Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-5.3.4.17

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.4666	0.315
27DAP/17DAP	1.92272	0.187
39DAP/27DAP	3.29256	0.593
41DAP/39DAP	1.73987	0.516
42DAP/41DAP	1.15311	0.962
43DAP/42DAP	0.84823	0.658
47DAP/43DAP	0.26996	0.043
52DAP/47DAP	1.12656	0.739
57DAP/52DAP	0.82973	0.879

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.80674	0.062
17DAP/reference	0.8749	0.022
27DAP/reference	0.92548	0.24
39DAP/reference	0.91099	0.124
41DAP/reference	0.98388	0.814
42DAP/reference	1.25926	0.068
43DAP/reference	1.00792	1
47DAP/reference	0.84612	0.003
52DAP/reference	1.0079	0.749
57DAP/reference	1.15321	0.249

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.71785	0.219
27DAP/17DAP	1.21365	0.411
39DAP/27DAP	3.3126	0.048
41DAP/39DAP	4.97963	0.005
42DAP/41DAP	0.60609	0.01
43DAP/42DAP	0.39414	0.019
47DAP/43DAP	1.08592	0.788
52DAP/47DAP	1.32971	0.883
57DAP/52DAP	0.56815	0.198
57DAP/7DAP	0.98226	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.6589	0.06
17DAP/reference	1.40307	0.244
27DAP/reference	2.29876	0.035
39DAP/reference	2.5262	0.069
41DAP/reference	1.0758	0.812
42DAP/reference	2.43572	0.1
43DAP/reference	1.55773	0.511
47DAP/reference	1.76067	0.109
52DAP/reference	3.11655	0.009
57DAP/reference	3.40029	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.66467	0.018
17DAP/reference	1.17713	0.824
27DAP/reference	0.92572	0.366
39DAP/reference	1.69834	0.124
41DAP/reference	1.30351	0.027
42DAP/reference	2.03318	0.022
43DAP/reference	1.92425	0.023
47DAP/reference	2.49358	0.009
52DAP/reference	1.33357	0.006
57DAP/reference	2.16045	0.026

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.78803	0.016
17DAP/reference	1.21258	0.865
27DAP/reference	1.826	0.531
39DAP/reference	1.71394	0.087
41DAP/reference	1.65936	0.031
42DAP/reference	5.04253	0.013
43DAP/reference	3.76365	0.023
47DAP/reference	0.84261	0.084
52DAP/reference	2.78421	0.115
57DAP/reference	1.99796	0.209

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.85016	0.708
26DAP/20DAP	1.25885	N/A
34DAP/26DAP	1.55105	N/A
51DAP/34DAP	1.0295	1
52DAP/51DAP	0.76913	1
53DAP/52DAP	1.07935	0.565
55DAP/53DAP	0.93671	0.746
57DAP/55DAP	0.98604	0.914
62DAP/57DAP	0.88728	0.871
68DAP/62DAP	1.52272	0.03
68DAP/14DAP	1.1861	0.042

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	5.02591	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	15.4047	0.015
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	1.04705	N/A
Mature Eggplant/Ripe Tomato	0.22243	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.95391	0.961
1-1-2/M82	1.21775	1
12-2/M82	1.31357	1
12-4/M82	1.38436	1
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	4.55581	N/A
2-6/M82	1.2183	0.425
3-2/M82	2.1711	0.84
4-1-1/M82	2.15764	1
4-1/M82	1.39644	N/A
4-3-2/M82	1.2534	N/A
4-3/M82	0.56552	N/A
5-3/M82	1.53543	0.572
6-2/M82	5.36294	0.235
6-3/M82	1.88051	1
7-1/M82	0.1741	N/A
7-2/M82	1.37763	N/A
9-3-2/M82	2.45869	0.196

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.97429	1
IL2-6/WTpooled	0.76063	0.383
IL7-5/WTpooled	1.17529	0.75
IL7-3/WTpooled	1.00549	1
IL12-4/WTpooled	1.05091	0.785
IL1-4/WTpooled	1.07964	1
WT/WTpooled	1.07096	0.999

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	2.25337	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.98794	1
DC3000/delta hrp 6h	1.05152	1
DC3000/delta hrp 12h	0.9158	1
DC3000/delta hrp 24h	1.69979	0.039

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	2.13577	N/A
DC3000 delta B/DC3000 delta AB	4.62924	0.062

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.97137	0.228
Exp 36h	1.6566	0.693
Exp 60h	3.06009	0.221

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)	0.36386	0.246
transgenic ySAMdc/azygous control (breaker)	0.47703	0.139
transgenic ySAMdc/azygous control (red)	1.05597	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.01422	0.687

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.09922	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.49418	1
Manapal/WT (break)	0.37917	0.333
Manapal/WT (red)	0.43562	0.315