Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.1.9.9

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.27169	0.463
27DAP/17DAP	0.78536	0.462
39DAP/27DAP	1.24413	0.655
41DAP/39DAP	0.85572	0.412
42DAP/41DAP	0.82619	0.774
43DAP/42DAP	0.90395	0.743
47DAP/43DAP	1.03695	0.926
52DAP/47DAP	1.22294	0.541
57DAP/52DAP	1.10679	0.977

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90682	0.224
17DAP/reference	0.67265	0.046
27DAP/reference	0.81514	0.223
39DAP/reference	0.76409	0.194
41DAP/reference	0.62709	0.049
42DAP/reference	0.80606	0.025
43DAP/reference	0.83493	0.018
47DAP/reference	0.94684	0.279
52DAP/reference	1.46244	0.021
57DAP/reference	1.153	0.073

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.00465	1
27DAP/17DAP	1.02804	0.9
39DAP/27DAP	0.99537	1
41DAP/39DAP	0.9793	0.959
42DAP/41DAP	0.9777	0.787
43DAP/42DAP	1.04968	0.176
47DAP/43DAP	0.94267	0.357
52DAP/47DAP	0.98806	0.935
57DAP/52DAP	1.02652	0.806
57DAP/7DAP	1.10506	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98547	0.495
17DAP/reference	1.03538	0.199
27DAP/reference	1.02274	0.371
39DAP/reference	0.99647	0.745
41DAP/reference	0.89263	0.044
42DAP/reference	0.83687	0.013
43DAP/reference	0.95776	0.351
47DAP/reference	0.93224	0.222
52DAP/reference	0.91562	0.137
57DAP/reference	0.91359	0.066

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.66093	0.129
17DAP/reference	0.6716	0.052
27DAP/reference	1.20691	0.323
39DAP/reference	1.22559	0.543
41DAP/reference	0.97574	0.459
42DAP/reference	1.06732	0.488
43DAP/reference	0.70951	0.056
47DAP/reference	0.7295	0.015
52DAP/reference	1.16288	0.014
57DAP/reference	0.60337	0.068

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94739	0.249
17DAP/reference	0.90083	0.389
27DAP/reference	1.05662	0.621
39DAP/reference	1.0352	0.353
41DAP/reference	1.04293	0.397
42DAP/reference	1.20518	0.226
43DAP/reference	1.41484	0.105
47DAP/reference	0.91874	0.371
52DAP/reference	0.9485	0.551
57DAP/reference	2.1735	0.018

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.85567	0.773
26DAP/20DAP	0.91115	0.512
34DAP/26DAP	1.02075	1
51DAP/34DAP	0.93863	0.555
52DAP/51DAP	1.08969	0.367
53DAP/52DAP	0.96723	0.848
55DAP/53DAP	1.06583	0.301
57DAP/55DAP	0.97347	0.851
62DAP/57DAP	1.15836	0.833
68DAP/62DAP	5.55636	0.042
68DAP/14DAP	12.1418	0.016

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.92344	0.175

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.04367
Mature Green Tomato/Ripe Tomato	3.01247	0.018
Immature Eggplant/Mature Eggplant	0.33548
Ripe Pepper/Ripe Tomato	0.44719
Mature Eggplant/Ripe Tomato	0.53039	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.91805	1
12-2/M82	N/A	N/A
12-4/M82	1.02798	1
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	1.00255
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	0.81229	1
4-3-2/M82	0.88755	0.487
4-3/M82	1.17629	1
5-3/M82	1.3294	0.496
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	1.16564
7-2/M82	0.77285	0.599
9-3-2/M82	0.93024	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.33308	0.365
IL2-6/WTpooled	0.99138	1
IL7-5/WTpooled	1.03574	1
IL7-3/WTpooled	1.43288	1
IL12-4/WTpooled	1.04475	0.891
IL1-4/WTpooled	1.17257	1
WT/WTpooled	0.92415	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	1.14566	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.90502	0.941
DC3000/delta hrp 6h	1.11272	1
DC3000/delta hrp 12h	0.9333	1
DC3000/delta hrp 24h	0.82871	0.145

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.04691	0.183
DC3000 delta B/DC3000 delta AB	1.08155	0.42

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.95196	1
Exp 36h	0.90139	0.661
Exp 60h	0.88849	0.32

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00256	1
Var 0h	0.49365	1
Var 12h I row2-row1	1.08482	0.348
Var 12h NI row2-row1	0.85047	0.713
Var 36h I row2-row1	1.02695	1
Var 36h NI row2-row1	1.14163	1
Var 60h I row2-row1	1.36252	1
Var 60h NI row2-row1	1.0593	0.904
Time course 0hI-0hNI	1.02397	0.852
Time course 12hI-12hNI	0.99152	0.968
Time course 36hI-36hNI	0.95132	0.45
Time course 60hI-60hNI	0.88751	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)	0.99525	0.931
transgenic ySAMdc/azygous control (breaker)	0.78799	0.15
transgenic ySAMdc/azygous control (red)	1.33792	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.00384	0.766

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.16769	0.093
Manapal/WT (break)	1.7724	0.14
Manapal/WT (red)	1.59103	0.164