Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-1.1.20.18

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.73014	0.226
27DAP/17DAP	1.28302	0.859
39DAP/27DAP	0.83883	0.449
41DAP/39DAP	1.50371	0.38
42DAP/41DAP	0.80684	1
43DAP/42DAP	1.25197	0.999
47DAP/43DAP	1.01371	0.851
52DAP/47DAP	0.77255	0.526
57DAP/52DAP	0.96844	0.927

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.82958	0.172
17DAP/reference	0.77033	0.043
27DAP/reference	1.04859	0.909
39DAP/reference	0.81087	0.034
41DAP/reference	0.59477	0.018
42DAP/reference	0.84019	0.012
43DAP/reference	0.90401	0.163
47DAP/reference	1.04497	1
52DAP/reference	1.32168	0.016
57DAP/reference	1.28003	0.014

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.90742	0.56
27DAP/17DAP	1.86635	0.653
39DAP/27DAP	1.05507	1
41DAP/39DAP	1.09609	1
42DAP/41DAP	0.99172	0.774
43DAP/42DAP	1.01786	0.875
47DAP/43DAP	1.3044	0.788
52DAP/47DAP	0.93695	0.905
57DAP/52DAP	1.18568	0.699
57DAP/7DAP	N/A	N/A

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.39361	0.147
17DAP/reference	1.92901	0.007
27DAP/reference	1.50548	0.01
39DAP/reference	1.81024	0.005
41DAP/reference	1.79001	0.024
42DAP/reference	1.89419	0.008
43DAP/reference	2.45998	0.009
47DAP/reference	1.39027	0.386
52DAP/reference	2.10664	0.007
57DAP/reference	1.74119	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.69907	0.032
17DAP/reference	0.6185	0.003
27DAP/reference	0.79004	0.044
39DAP/reference	1.03351	0.978
41DAP/reference	1.00522	0.735
42DAP/reference	0.86264	0.037
43DAP/reference	0.7025	0.04
47DAP/reference	0.85156	0.083
52DAP/reference	0.85722	0.078
57DAP/reference	0.62768	0.004

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.37942	0.049
17DAP/reference	0.99033	0.647
27DAP/reference	1.90822	0.024
39DAP/reference	1.62868	0.015
41DAP/reference	1.64566	0.009
42DAP/reference	1.55779	0.022
43DAP/reference	1.67873	0.01
47DAP/reference	0.91448	0.183
52DAP/reference	1.81243	0.082
57DAP/reference	1.7443	0.151

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.58273	0.773
26DAP/20DAP	N/A	N/A
34DAP/26DAP	N/A	N/A
51DAP/34DAP	0.77838	0.217
52DAP/51DAP	1.11238	0.783
53DAP/52DAP	0.80203	0.27
55DAP/53DAP	0.65752	0.404
57DAP/55DAP	0.85137	0.452
62DAP/57DAP	1.10147	1
68DAP/62DAP	1.37169	0.124
68DAP/14DAP	1.3362	0.384

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.89087	0.52

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.48439	0.109
Mature Green Tomato/Ripe Tomato	N/A	N/A
Immature Eggplant/Mature Eggplant	2.3815	0.05
Ripe Pepper/Ripe Tomato	0.51795	0.224
Mature Eggplant/Ripe Tomato	0.46024	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.97891	N/A
1-1-2/M82	1.14046	N/A
12-2/M82	N/A	N/A
12-4/M82	1.03078	1
1-3/M82	0.96094	N/A
2-1-1/M82	0.75098	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	0.9544	N/A
5-3/M82	1.0477	1
6-2/M82	N/A	N/A
6-3/M82	1.01341	N/A
7-1/M82	N/A	N/A
7-2/M82	0.94426	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	0.64911	0.243
IL2-6/WTpooled	0.92531	1
IL7-5/WTpooled	0.50631	0.559
IL7-3/WTpooled	1.38432	0.362
IL12-4/WTpooled	1.23686	0.646
IL1-4/WTpooled	0.85276	0.444
WT/WTpooled	1.06862	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	1.00323	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.85404	1
DC3000/delta hrp 6h	0.90918	0.95
DC3000/delta hrp 12h	0.88271	1
DC3000/delta hrp 24h	0.97811	0.897

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.25265	N/A
DC3000 delta B/DC3000 delta AB	N/A	N/A

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	1.19364	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.83235	1
Var 0h	N/A	N/A
Var 12h I row2-row1	1.37267	0.443
Var 12h NI row2-row1	1.07706	1
Var 36h I row2-row1	1.04316	1
Var 36h NI row2-row1	2.37157	1
Var 60h I row2-row1	0.80017	N/A
Var 60h NI row2-row1	0.60852	0.69
Time course 0hI-0hNI	0.93233	0.671
Time course 12hI-12hNI	0.86947	0.991
Time course 36hI-36hNI	0.91366	0.373
Time course 60hI-60hNI	1.12162	0.359

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)	0.90746	0.362
transgenic ySAMdc/azygous control (breaker)	1.02514	1
transgenic ySAMdc/azygous control (red)	0.86162	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.28382	0.039

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.08682	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.8775	1
Manapal/WT (break)	0.71145	0.285
Manapal/WT (red)	0.92028	0.607