Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-1.1.8.1

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.34221	0.477
27DAP/17DAP	0.97977	1
39DAP/27DAP	0.86172	0.462
41DAP/39DAP	1.6143	0.328
42DAP/41DAP	1.14328	0.82
43DAP/42DAP	1.41719	0.14
47DAP/43DAP	1.61971	0.369
52DAP/47DAP	1.1816	0.709
57DAP/52DAP	0.97565	0.957

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97024	0.513
17DAP/reference	1.08739	0.039
27DAP/reference	0.94777	0.265
39DAP/reference	1.03768	0.593
41DAP/reference	1.015	0.963
42DAP/reference	0.93334	0.062
43DAP/reference	0.98366	0.763
47DAP/reference	0.91282	0.042
52DAP/reference	0.85297	0.135
57DAP/reference	0.85838	0.101

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.08144	0.326
27DAP/17DAP	1.14206	0.706
39DAP/27DAP	1.82635	0.046
41DAP/39DAP	0.46084	0.013
42DAP/41DAP	3.9103	0.002
43DAP/42DAP	3.69317	0.013
47DAP/43DAP	0.92911	0.722
52DAP/47DAP	1.01557	0.935
57DAP/52DAP	1.07408	1
57DAP/7DAP	4.66812	N/A

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.71861	0.078
17DAP/reference	0.69568	0.013
27DAP/reference	0.9518	0.325
39DAP/reference	1.35952	0.01
41DAP/reference	1.15838	0.241
42DAP/reference	1.27129	0.016
43DAP/reference	1.16987	0.066
47DAP/reference	1.249	0.413
52DAP/reference	0.89907	0.213
57DAP/reference	0.79938	0.047

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92376	0.197
17DAP/reference	0.92127	0.07
27DAP/reference	0.9715	0.519
39DAP/reference	1.00175	0.745
41DAP/reference	0.82985	0.019
42DAP/reference	1.09285	0.351
43DAP/reference	1.2918	0.562
47DAP/reference	1.05781	0.544
52DAP/reference	0.96022	0.239
57DAP/reference	0.93616	0.318

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.76885	0.077
17DAP/reference	0.81101	0.3
27DAP/reference	0.70919	0.069
39DAP/reference	0.85601	0.05
41DAP/reference	0.80689	0.02
42DAP/reference	1.55679	0.045
43DAP/reference	1.2674	0.202
47DAP/reference	0.97084	0.509
52DAP/reference	1.21029	0.278
57DAP/reference	1.07341	1

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.00772	1
26DAP/20DAP	0.77834	0.244
34DAP/26DAP	1.08176	1
51DAP/34DAP	1.30455	0.105
52DAP/51DAP	1.19048	0.121
53DAP/52DAP	3.73335	0.043
55DAP/53DAP	0.97926	0.864
57DAP/55DAP	0.76879	0.09
62DAP/57DAP	0.77154	0.28
68DAP/62DAP	1.33355	0.413
68DAP/14DAP	1.05381	0.656

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	2.74284	0.021

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.23727	0.176
Mature Green Tomato/Ripe Tomato	0.29893	0.019
Immature Eggplant/Mature Eggplant	0.34502	0.062
Ripe Pepper/Ripe Tomato	0.97129	1
Mature Eggplant/Ripe Tomato	1.94842	0.268

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.90938	0.944
1-1-2/M82	1.11878	1
12-2/M82	N/A	N/A
12-4/M82	0.923	0.619
1-3/M82	N/A	N/A
2-1-1/M82	0.49675	N/A
2-1/M82	N/A	N/A
2-6/M82	1.43621	N/A
3-2/M82	0.17823	0.455
4-1-1/M82	N/A	N/A
4-1/M82	1.48526	N/A
4-3-2/M82	0.63856	N/A
4-3/M82	1.33105	0.268
5-3/M82	1.02433	1
6-2/M82	N/A	N/A
6-3/M82	0.94592	N/A
7-1/M82	1.09644	N/A
7-2/M82	1.07328	1
9-3-2/M82	1.70686	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.12325	0.493
IL2-6/WTpooled	0.70071	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.4121	N/A
IL12-4/WTpooled	0.82048	0.71
IL1-4/WTpooled	1.11925	1
WT/WTpooled	0.97137	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	0.76328	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.86509	0.288
DC3000/delta hrp 6h	0.94856	0.95
DC3000/delta hrp 12h	1.1697	1
DC3000/delta hrp 24h	2.0242	0.453

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.53319	0.229
DC3000 delta B/DC3000 delta AB	1.36902	0.167

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.05275	1
Exp 36h	1.20776	1
Exp 60h	1.16602	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	1.05656	1
Var 0h	1.0027	1
Var 12h I row2-row1	1.59942	0.216
Var 12h NI row2-row1	0.90786	0.82
Var 36h I row2-row1	0.9848	1
Var 36h NI row2-row1	0.89125	0.706
Var 60h I row2-row1	0.82521	0.285
Var 60h NI row2-row1	1.10594	0.904
Time course 0hI-0hNI	0.97455	0.898
Time course 12hI-12hNI	0.83379	0.142
Time course 36hI-36hNI	0.98721	0.559
Time course 60hI-60hNI	1.64983	0.008

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)	0.91941	0.33
transgenic ySAMdc/azygous control (breaker)	0.97052	0.49
transgenic ySAMdc/azygous control (red)	0.9485	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.99588	0.806

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.76729	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.58963	0.172
Manapal/WT (break)	1.16753	1
Manapal/WT (red)	1.13415	0.413