Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.4.1.17

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.95189	0.689
27DAP/17DAP	0.99752	0.975
39DAP/27DAP	1.75267	0.031
41DAP/39DAP	0.58944	0.045
42DAP/41DAP	1.30719	0.404
43DAP/42DAP	1.03682	0.937
47DAP/43DAP	1.01554	0.89
52DAP/47DAP	1.32973	0.538
57DAP/52DAP	1.32425	0.817

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.2758	0.014
17DAP/reference	1.06738	0.306
27DAP/reference	1.00206	0.923
39DAP/reference	1.08182	0.114
41DAP/reference	1.03741	0.714
42DAP/reference	1.17823	0.072
43DAP/reference	1.10409	0.035
47DAP/reference	1.22877	0.001
52DAP/reference	1.05424	0.476
57DAP/reference	1.0962	0.249

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.617	0.277
27DAP/17DAP	0.90434	0.887
39DAP/27DAP	1.95552
41DAP/39DAP	1.7397	0.04
42DAP/41DAP	1.20464	0.947
43DAP/42DAP	0.78551
47DAP/43DAP	2.34883	0.035
52DAP/47DAP	1.23221	0.573
57DAP/52DAP	N/A	N/A
57DAP/7DAP	0.44838

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.12853	0.292
17DAP/reference	1.00885	1
27DAP/reference	1.05774	0.664
39DAP/reference	1.04056	0.669
41DAP/reference	1.02672	0.891
42DAP/reference	0.93481	0.248
43DAP/reference	0.87929	0.091
47DAP/reference	1.11095	0.45
52DAP/reference	0.93347	0.232
57DAP/reference	0.92376	0.191

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.22576	0.124
17DAP/reference	1.37546	0.014
27DAP/reference	1.89112	0.015
39DAP/reference	1.68826	0.026
41DAP/reference	1.31064	0.088
42DAP/reference	1.39245	0.086
43DAP/reference	1.30247	0.033
47DAP/reference	1.50778	0.042
52DAP/reference	1.28537	0.069
57DAP/reference	1.22684	0.462

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.08851	0.101
17DAP/reference	1.14279	0.191
27DAP/reference	0.90027	0.119
39DAP/reference	1.05591	0.483
41DAP/reference	0.97713	0.618
42DAP/reference	1.07669	0.701
43DAP/reference	1.33389	0.403
47DAP/reference	1.28656	0.038
52DAP/reference	0.99257	0.675
57DAP/reference	1.70851	0.069

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.02106	1
26DAP/20DAP	N/A	N/A
34DAP/26DAP	N/A	N/A
51DAP/34DAP	0.56871
52DAP/51DAP	0.96154	1
53DAP/52DAP	1.56639
55DAP/53DAP	1.45992	0.076
57DAP/55DAP	1.21141	0.818
62DAP/57DAP	0.99982	1
68DAP/62DAP	0.85809	0.609
68DAP/14DAP	0.90688	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.16266

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.14022	0.666
Mature Green Tomato/Ripe Tomato	1.314	0.053
Immature Eggplant/Mature Eggplant	1.00208	1
Ripe Pepper/Ripe Tomato	0.82097	1
Mature Eggplant/Ripe Tomato	0.87284	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.79824	0.708
1-1-2/M82	1.30605	1
12-2/M82	0.81036	0.678
12-4/M82	0.83362	0.619
1-3/M82	1.77012	0.479
2-1-1/M82	0.82845	0.465
2-1/M82	0.67487	0.322
2-6/M82	0.94776	1
3-2/M82	1.18574	0.426
4-1-1/M82	1.05173	1
4-1/M82	1.2322	1
4-3-2/M82	1.46556	0.508
4-3/M82	1.45478	0.268
5-3/M82	1.2287	0.467
6-2/M82	1.09607
6-3/M82	1.07827	1
7-1/M82	1.02711	1
7-2/M82	1.08354	1
9-3-2/M82	1.03781	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.9867	1
IL2-6/WTpooled	0.79293	0.358
IL7-5/WTpooled	1.22448	0.792
IL7-3/WTpooled	0.98814	0.418
IL12-4/WTpooled	1.04039	0.595
IL1-4/WTpooled	1.08762	1
WT/WTpooled	0.9509	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	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.08384	0.921
DC3000/delta hrp 6h	1.0581	1
DC3000/delta hrp 12h	1.01149	1
DC3000/delta hrp 24h	1.12664	0.453

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	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	0.84051	1
Exp 36h	1.13837	1
Exp 60h	1.1003	1

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)	1.00946	1
transgenic ySAMdc/azygous control (breaker)	1.62125	0.166
transgenic ySAMdc/azygous control (red)	1.31194	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.14999	0.035

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.83813	0.241

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.86859	1
Manapal/WT (break)	0.73994	1
Manapal/WT (red)	1.92748	0.164