Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-7.4.5.8

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.70579	0.159
27DAP/17DAP	0.52863	0.04
39DAP/27DAP	0.51528	0.327
41DAP/39DAP	1.20007	0.844
42DAP/41DAP	0.95986	1
43DAP/42DAP	1.37274	0.861
47DAP/43DAP	0.88928	0.705
52DAP/47DAP	1.33988	0.649
57DAP/52DAP	0.94603	0.94

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.8855	0.154
17DAP/reference	1.07869	0.355
27DAP/reference	0.95541	0.514
39DAP/reference	1.11401	0.224
41DAP/reference	1.17001	0.111
42DAP/reference	1.12372	0.144
43DAP/reference	1.07435	0.083
47DAP/reference	1.10162	0.575
52DAP/reference	1.05874	0.991
57DAP/reference	0.96379	0.526

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.79671	0.05
27DAP/17DAP	1.04922	0.798
39DAP/27DAP	0.99981	1
41DAP/39DAP	0.97785	0.973
42DAP/41DAP	1.00307	1
43DAP/42DAP	1.08376	0.079
47DAP/43DAP	0.94578	0.677
52DAP/47DAP	0.94881	0.739
57DAP/52DAP	0.8414	0.091
57DAP/7DAP	0.94159	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00904	1
17DAP/reference	0.90078	0.108
27DAP/reference	0.77692	0.01
39DAP/reference	0.97526	0.552
41DAP/reference	0.95538	0.298
42DAP/reference	0.74449	0.014
43DAP/reference	0.74064	0.015
47DAP/reference	0.87476	0.293
52DAP/reference	0.72314	0.019
57DAP/reference	0.81344	0.012

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.18341	0.141
17DAP/reference	1.48453	0.011
27DAP/reference	1.35431	0.07
39DAP/reference	1.43583	0.019
41DAP/reference	1.41617	0.074
42DAP/reference	1.22629	0.096
43DAP/reference	1.38924	0.128
47DAP/reference	1.16833	0.076
52DAP/reference	1.34299	0.008
57DAP/reference	1.1347	0.172

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00569	0.804
17DAP/reference	1.08266	0.443
27DAP/reference	0.80878	0.039
39DAP/reference	0.77341	0.022
41DAP/reference	1.00882	0.754
42DAP/reference	0.95298	0.552
43DAP/reference	0.85436	0.143
47DAP/reference	1.01636	1
52DAP/reference	0.85103	0.277
57DAP/reference	0.89951	0.184

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.54883	0.26
26DAP/20DAP	0.899	0.317
34DAP/26DAP	1.03074	1
51DAP/34DAP	1.05136	0.785
52DAP/51DAP	0.8852	1
53DAP/52DAP	0.98353	0.929
55DAP/53DAP	0.97742	0.807
57DAP/55DAP	1.21886	0.188
62DAP/57DAP	0.90347	0.871
68DAP/62DAP	0.81503	0.579
68DAP/14DAP	0.74474	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.00088	0.737

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.00913	1
Mature Green Tomato/Ripe Tomato	N/A	N/A
Immature Eggplant/Mature Eggplant	0.93601	0.448
Ripe Pepper/Ripe Tomato	0.49765	0.293
Mature Eggplant/Ripe Tomato	1.6295	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.80955	0.804
12-2/M82	N/A	N/A
12-4/M82	1.66806	N/A
1-3/M82	0.71683	N/A
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	1.185	N/A
3-2/M82	0.96933	N/A
4-1-1/M82	0.93394	N/A
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	0.72347	N/A
5-3/M82	0.92665	1
6-2/M82	0.96698	N/A
6-3/M82	N/A	N/A
7-1/M82	1.15734	N/A
7-2/M82	1.08211	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	1.00576	1
IL2-6/WTpooled	0.90082	1
IL7-5/WTpooled	0.92468	N/A
IL7-3/WTpooled	0.96916	1
IL12-4/WTpooled	0.82863	0.71
IL1-4/WTpooled	1.13626	1
WT/WTpooled	0.92582	0.67

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	1.38314	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.01638	1
DC3000/delta hrp 6h	1.01206	0.95
DC3000/delta hrp 12h	1.05044	1
DC3000/delta hrp 24h	0.59844	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.09636	0.515
DC3000 delta B/DC3000 delta AB	1.19879	0.225

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.85802	1
Exp 36h	1.13169	1
Exp 60h	1.1515	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	0.95306	1
Var 0h	1.32056	0.936
Var 12h I row2-row1	0.97998	0.948
Var 12h NI row2-row1	0.88107	0.627
Var 36h I row2-row1	1.14596	0.298
Var 36h NI row2-row1	0.86052	0.421
Var 60h I row2-row1	0.95466	0.832
Var 60h NI row2-row1	1.04744	0.904
Time course 0hI-0hNI	0.99942	1
Time course 12hI-12hNI	1.02957	0.709
Time course 36hI-36hNI	1.10637	0.114
Time course 60hI-60hNI	1.79763	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)	0.98717	0.662
transgenic ySAMdc/azygous control (breaker)	0.63959	0.134
transgenic ySAMdc/azygous control (red)	0.96444	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.06806	0.495

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.88019	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.77356	1
Manapal/WT (break)	1.09558	0.183
Manapal/WT (red)	N/A	N/A