Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-3.3.6.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.40369	0.498
27DAP/17DAP	0.99751	0.882
39DAP/27DAP	1.03112	0.899
41DAP/39DAP	0.95551	0.811
42DAP/41DAP	0.94457	1
43DAP/42DAP	0.92918	0.801
47DAP/43DAP	1.11192	0.463
52DAP/47DAP	0.90459	0.698
57DAP/52DAP	1.13524	0.92

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98992	0.707
17DAP/reference	1.01368	0.565
27DAP/reference	0.97847	0.359
39DAP/reference	1.03731	0.691
41DAP/reference	0.97209	0.267
42DAP/reference	0.91414	0.005
43DAP/reference	0.96124	0.429
47DAP/reference	0.94442	0.106
52DAP/reference	0.90742	0.258
57DAP/reference	0.93841	0.235

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.3243	0.312
27DAP/17DAP	1.04743	0.957
39DAP/27DAP	1.08218	0.751
41DAP/39DAP	0.90237	0.696
42DAP/41DAP	1.00572	0.876
43DAP/42DAP	0.83373	0.034
47DAP/43DAP	1.0483	0.948
52DAP/47DAP	1.13025	0.624
57DAP/52DAP	1.04407	0.874
57DAP/7DAP	1.14482	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96436	0.613
17DAP/reference	1.03571	1
27DAP/reference	0.94721	0.348
39DAP/reference	1.21836	0.175
41DAP/reference	1.00575	0.811
42DAP/reference	1.20072	0.233
43DAP/reference	1.3282	0.009
47DAP/reference	0.97506	0.671
52DAP/reference	1.00424	0.621
57DAP/reference	1.1863	0.1

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93116	0.518
17DAP/reference	0.96256	0.434
27DAP/reference	1.06366	0.834
39DAP/reference	0.98111	0.497
41DAP/reference	0.96089	0.403
42DAP/reference	0.95978	0.237
43DAP/reference	1.02857	0.751
47DAP/reference	0.94742	0.05
52DAP/reference	0.99144	0.619
57DAP/reference	0.99976	0.834

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.09399	0.224
17DAP/reference	0.97568	0.624
27DAP/reference	0.95435	0.397
39DAP/reference	1.06657	0.318
41DAP/reference	1.23826	0.104
42DAP/reference	1.01921	1
43DAP/reference	1.25077	0.381
47DAP/reference	0.97718	0.478
52DAP/reference	1.15324	0.592
57DAP/reference	0.86737	0.122

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.93858	0.841
26DAP/20DAP	1.50178	0.19
34DAP/26DAP	0.90832	0.771
51DAP/34DAP	1.38968	0.072
52DAP/51DAP	0.87099	1
53DAP/52DAP	1.03191	1
55DAP/53DAP	0.73195	0.072
57DAP/55DAP	1.15704	0.779
62DAP/57DAP	0.98708	0.994
68DAP/62DAP	0.99792	0.914
68DAP/14DAP	1.14884	0.504

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.67741	0.031

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.84999	0.318
Mature Green Tomato/Ripe Tomato	1.58416	0.077
Immature Eggplant/Mature Eggplant	1.27924	0.078
Ripe Pepper/Ripe Tomato	1.64255	1
Mature Eggplant/Ripe Tomato	2.32289	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.05541	N/A
1-1-2/M82	0.98515	N/A
12-2/M82	N/A	N/A
12-4/M82	0.82195	0.619
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	0.7369	N/A
2-6/M82	0.8413	N/A
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	1.17192	N/A
4-3/M82	1.76536	1
5-3/M82	0.97705	1
6-2/M82	1.2828	N/A
6-3/M82	0.93257	1
7-1/M82	1.08363	N/A
7-2/M82	0.93018	N/A
9-3-2/M82	0.81497	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.95964	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.89282	1
IL12-4/WTpooled	0.92433	0.539
IL1-4/WTpooled	0.89099	0.457
WT/WTpooled	1.0175	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	0.99217	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.05283	0.914
DC3000/delta hrp 6h	0.96958	0.95
DC3000/delta hrp 12h	1.06233	1
DC3000/delta hrp 24h	0.83034	0.067

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.19792	0.384
DC3000 delta B/DC3000 delta AB	1.13073	0.321

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.89316	1
Exp 36h	1.27089	0.693
Exp 60h	1.09087	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	1.04277	1
Var 0h	1.06256	0.782
Var 12h I row2-row1	1.09518	0.506
Var 12h NI row2-row1	1.2012	1
Var 36h I row2-row1	0.82865	1
Var 36h NI row2-row1	1.24188	0.482
Var 60h I row2-row1	0.705	0.287
Var 60h NI row2-row1	1.15547	0.904
Time course 0hI-0hNI	1.00416	1
Time course 12hI-12hNI	1.02894	0.762
Time course 36hI-36hNI	1.00386	0.73
Time course 60hI-60hNI	0.76462	0.026

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)	1.33929	0.221
transgenic ySAMdc/azygous control (breaker)	1.01114	1
transgenic ySAMdc/azygous control (red)	0.92246	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.99822	0.858

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.95109	0.431

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.77971	0.172
Manapal/WT (break)	0.64689	0.299
Manapal/WT (red)	1.11013	1