Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.4.4.13

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.128	0.523
27DAP/17DAP	1.03215	0.93
39DAP/27DAP	0.93836	0.62
41DAP/39DAP	0.97111	0.876
42DAP/41DAP	0.89777	1
43DAP/42DAP	1.10042	0.991
47DAP/43DAP	0.95429	0.804
52DAP/47DAP	0.93609	0.8
57DAP/52DAP	0.99807	0.985

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.957	0.097
17DAP/reference	0.99502	0.904
27DAP/reference	1.01365	0.735
39DAP/reference	0.98279	0.6
41DAP/reference	1.01082	0.808
42DAP/reference	1.00688	1
43DAP/reference	1.00512	0.928
47DAP/reference	0.99503	0.636
52DAP/reference	0.95817	0.393
57DAP/reference	1.08443	0.211

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.14145	0.662
27DAP/17DAP	1.0516	0.9
39DAP/27DAP	0.93883	0.507
41DAP/39DAP	1.01235	0.895
42DAP/41DAP	1.00075	0.932
43DAP/42DAP	1.0237	0.049
47DAP/43DAP	0.98893	0.93
52DAP/47DAP	0.97182	0.801
57DAP/52DAP	0.95103	0.395
57DAP/7DAP	0.96879	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.82835
17DAP/reference	0.93427	0.072
27DAP/reference	0.9234	0.03
39DAP/reference	0.9801	0.354
41DAP/reference	0.98693	0.538
42DAP/reference	1.06107	0.046
43DAP/reference	0.95045	0.072
47DAP/reference	0.89533	0.293
52DAP/reference	0.96382	0.398
57DAP/reference	0.90923	0.128

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04598	0.732
17DAP/reference	0.93486	0.326
27DAP/reference	1.08935	0.573
39DAP/reference	0.99169	0.569
41DAP/reference	0.93128	0.373
42DAP/reference	1.0187	0.951
43DAP/reference	1.02086	1
47DAP/reference	0.9776	0.227
52DAP/reference	1.11047	0.882
57DAP/reference	0.91995	0.125

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03051	0.433
17DAP/reference	0.95934	0.129
27DAP/reference	1.10904
39DAP/reference	0.97899	0.328
41DAP/reference	0.94591	0.264
42DAP/reference	0.91901	0.019
43DAP/reference	0.97399	0.432
47DAP/reference	1.00834	1
52DAP/reference	0.97066	0.623
57DAP/reference	0.96499	0.268

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.96298	0.961
26DAP/20DAP	0.93619	0.512
34DAP/26DAP	0.97246	0.826
51DAP/34DAP	1.0075	0.949
52DAP/51DAP	0.97755	1
53DAP/52DAP	1.04413	0.845
55DAP/53DAP	0.91398	0.417
57DAP/55DAP	1.20981
62DAP/57DAP	1.55461
68DAP/62DAP	0.99578	0.939
68DAP/14DAP	1.34385	0.161

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.96766	0.576

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.12939	0.417
Mature Green Tomato/Ripe Tomato	0.74568	0.04
Immature Eggplant/Mature Eggplant	1.26918	0.181
Ripe Pepper/Ripe Tomato	1.41901	1
Mature Eggplant/Ripe Tomato	1.87117

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.97305	0.961
1-1-2/M82	0.98583	0.754
12-2/M82	1.0008	1
12-4/M82	0.994	1
1-3/M82	0.94826	0.378
2-1-1/M82	0.86218	0.465
2-1/M82	1.12414	1
2-6/M82	0.96917	1
3-2/M82	1.00018	1
4-1-1/M82	1.01948	1
4-1/M82	0.97677	1
4-3-2/M82	0.96235	1
4-3/M82	0.93578	0.72
5-3/M82	1.02725	1
6-2/M82	1.05323	1
6-3/M82	0.99526	1
7-1/M82	1.0534	1
7-2/M82	0.93707	0.599
9-3-2/M82	0.89605	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.41379
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	0.86343	0.581
IL1-4/WTpooled	1.02676	1
WT/WTpooled	0.95159	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	2.25057	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.03843	0.921
DC3000/delta hrp 6h	1.11193	1
DC3000/delta hrp 12h	1.02189	1
DC3000/delta hrp 24h	1.01889	0.71

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.26829	0.042
DC3000 delta B/DC3000 delta AB	1.19037	0.167

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.39112	1
Exp 36h	1.51935	0.693
Exp 60h	2.06284	0.399

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	0.98422	1
Var 12h I row2-row1	N/A	N/A
Var 12h NI row2-row1	N/A	N/A
Var 36h I row2-row1	N/A	N/A
Var 36h NI row2-row1	N/A	N/A
Var 60h I row2-row1	N/A	N/A
Var 60h NI row2-row1	N/A	N/A
Time course 0hI-0hNI	N/A	N/A
Time course 12hI-12hNI	N/A	N/A
Time course 36hI-36hNI	N/A	N/A
Time course 60hI-60hNI	N/A	N/A

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)	1.03196	0.931
transgenic ySAMdc/azygous control (breaker)	1.38875	1
transgenic ySAMdc/azygous control (red)	1.53975	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.97581	0.196

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.86643	0.255

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.89328	0.14
Manapal/WT (break)	1.44096	1
Manapal/WT (red)	0.56352	0.36