Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-1.3.17.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.92752	0.543
27DAP/17DAP	1.12452	0.864
39DAP/27DAP	1.16347	0.643
41DAP/39DAP	1.00279	0.949
42DAP/41DAP	1.21707	0.894
43DAP/42DAP	1.21778	0.772
47DAP/43DAP	0.82319	0.467
52DAP/47DAP	1.56105	0.436
57DAP/52DAP	1.25903	0.92

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.1562	0.814
17DAP/reference	0.79959	0.008
27DAP/reference	1.19758	0.156
39DAP/reference	0.77301	0.032
41DAP/reference	0.69484	0.014
42DAP/reference	1.04785	0.587
43DAP/reference	0.98377	0.745
47DAP/reference	1.28577	0.495
52DAP/reference	1.78399	0.026
57DAP/reference	1.88259	0.009

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.98103	0.782
27DAP/17DAP	0.84031	0.241
39DAP/27DAP	0.71831	0.181
41DAP/39DAP	1.04674	0.896
42DAP/41DAP	1.05187	0.904
43DAP/42DAP	0.72579	0.049
47DAP/43DAP	1.38115	0.934
52DAP/47DAP	1.35459	0.441
57DAP/52DAP	1.55077	0.091
57DAP/7DAP	1.09823	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.75678	0.095
17DAP/reference	0.66063	0.011
27DAP/reference	0.8699	0.042
39DAP/reference	0.84636	0.064
41DAP/reference	0.9212	0.259
42DAP/reference	0.74079	0.014
43DAP/reference	0.8035	0.018
47DAP/reference	0.99771	0.671
52DAP/reference	0.83367	0.066
57DAP/reference	0.82781	0.064

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.74392	0.067
17DAP/reference	0.74227	0.023
27DAP/reference	1.0746	0.847
39DAP/reference	1.08453	0.239
41DAP/reference	1.3842	0.005
42DAP/reference	1.261	0.04
43DAP/reference	0.70362	0.077
47DAP/reference	0.97057	0.459
52DAP/reference	1.03846	1
57DAP/reference	0.68999	0.004

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.872	0.065
17DAP/reference	0.92522	0.47
27DAP/reference	0.7817	0.063
39DAP/reference	0.9073	0.246
41DAP/reference	1.01964	1
42DAP/reference	1.13839	0.802
43DAP/reference	1.13097	0.59
47DAP/reference	1.20186	0.461
52DAP/reference	0.71002	0.086
57DAP/reference	1.83008	0.025

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	N/A	N/A
26DAP/20DAP	1.02664	1
34DAP/26DAP	0.9687	0.92
51DAP/34DAP	0.80139	N/A
52DAP/51DAP	0.83554	1
53DAP/52DAP	0.83066	0.581
55DAP/53DAP	1.4396	0.527
57DAP/55DAP	0.73713	0.176
62DAP/57DAP	1.40316	0.622
68DAP/62DAP	3.20418	0.017
68DAP/14DAP	3.76012	0.019

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.02746	0.821

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.97634	0.715
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.39734	N/A
Mature Eggplant/Ripe Tomato	1.02399	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.30987	N/A
1-1-2/M82	1.07432	0.977
12-2/M82	N/A	N/A
12-4/M82	1.22584	1
1-3/M82	N/A	N/A
2-1-1/M82	1.31859	N/A
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	N/A	N/A
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	1.01151	1
5-3/M82	0.92839	1
6-2/M82	0.7205	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.79334	N/A
IL2-6/WTpooled	1.21795	0.788
IL7-5/WTpooled	0.52031	N/A
IL7-3/WTpooled	0.86195	0.294
IL12-4/WTpooled	1.26525	0.624
IL1-4/WTpooled	0.95288	N/A
WT/WTpooled	1.02951	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	0.96115	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.0197	0.921
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	1.25246	1
DC3000/delta hrp 24h	0.74735	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.63332	0.059
DC3000 delta B/DC3000 delta AB	0.47048	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	N/A	N/A
Exp 60h	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
self-self	1.0005	1
Var 0h	0.87949	1
Var 12h I row2-row1	0.75647	0.338
Var 12h NI row2-row1	0.91763	0.494
Var 36h I row2-row1	0.91567	1
Var 36h NI row2-row1	1.09816	1
Var 60h I row2-row1	1.29373	0.562
Var 60h NI row2-row1	0.97284	1
Time course 0hI-0hNI	1.00935	1
Time course 12hI-12hNI	0.93635	0.377
Time course 36hI-36hNI	0.82543	0.068
Time course 60hI-60hNI	0.12909	0.005

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)	N/A	N/A
transgenic ySAMdc/azygous control (breaker)	N/A	N/A
transgenic ySAMdc/azygous control (red)	N/A	N/A

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.04205	1

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)	0.97864	0.863