Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.1.3.1

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.91125	0.046
27DAP/17DAP	1.09586	0.873
39DAP/27DAP	2.03561	0.042
41DAP/39DAP	0.75712	0.158
42DAP/41DAP	2.17274	0.502
43DAP/42DAP	1.32037	0.956
47DAP/43DAP	0.85117	0.484
52DAP/47DAP	1.09124	0.991
57DAP/52DAP	0.76144	0.666

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.76879	0.024
17DAP/reference	0.91779	0.194
27DAP/reference	1.03038	0.782
39DAP/reference	0.83756	0.088
41DAP/reference	0.84005	0.01
42DAP/reference	1.25281	0.029
43DAP/reference	1.02402	0.861
47DAP/reference	1.08596	1
52DAP/reference	0.77841	0.069
57DAP/reference	0.81912	0.248

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.9392	0.036
27DAP/17DAP	0.85435	0.312
39DAP/27DAP	0.94943	0.66
41DAP/39DAP	0.94501	0.849
42DAP/41DAP	0.99906	0.841
43DAP/42DAP	1.82933	0.014
47DAP/43DAP	1.05288	0.827
52DAP/47DAP	0.78432	0.101
57DAP/52DAP	0.61789	0.067
57DAP/7DAP	1.1085	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.09203	0.472
17DAP/reference	1.06913	0.018
27DAP/reference	1.03206	0.551
39DAP/reference	2.1571	0.005
41DAP/reference	1.29617	0.034
42DAP/reference	2.49239	0.007
43DAP/reference	3.36891	0.006
47DAP/reference	3.82272	0.014
52DAP/reference	2.74934	0.007
57DAP/reference	2.89996	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.68622	0.006
17DAP/reference	1.06625	0.961
27DAP/reference	1.04556	0.988
39DAP/reference	1.31469	0.182
41DAP/reference	0.99135	0.615
42DAP/reference	1.52939	0.008
43DAP/reference	0.9706	0.561
47DAP/reference	1.57676	0.008
52DAP/reference	1.02342	0.168
57DAP/reference	1.11577	0.916

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.83258	0.033
17DAP/reference	1.18568	0.17
27DAP/reference	1.21456	0.029
39DAP/reference	1.24296	0.036
41DAP/reference	1.25932	0.015
42DAP/reference	2.36097	0.007
43DAP/reference	2.61076	0.007
47DAP/reference	1.41931	0.008
52DAP/reference	1.75604	0.041
57DAP/reference	1.359	0.228

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.89634	1
26DAP/20DAP	1.95811	0.099
34DAP/26DAP	1.02221	1
51DAP/34DAP	0.74194	0.066
52DAP/51DAP	0.89598	1
53DAP/52DAP	1.00676	0.961
55DAP/53DAP	0.84923	0.181
57DAP/55DAP	0.84119	0.327
62DAP/57DAP	1.04485	1
68DAP/62DAP	0.67513	0.177
68DAP/14DAP	0.66478	0.09

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.388	0.064

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.95847	0.648
Mature Green Tomato/Ripe Tomato	1.45796	0.095
Immature Eggplant/Mature Eggplant	0.91951	0.366
Ripe Pepper/Ripe Tomato	2.09748	0.258
Mature Eggplant/Ripe Tomato	2.82093	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.08444	1
1-1-2/M82	0.95228
12-2/M82	0.93404	0.955
12-4/M82	1.22175	1
1-3/M82	1.11141	0.479
2-1-1/M82	0.88432	0.465
2-1/M82	0.58253	0.322
2-6/M82	0.97337	1
3-2/M82	1.18724	0.388
4-1-1/M82	1.17443	1
4-1/M82	0.8724
4-3-2/M82	1.87134	0.262
4-3/M82	1.05881	1
5-3/M82	0.99284	1
6-2/M82	1.10545	1
6-3/M82	1.06565	1
7-1/M82	0.99909	1
7-2/M82	1.05383	1
9-3-2/M82	1.24202

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.90426	0.321
IL2-6/WTpooled	1.00679	1
IL7-5/WTpooled	0.82581	1
IL7-3/WTpooled	1.03647	1
IL12-4/WTpooled	0.7928	0.71
IL1-4/WTpooled	1.0607	1
WT/WTpooled	0.97002	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	1.03751	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.99823	1
DC3000/delta hrp 6h	1.28918	1
DC3000/delta hrp 12h	1.15677	1
DC3000/delta hrp 24h	1.11861	0.655

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.98287	1
DC3000 delta B/DC3000 delta AB	1.01115	0.748

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.19802	1
Exp 36h	0.95596	0.943
Exp 60h	1.17412	1

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

hybridization	ratio	FDR (corrected p value)
self-self	N/A	N/A
Var 0h	1.15133	0.421
Var 12h I row2-row1	0.86577	0.39
Var 12h NI row2-row1	1.16682	1
Var 36h I row2-row1	1.21631	0.368
Var 36h NI row2-row1	0.97972	0.852
Var 60h I row2-row1	0.94812	0.952
Var 60h NI row2-row1	1.26878	0.904
Time course 0hI-0hNI	1.15411	0.63
Time course 12hI-12hNI	0.98856	0.991
Time course 36hI-36hNI	0.8225	0.187
Time course 60hI-60hNI	1.92042	0.015

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)	0.8168	0.377
transgenic ySAMdc/azygous control (breaker)	0.26745	0.119
transgenic ySAMdc/azygous control (red)	1.08046	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.20988	0.073

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.14827	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.96951	1
Manapal/WT (break)	0.9638	1
Manapal/WT (red)	0.49799	0.181