Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.4.12.13

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.93044	0.578
27DAP/17DAP	1.0399	1
39DAP/27DAP	1.01182	0.82
41DAP/39DAP	1.29599	0.278
42DAP/41DAP	1.31089	0.481
43DAP/42DAP	1.01747	0.94
47DAP/43DAP	0.86664	0.568
52DAP/47DAP	1.18942	0.699
57DAP/52DAP	0.94436	0.938

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95927	0.3
17DAP/reference	0.92592	0.057
27DAP/reference	0.87412	0.035
39DAP/reference	0.96775	0.391
41DAP/reference	0.95888	0.434
42DAP/reference	0.96014	0.107
43DAP/reference	1.07366	0.252
47DAP/reference	0.93044	0.065
52DAP/reference	0.91716	0.3
57DAP/reference	0.95071	0.156

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.83075	0.245
27DAP/17DAP	1.06342	0.887
39DAP/27DAP	1.0321	0.751
41DAP/39DAP	0.98836	1
42DAP/41DAP	1.03132	0.824
43DAP/42DAP	0.96595	0.684
47DAP/43DAP	1.08507	0.749
52DAP/47DAP	1.01696	0.956
57DAP/52DAP	1.04716	0.745
57DAP/7DAP	1.10943	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87651	0.203
17DAP/reference	0.91878	0.028
27DAP/reference	0.88622	0.01
39DAP/reference	0.89167	0.02
41DAP/reference	0.87271	0.022
42DAP/reference	0.88882	0.012
43DAP/reference	0.80879	0.011
47DAP/reference	0.79443	0.036
52DAP/reference	0.82154	0.012
57DAP/reference	0.8076	0.008

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91054	0.248
17DAP/reference	0.95601	0.253
27DAP/reference	0.92823	0.257
39DAP/reference	0.81984	0.047
41DAP/reference	0.90096	0.194
42DAP/reference	0.82056	0.016
43DAP/reference	1.03694	0.89
47DAP/reference	0.9807	0.487
52DAP/reference	0.95615	0.239
57DAP/reference	1.09471	0.494

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.83662	0.061
17DAP/reference	0.94194	0.243
27DAP/reference	0.84374	0.036
39DAP/reference	0.82739	0.01
41DAP/reference	0.85085	0.024
42DAP/reference	0.8426	0.028
43DAP/reference	0.8659	0.079
47DAP/reference	1.02781	0.847
52DAP/reference	0.84791	0.189
57DAP/reference	0.78375	0.031

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.96194	1
26DAP/20DAP	1.50626	0.099
34DAP/26DAP	1.12654	0.819
51DAP/34DAP	0.89859	0.328
52DAP/51DAP	0.9326	1
53DAP/52DAP	1.07728	0.623
55DAP/53DAP	1.09059	0.361
57DAP/55DAP	0.88424	0.437
62DAP/57DAP	0.94424	0.871
68DAP/62DAP	0.99214	0.834
68DAP/14DAP	1.06116	0.85

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.61313	0.065

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	7.29529	0.058
Mature Green Tomato/Ripe Tomato	0.86206	0.256
Immature Eggplant/Mature Eggplant	16.7842	0.05
Ripe Pepper/Ripe Tomato	4.41464	0.256
Mature Eggplant/Ripe Tomato	1.70827	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.02914	1
1-1-2/M82	0.94644	1
12-2/M82	1.20995	1
12-4/M82	0.94464	1
1-3/M82	1.0049	1
2-1-1/M82	1.22577	0.764
2-1/M82	1.58611	0.345
2-6/M82	0.96811	1
3-2/M82	0.99716	1
4-1-1/M82	1.05608	1
4-1/M82	0.92177	0.737
4-3-2/M82	0.97339	1
4-3/M82	1.03783	1
5-3/M82	1.14094	1
6-2/M82	1.01724	1
6-3/M82	1.00992	1
7-1/M82	1.0268	1
7-2/M82	0.97629	0.54
9-3-2/M82	1.0902	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.59393	0.243
IL2-6/WTpooled	1.06846	0.788
IL7-5/WTpooled	0.73785	1
IL7-3/WTpooled	0.71962	0.31
IL12-4/WTpooled	0.9428	1
IL1-4/WTpooled	0.75434	0.435
WT/WTpooled	1.04599	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	1.75266	0.193

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.01058	1
DC3000/delta hrp 6h	1.03961	1
DC3000/delta hrp 12h	1.06467	1
DC3000/delta hrp 24h	1.12229	0.221

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.41851	0.16
DC3000 delta B/DC3000 delta AB	1.30309	0.198

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.34162	1
Exp 36h	1.58246	1
Exp 60h	1.41567	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01231	1
Var 0h	0.54044	1
Var 12h I row2-row1	0.84486	0.627
Var 12h NI row2-row1	1.20147	0.649
Var 36h I row2-row1	1.14705	1
Var 36h NI row2-row1	0.69576	0.522
Var 60h I row2-row1	0.65659	0.285
Var 60h NI row2-row1	0.78037	0.408
Time course 0hI-0hNI	1.08928	0.603
Time course 12hI-12hNI	1.10999	0.145
Time course 36hI-36hNI	2.21448	0.004
Time course 60hI-60hNI	19.8919	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)	1.34784	0.722
transgenic ySAMdc/azygous control (breaker)	0.23871	0.131
transgenic ySAMdc/azygous control (red)	1.66007	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.0182	0.854

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.40923	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	66.2458	0.09
Manapal/WT (break)	1.32757	1
Manapal/WT (red)	2.73381	0.222