DAP/reference	0.88612	0.081
42DAP/reference	0.89836	0.042
43DAP/reference	0.95691	0.292
47DAP/reference	0.92979	0.073
52DAP/reference	0.90415	0.027
57DAP/reference	0.95364	0.194

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.89217	0.03
17DAP/reference	0.92324	0.189
27DAP/reference	0.87169	0.026
39DAP/reference	0.88055	0.007
41DAP/reference	0.90878	0.07
42DAP/reference	0.87248	0.015
43DAP/reference	0.89928	0.025
47DAP/reference	0.90975	0.145
52DAP/reference	0.90642	0.144
57DAP/reference	0.84342	0.019

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.01574	0.966
26DAP/20DAP	1.07921	0.663
34DAP/26DAP	1.04477	1
51DAP/34DAP	1.06293	0.535
52DAP/51DAP	0.99698	1
53DAP/52DAP	1.1265	0.47
55DAP/53DAP	0.9923	0.908
57DAP/55DAP	1.08991	0.898
62DAP/57DAP	1.19211	0.8
68DAP/62DAP	0.9601	0.787
68DAP/14DAP	1.22811	0.041

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.00235	1

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.87471	0.401
Mature Green Tomato/Ripe Tomato	0.89491	0.317
Immature Eggplant/Mature Eggplant	1.00893	1
Ripe Pepper/Ripe Tomato	0.96851	1
Mature Eggplant/Ripe Tomato	0.63373	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.96218	0.944
1-1-2/M82	0.88473	1
12-2/M82	0.99935	1
12-4/M82	0.99935	1
1-3/M82	0.96202	0.441
2-1-1/M82	0.85659	0.465
2-1/M82	0.92389	1
2-6/M82	0.93175	1
3-2/M82	0.98699	1
4-1-1/M82	0.96475	1
4-1/M82	0.97877	1
4-3-2/M82	0.89643	0.698
4-3/M82	0.92928	1
5-3/M82	0.95229	1
6-2/M82	1.13067	1
6-3/M82	1.04888	1
7-1/M82	1.00108
7-2/M82	0.91369	0.881
9-3-2/M82	1.0095	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.14017	0.659
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.19717	1
IL12-4/WTpooled	1.02546	1
IL1-4/WTpooled	1.30541	1
WT/WTpooled	1.00304	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	0.89493	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.96704	1
DC3000/delta hrp 6h	1.32406	1
DC3000/delta hrp 12h	1.10695	1
DC3000/delta hrp 24h	1.08364	0.336

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.21025	0.042
DC3000 delta B/DC3000 delta AB	1.12168	0.415

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.88028	1
Exp 36h	1.1506	0.409
Exp 60h	1.14685	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99123	1
Var 0h	0.60529	0.457
Var 12h I row2-row1	1.12778	0.283
Var 12h NI row2-row1	1.09655	1
Var 36h I row2-row1	1.08082	1
Var 36h NI row2-row1	0.93552	0.706
Var 60h I row2-row1	0.9974	1
Var 60h NI row2-row1	1.04024	0.904
Time course 0hI-0hNI	1.04872	0.867
Time course 12hI-12hNI	1.04601	0.741
Time course 36hI-36hNI	1.05329	0.355
Time course 60hI-60hNI	1.63132	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)	0.95449	0.614
transgenic ySAMdc/azygous control (breaker)	1.25891	0.248
transgenic ySAMdc/azygous control (red)	1.22552	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.96437	0.104

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.07185	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.99036	1
Manapal/WT (break)	0.78695	1
Manapal/WT (red)	0.94519	0.728