Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-8.1.20.21

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	61.7769	0.01
27DAP/17DAP	1.33674	0.793
39DAP/27DAP	1.34182	0.927
41DAP/39DAP	0.42544	0.042
42DAP/41DAP	0.60787	0.774
43DAP/42DAP	0.64932	0.477
47DAP/43DAP	0.7559	0.231
52DAP/47DAP	0.86727	0.618
57DAP/52DAP	1.53427	0.784

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.42576	0.025
17DAP/reference	14.1525	0.011
27DAP/reference	11.2672	0.007
39DAP/reference	6.17279	0.021
41DAP/reference	5.17572	0.01
42DAP/reference	1.84835	0.001
43DAP/reference	0.82981	0.073
47DAP/reference	2.00678	0.007
52DAP/reference	2.86468	0.008
57DAP/reference	3.05333	0.008

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	2.95448	0.036
27DAP/17DAP	1.25911	0.131
39DAP/27DAP	0.61847	0.028
41DAP/39DAP	0.71037	0.31
42DAP/41DAP	1.19	0.879
43DAP/42DAP	0.53659	0.02
47DAP/43DAP	0.85484	0.031
52DAP/47DAP	1.19312	0.467
57DAP/52DAP	0.93313	0.545
57DAP/7DAP	0.93844	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.30767	0.747
17DAP/reference	6.70719	0.006
27DAP/reference	5.62926	0.006
39DAP/reference	4.66438	0.006
41DAP/reference	2.61661	0.008
42DAP/reference	1.79785	0.076
43DAP/reference	0.46667	0.012
47DAP/reference	1.20434	0.504
52DAP/reference	0.58285	0.014
57DAP/reference	0.59748	0.009

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.15405	0.005
17DAP/reference	6.69629	0.007
27DAP/reference	5.94041	0.012
39DAP/reference	4.63558	0.011
41DAP/reference	1.96364	0.005
42DAP/reference	3.31375	0.007
43DAP/reference	2.48647	0.018
47DAP/reference	2.38632	0.036
52DAP/reference	3.7365	0.006
57DAP/reference	0.89252	0.226

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.30773	0.037
17DAP/reference	1.71497	0.117
27DAP/reference	4.84626	0.008
39DAP/reference	2.6905	0.005
41DAP/reference	1.57188	0.008
42DAP/reference	1.02533	1
43DAP/reference	0.74568	0.088
47DAP/reference	0.56566	0.014
52DAP/reference	0.75795	0.158
57DAP/reference	3.31998	0.012

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.31726	0.966
26DAP/20DAP	0.895	0.512
34DAP/26DAP	1.09645	0.819
51DAP/34DAP	1.18386	0.06
52DAP/51DAP	0.86779	0.151
53DAP/52DAP	1.17507	0.47
55DAP/53DAP	1.04163	1
57DAP/55DAP	0.99804	0.955
62DAP/57DAP	0.7934	0.088
68DAP/62DAP	1.10719	1
68DAP/14DAP	2.20116	0.026

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	2.5008	0.015

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.00981	1
Mature Green Tomato/Ripe Tomato	8.75372	0.015
Immature Eggplant/Mature Eggplant	6.77922	0.049
Ripe Pepper/Ripe Tomato	0.13307	0.224
Mature Eggplant/Ripe Tomato	0.22847	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.62289	0.841
1-1-2/M82	0.9495	1
12-2/M82	1.06228	1
12-4/M82	0.84328	1
1-3/M82	2.35923	0.479
2-1-1/M82	1.08869	1
2-1/M82	0.99911	1
2-6/M82	0.72967	1
3-2/M82	1.35704	N/A
4-1-1/M82	1.49783	1
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	0.85833	1
5-3/M82	1.04615	1
6-2/M82	0.96886	1
6-3/M82	0.9933	1
7-1/M82	N/A	N/A
7-2/M82	0.96597	0.881
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	N/A	N/A
WT/WTpooled	N/A	N/A

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	1.31685	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.96035	1
DC3000/delta hrp 6h	0.95048	0.95
DC3000/delta hrp 12h	1.30121	1
DC3000/delta hrp 24h	0.35814	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.94203	0.513
DC3000 delta B/DC3000 delta AB	1.02356	0.609

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.118	1
Exp 36h	0.8043	0.471
Exp 60h	0.754	0.386

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

hybridization	ratio	FDR (corrected p value)
self-self	1.03063	1
Var 0h	N/A	N/A
Var 12h I row2-row1	0.86663	0.627
Var 12h NI row2-row1	0.84369	0.713
Var 36h I row2-row1	0.99051	1
Var 36h NI row2-row1	1.67264	0.253
Var 60h I row2-row1	1.40988	0.562
Var 60h NI row2-row1	1.03932	0.904
Time course 0hI-0hNI	1.09926	0.764
Time course 12hI-12hNI	0.93141	0.526
Time course 36hI-36hNI	0.6053	0.023
Time course 60hI-60hNI	0.14261	0.006

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)	1.05968	0.699
transgenic ySAMdc/azygous control (breaker)	1.00571	1
transgenic ySAMdc/azygous control (red)	0.69974	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.46398	0.247

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.6901	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.89029	1
Manapal/WT (break)	0.69198	0.333
Manapal/WT (red)	0.80569	0.274