Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-2.3.4.6

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.89406	0.405
27DAP/17DAP	0.91789	0.839
39DAP/27DAP	0.90723	0.583
41DAP/39DAP	1.35807	0.331
42DAP/41DAP	1.10521	0.949
43DAP/42DAP	0.96978	0.91
47DAP/43DAP	0.87176	0.628
52DAP/47DAP	1.22901	0.776
57DAP/52DAP	0.85142	0.827

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02244	0.928
17DAP/reference	1.01896	0.696
27DAP/reference	0.99865	0.904
39DAP/reference	1.00132	1
41DAP/reference	0.99485	0.814
42DAP/reference	0.8974	0.019
43DAP/reference	1.04514	0.36
47DAP/reference	0.92965	0.065
52DAP/reference	0.83493	0.079
57DAP/reference	0.73588	0.022

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.95544	0.578
27DAP/17DAP	0.98205	0.919
39DAP/27DAP	1.09369	0.388
41DAP/39DAP	1.05111	0.763
42DAP/41DAP	1.04856	0.622
43DAP/42DAP	0.96119	0.538
47DAP/43DAP	1.13638	0.293
52DAP/47DAP	0.91354	0.546
57DAP/52DAP	0.90867	0.321
57DAP/7DAP	0.87366	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94037	0.361
17DAP/reference	0.88239	0.094
27DAP/reference	0.85654	0.011
39DAP/reference	0.84736	0.017
41DAP/reference	0.82559	0.047
42DAP/reference	0.81663	0.02
43DAP/reference	0.8053	0.035
47DAP/reference	0.86667	0.383
52DAP/reference	0.77465	0.027
57DAP/reference	0.8458	0.086

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.15518	0.059
17DAP/reference	1.03244	0.824
27DAP/reference	0.8639	0.111
39DAP/reference	0.70318	0.009
41DAP/reference	0.88466	0.183
42DAP/reference	0.89544	0.169
43DAP/reference	1.01919	1
47DAP/reference	0.88925	0.069
52DAP/reference	1.19514	0.444
57DAP/reference	1.26613	0.007

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96294	0.422
17DAP/reference	0.94021	0.508
27DAP/reference	0.83193	0.044
39DAP/reference	0.84463	0.019
41DAP/reference	0.9337	0.237
42DAP/reference	0.74912	0.025
43DAP/reference	0.85589	0.171
47DAP/reference	0.98582	0.574
52DAP/reference	0.83324	0.25
57DAP/reference	0.67734	0.017

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.1057	0.966
26DAP/20DAP	1.47937	0.315
34DAP/26DAP	0.99631	1
51DAP/34DAP	1.11097	0.352
52DAP/51DAP	0.95001	1
53DAP/52DAP	0.96275	0.797
55DAP/53DAP	0.81943	0.243
57DAP/55DAP	1.02573	0.997
62DAP/57DAP	1.11491	0.767
68DAP/62DAP	1.11119	0.813
68DAP/14DAP	0.94367	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.55702	0.019

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.0965	1
Mature Green Tomato/Ripe Tomato	0.91772	0.446
Immature Eggplant/Mature Eggplant	1.75733	0.05
Ripe Pepper/Ripe Tomato	1.16186	1
Mature Eggplant/Ripe Tomato	1.29935	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.92628	0.736
1-1-2/M82	0.86613	1
12-2/M82	1.24467	N/A
12-4/M82	0.90977	1
1-3/M82	0.83392	0.378
2-1-1/M82	1.13556	N/A
2-1/M82	N/A	N/A
2-6/M82	1.06486	0.695
3-2/M82	0.53656	N/A
4-1-1/M82	0.79917	1
4-1/M82	1.05311	N/A
4-3-2/M82	0.83076	0.698
4-3/M82	0.86337	N/A
5-3/M82	0.97302	1
6-2/M82	0.96924	N/A
6-3/M82	1.11483	N/A
7-1/M82	0.92356	N/A
7-2/M82	0.90704	0.881
9-3-2/M82	1.12789	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.04827	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.6405	0.298
IL12-4/WTpooled	1.1513	0.646
IL1-4/WTpooled	1.01867	N/A
WT/WTpooled	0.95096	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	0.93418	0.341

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.95042	1
DC3000/delta hrp 6h	1.06297	1
DC3000/delta hrp 12h	1.0973	1
DC3000/delta hrp 24h	1.28695	0.063

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.9454	0.691
DC3000 delta B/DC3000 delta AB	0.95357	0.575

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.05379	1
Exp 36h	1.13636	0.693
Exp 60h	1.05316	0.563

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	N/A	N/A
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)	1.02571	0.541
transgenic ySAMdc/azygous control (breaker)	1.01612	1
transgenic ySAMdc/azygous control (red)	0.78697	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.03175	0.223

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.01031	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.92568	1
Manapal/WT (break)	0.95077	1
Manapal/WT (red)	1.13761	1