Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.2.2.1

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.98764	0.779
27DAP/17DAP	1.12978	0.854
39DAP/27DAP	0.78506	0.507
41DAP/39DAP	1.36654	0.511
42DAP/41DAP	1.50463	0.145
43DAP/42DAP	0.69843	0.456
47DAP/43DAP	0.56559	0.099
52DAP/47DAP	0.81141	0.612
57DAP/52DAP	1.20306	0.977

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.79618	0.073
17DAP/reference	0.788	0.007
27DAP/reference	0.9581	0.525
39DAP/reference	0.84489	0.02
41DAP/reference	0.71267	0.011
42DAP/reference	0.90688	0.091
43DAP/reference	0.91594	0.287
47DAP/reference	0.89058	0.137
52DAP/reference	1.14251	0.256
57DAP/reference	1.33985	0.017

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.97126	0.679
27DAP/17DAP	1.15995	0.73
39DAP/27DAP	0.70224	0.039
41DAP/39DAP	1.09616	0.799
42DAP/41DAP	1.053	1
43DAP/42DAP	1.16013	0.554
47DAP/43DAP	0.95251	0.805
52DAP/47DAP	1.26143	0.504
57DAP/52DAP	1.4588	0.116
57DAP/7DAP	1.84527	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.21862	0.298
17DAP/reference	1.30152	0.134
27DAP/reference	1.06802	0.974
39DAP/reference	1.25931	0.314
41DAP/reference	0.9739	0.489
42DAP/reference	0.91401	0.042
43DAP/reference	0.96083	0.403
47DAP/reference	1.02727	0.932
52DAP/reference	1.24024	0.212
57DAP/reference	1.16041	0.438

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.75643	0.069
17DAP/reference	0.77987	0.034
27DAP/reference	0.93868	0.317
39DAP/reference	0.97701	0.485
41DAP/reference	1.14602	0.072
42DAP/reference	0.98745	0.534
43DAP/reference	0.90237	0.298
47DAP/reference	0.89475	0.043
52DAP/reference	0.93992	0.22
57DAP/reference	0.74372	0.032

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94237	0.362
17DAP/reference	0.85531	0.308
27DAP/reference	1.34252	0.298
39DAP/reference	1.05885	0.912
41DAP/reference	1.04875	0.621
42DAP/reference	1.12764	0.321
43DAP/reference	1.0624	0.755
47DAP/reference	1.06084	1
52DAP/reference	1.14697	0.851
57DAP/reference	1.28507	0.05

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	3.15819	0.966
26DAP/20DAP	1.50666	0.453
34DAP/26DAP	1.44367
51DAP/34DAP	0.83301	0.624
52DAP/51DAP	1.64288	0.039
53DAP/52DAP	0.9274	0.807
55DAP/53DAP	1.13328	0.755
57DAP/55DAP	0.76929	0.225
62DAP/57DAP	1.25907	0.515
68DAP/62DAP	1.59148	0.153
68DAP/14DAP	2.46345	0.027

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.64971	0.031

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.62267
Immature Eggplant/Mature Eggplant	0.11885	0.057
Ripe Pepper/Ripe Tomato	0.64258	0.293
Mature Eggplant/Ripe Tomato	3.79776	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.99191	0.944
1-1-2/M82	0.76403
12-2/M82	1.10825	1
12-4/M82	1.64845
1-3/M82	N/A	N/A
2-1-1/M82	1.13111
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	0.75062
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	0.96653	0.72
5-3/M82	0.91291	1
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	0.95533	0.578
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.86476
IL2-6/WTpooled	0.85975	1
IL7-5/WTpooled	1.07987	1
IL7-3/WTpooled	1.21532	0.362
IL12-4/WTpooled	1.14764	0.532
IL1-4/WTpooled	0.86269	0.562
WT/WTpooled	1.0385	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	1.00389	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.92193	1
DC3000/delta hrp 6h	0.83311	0.95
DC3000/delta hrp 12h	1.18925	1
DC3000/delta hrp 24h	0.68292	0.039

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.4322
DC3000 delta B/DC3000 delta AB	0.7441	0.023

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.60798	1
Exp 36h	0.88308	0.749
Exp 60h	0.70584	0.29

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99433	1
Var 0h	1.37057	0.594
Var 12h I row2-row1	1.01111	1
Var 12h NI row2-row1	1.19322	1
Var 36h I row2-row1	0.79353	0.805
Var 36h NI row2-row1	0.42837	1
Var 60h I row2-row1	N/A	N/A
Var 60h NI row2-row1	0.95319	1
Time course 0hI-0hNI	0.93527	0.555
Time course 12hI-12hNI	0.9749	0.864
Time course 36hI-36hNI	0.67184	0.023
Time course 60hI-60hNI	0.41651	0.007

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)	1.59799	0.297
transgenic ySAMdc/azygous control (breaker)	1.19937	1
transgenic ySAMdc/azygous control (red)	1.27764	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.99669	0.694

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.12912	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.75081	0.172
Manapal/WT (break)	1.00491	1
Manapal/WT (red)	0.92519	0.728