Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-5.3.11.18

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.14014	0.904
27DAP/17DAP	1.00197	1
39DAP/27DAP	1.63383	0.182
41DAP/39DAP	0.90389	0.586
42DAP/41DAP	0.81945	0.774
43DAP/42DAP	1.01067	0.937
47DAP/43DAP	0.76206	0.308
52DAP/47DAP	1.80401	0.228
57DAP/52DAP	1.10045	0.996

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96665	0.513
17DAP/reference	0.95328	0.536
27DAP/reference	0.99113	0.779
39DAP/reference	0.9765	0.75
41DAP/reference	0.87988	0.013
42DAP/reference	1.21928	0.001
43DAP/reference	1.12311	0.028
47DAP/reference	0.97556	0.322
52DAP/reference	0.80332	0.069
57DAP/reference	0.94967	0.248

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.85282	0.219
27DAP/17DAP	0.94746	0.537
39DAP/27DAP	1.04899	0.611
41DAP/39DAP	0.92776	0.713
42DAP/41DAP	1.20848	0.067
43DAP/42DAP	1.09288	0.147
47DAP/43DAP	1.026	0.92
52DAP/47DAP	0.85393	0.23
57DAP/52DAP	1.08947	0.466
57DAP/7DAP	1.22925	0.22

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.35943	0.227
17DAP/reference	1.07935	0.009
27DAP/reference	1.31876	0.006
39DAP/reference	1.05449	0.46
41DAP/reference	1.09714	0.35
42DAP/reference	1.1826	0.008
43DAP/reference	1.87186	0.074
47DAP/reference	1.7204	0.019
52DAP/reference	N/A	N/A
57DAP/reference	1.13311	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97312	0.688
17DAP/reference	0.81581	0.025
27DAP/reference	1.28621	0.178
39DAP/reference	0.90261	0.099
41DAP/reference	1.07387	0.548
42DAP/reference	1.06704	0.649
43DAP/reference	0.7575	0.033
47DAP/reference	0.9173	0.055
52DAP/reference	0.64864	0.003
57DAP/reference	0.57522	0.002

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.13778	0.19
17DAP/reference	0.85795	0.182
27DAP/reference	1.13415	0.198
39DAP/reference	1.46967	0.009
41DAP/reference	1.14817	0.06
42DAP/reference	1.48658	0.01
43DAP/reference	1.44344	0.026
47DAP/reference	0.80657	0.007
52DAP/reference	1.20518	0.33
57DAP/reference	1.04999	0.706

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.07506	0.966
26DAP/20DAP	1.0375	0.896
34DAP/26DAP	0.94315	0.675
51DAP/34DAP	1.14131	0.251
52DAP/51DAP	0.97643	1
53DAP/52DAP	1.1036	0.643
55DAP/53DAP	0.91806	0.489
57DAP/55DAP	1.03375	0.881
62DAP/57DAP	0.96077	0.871
68DAP/62DAP	1.18338	0.549
68DAP/14DAP	1.33588	0.384

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	2.61649	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.68935	0.179
Mature Green Tomato/Ripe Tomato	N/A	N/A
Immature Eggplant/Mature Eggplant	1.8748	0.05
Ripe Pepper/Ripe Tomato	0.75653	1
Mature Eggplant/Ripe Tomato	0.35474	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.04913	0.877
1-1-2/M82	0.98511	1
12-2/M82	0.99993	1
12-4/M82	1.08948	1
1-3/M82	1.33062	0.479
2-1-1/M82	0.85657	0.784
2-1/M82	1.04851	1
2-6/M82	0.97356	1
3-2/M82	0.99368	1
4-1-1/M82	1.07123	1
4-1/M82	0.84572	N/A
4-3-2/M82	1.09242	1
4-3/M82	0.96345	1
5-3/M82	1.1041	0.572
6-2/M82	1.04732	1
6-3/M82	0.99374	1
7-1/M82	0.93734	0.476
7-2/M82	0.9826	1
9-3-2/M82	1.63755	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.28054	0.659
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.97706	1
IL12-4/WTpooled	0.87655	0.554
IL1-4/WTpooled	0.89323	0.457
WT/WTpooled	0.89947	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	1.21309	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.99214	1
DC3000/delta hrp 6h	0.77588	0.942
DC3000/delta hrp 12h	1.07655	1
DC3000/delta hrp 24h	1.00099	1

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.98074	1
DC3000 delta B/DC3000 delta AB	1.0393	0.544

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.1786	1
Exp 36h	1.31372	1
Exp 60h	1.19173	0.237

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

hybridization	ratio	FDR (corrected p value)
self-self	1.0084	1
Var 0h	1.04316	1
Var 12h I row2-row1	1.0992	0.196
Var 12h NI row2-row1	1.05386	0.649
Var 36h I row2-row1	0.78063	0.805
Var 36h NI row2-row1	0.89823	0.522
Var 60h I row2-row1	1.08881	1
Var 60h NI row2-row1	1.05975	0.904
Time course 0hI-0hNI	1.08759	0.574
Time course 12hI-12hNI	1.01777	0.818
Time course 36hI-36hNI	0.99064	0.665
Time course 60hI-60hNI	1.62657	0.015

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)	1.21431	0.455
transgenic ySAMdc/azygous control (breaker)	0.91183	0.49
transgenic ySAMdc/azygous control (red)	1.13649	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.22399	0.051

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.82415	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.23345	0.307
Manapal/WT (break)	1.09736	0.381
Manapal/WT (red)	0.9237	0.242