Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-7.3.4.15

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.95438	0.683
27DAP/17DAP	0.84418	0.611
39DAP/27DAP	0.81159	0.376
41DAP/39DAP	1.12088	0.334
42DAP/41DAP	1.05862	1
43DAP/42DAP	1.01669	0.937
47DAP/43DAP	0.90065	0.663
52DAP/47DAP	1.07042	0.869
57DAP/52DAP	1.0079	1

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95925	0.177
17DAP/reference	0.99934	1
27DAP/reference	1.00818	1
39DAP/reference	1.01127	0.771
41DAP/reference	0.97775	0.667
42DAP/reference	0.92887	0.011
43DAP/reference	0.99951	0.942
47DAP/reference	0.95347	0.077
52DAP/reference	0.92619	0.053
57DAP/reference	0.90356	0.035

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.02289	0.749
27DAP/17DAP	0.96181	0.508
39DAP/27DAP	1.04289	0.603
41DAP/39DAP	1.07473	0.682
42DAP/41DAP	1.00283	0.939
43DAP/42DAP	1.02174	0.382
47DAP/43DAP	1.01575	0.88
52DAP/47DAP	0.99735	0.97
57DAP/52DAP	1.04845	0.695
57DAP/7DAP	1.03198	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91892	0.146
17DAP/reference	0.90682	0.012
27DAP/reference	0.92121	0.019
39DAP/reference	0.95455	0.027
41DAP/reference	0.95713	0.103
42DAP/reference	0.90037	0.086
43DAP/reference	0.9024	0.126
47DAP/reference	0.9062	0.222
52DAP/reference	0.89948	0.024
57DAP/reference	0.91522	0.054

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98809	0.831
17DAP/reference	0.94608	0.367
27DAP/reference	1.07608	1
39DAP/reference	0.91096	0.359
41DAP/reference	1.06916	0.672
42DAP/reference	1.04896	0.596
43DAP/reference	1.01328	0.957
47DAP/reference	1.03413	0.572
52DAP/reference	0.97693	0.407
57DAP/reference	1.00007	1

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97445	0.249
17DAP/reference	0.97484	0.537
27DAP/reference	0.94228	0.03
39DAP/reference	0.96089	0.054
41DAP/reference	0.98823	0.682
42DAP/reference	0.90299	0.028
43DAP/reference	0.96063	0.143
47DAP/reference	0.99752	0.687
52DAP/reference	0.89197	0.142
57DAP/reference	0.9147	0.113

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.03139	0.966
26DAP/20DAP	0.91635	0.512
34DAP/26DAP	0.96969	0.893
51DAP/34DAP	1.02781	0.666
52DAP/51DAP	1.05017	0.596
53DAP/52DAP	1.01498	1
55DAP/53DAP	0.96867	0.735
57DAP/55DAP	1.02123	0.975
62DAP/57DAP	1.04055	0.868
68DAP/62DAP	1.02737	1
68DAP/14DAP	0.88061	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.92211	0.097

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.96408	0.66
Immature Eggplant/Mature Eggplant	0.92214	N/A
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	N/A	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.9679	0.944
1-1-2/M82	0.97064	1
12-2/M82	1.01041	1
12-4/M82	1.01753	1
1-3/M82	0.94489	0.501
2-1-1/M82	1.06058	0.764
2-1/M82	1.4273	1
2-6/M82	1.04347	1
3-2/M82	1.00658	1
4-1-1/M82	0.88788	0.985
4-1/M82	0.9553	1
4-3-2/M82	0.88573	0.487
4-3/M82	1.03498	1
5-3/M82	0.99328	1
6-2/M82	0.97464	1
6-3/M82	1.0048	1
7-1/M82	0.97667	1
7-2/M82	1.14306	0.385
9-3-2/M82	0.92061	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.24978	0.788
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	0.98865	1
IL1-4/WTpooled	0.94106	0.834
WT/WTpooled	0.95435	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	0.71854	0.497

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.95257	1
DC3000/delta hrp 6h	0.93619	0.95
DC3000/delta hrp 12h	1.18472	1
DC3000/delta hrp 24h	0.85859	0.225

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.82962	0.318
DC3000 delta B/DC3000 delta AB	1.23684	0.468

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.65261	0.328
Exp 36h	0.5353	0.434
Exp 60h	0.37323	0.249

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	0.98288	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)	1.29014	1
transgenic ySAMdc/azygous control (breaker)	1.28698	1
transgenic ySAMdc/azygous control (red)	2.21647	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.01004	0.556

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	2.59851	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	N/A	N/A
Manapal/WT (break)	N/A	N/A
Manapal/WT (red)	0.8365	0.424