Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-4.1.17.18

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.19267	0.901
27DAP/17DAP	2.06419	0.362
39DAP/27DAP	0.70273	0.458
41DAP/39DAP	1.3295	0.715
42DAP/41DAP	0.87285	1
43DAP/42DAP	5.21107	0.02
47DAP/43DAP	0.41286	0.049
52DAP/47DAP	1.22903	0.869
57DAP/52DAP	0.94671	0.932

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.90562	0.014
17DAP/reference	0.78524	0.111
27DAP/reference	0.79093	0.109
39DAP/reference	0.68278	0.02
41DAP/reference	0.70455	0.039
42DAP/reference	1.01738	0.707
43DAP/reference	0.57771	0.013
47DAP/reference	0.59954	0.001
52DAP/reference	0.60706	0.019
57DAP/reference	0.59633	0.01

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.79565	0.376
27DAP/17DAP	4.2237	0.02
39DAP/27DAP	0.69568	0.057
41DAP/39DAP	0.46588	0.013
42DAP/41DAP	0.97093	0.743
43DAP/42DAP	1.15536	0.324
47DAP/43DAP	1.11202	0.765
52DAP/47DAP	2.2837	0.05
57DAP/52DAP	1.46368	0.197
57DAP/7DAP	1.22698	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.76632	0.115
17DAP/reference	0.71832	0.028
27DAP/reference	1.0294	1
39DAP/reference	0.67483	0.017
41DAP/reference	0.81964	0.107
42DAP/reference	1.04274	0.612
43DAP/reference	1.08929	0.603
47DAP/reference	0.8631	0.293
52DAP/reference	0.65397	0.012
57DAP/reference	0.95565	0.353

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.60824	0.069
17DAP/reference	1.37138	0.081
27DAP/reference	1.14408	0.552
39DAP/reference	0.70627	0.062
41DAP/reference	1.03301	1
42DAP/reference	0.99599	0.655
43DAP/reference	0.79688	0.035
47DAP/reference	0.83753	0.051
52DAP/reference	0.64394	0.005
57DAP/reference	0.80871	0.099

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.75308	0.052
17DAP/reference	0.88374	0.243
27DAP/reference	0.82697	0.085
39DAP/reference	0.67226	0.015
41DAP/reference	0.74184	0.043
42DAP/reference	1.24069	0.158
43DAP/reference	0.88631	0.237
47DAP/reference	0.53307	0.005
52DAP/reference	0.99923	0.482
57DAP/reference	0.73477	0.064

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.82768	1
26DAP/20DAP	0.95519	1
34DAP/26DAP	1.36771	0.819
51DAP/34DAP	1.17628	0.73
52DAP/51DAP	1.89332	0.036
53DAP/52DAP	0.96076	0.862
55DAP/53DAP	1.07365	0.976
57DAP/55DAP	1.20923	0.955
62DAP/57DAP	1.18629	0.217
68DAP/62DAP	1.00025	0.863
68DAP/14DAP	1.18579	N/A

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.93058	0.269

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.18039	0.417
Mature Green Tomato/Ripe Tomato	0.8275	0.347
Immature Eggplant/Mature Eggplant	0.75933	0.254
Ripe Pepper/Ripe Tomato	0.36644	0.224
Mature Eggplant/Ripe Tomato	0.76911	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.17344	0.742
1-1-2/M82	0.96018	0.804
12-2/M82	0.79182	N/A
12-4/M82	1.4983	1
1-3/M82	0.82768	N/A
2-1-1/M82	0.73113	N/A
2-1/M82	0.75317	N/A
2-6/M82	1.11909	0.329
3-2/M82	0.97431	N/A
4-1-1/M82	0.88093	N/A
4-1/M82	1.38657	N/A
4-3-2/M82	0.75311	N/A
4-3/M82	1.27744	0.268
5-3/M82	1.14052	1
6-2/M82	N/A	N/A
6-3/M82	0.64285	N/A
7-1/M82	0.93621	N/A
7-2/M82	1.09725	0.385
9-3-2/M82	1.00259	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.90143	0.243
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	0.80284	1
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	0.78615	N/A
IL1-4/WTpooled	1.24396	0.399
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	1.02528	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.99647	1
DC3000/delta hrp 6h	0.88964	0.95
DC3000/delta hrp 12h	0.77188	1
DC3000/delta hrp 24h	0.92456	0.534

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.10807	0.25
DC3000 delta B/DC3000 delta AB	1.0925	0.449

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.87246	1
Exp 36h	0.7163	0.623
Exp 60h	1.06425	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.03011	1
Var 0h	1.07308	1
Var 12h I row2-row1	1.0411	0.283
Var 12h NI row2-row1	1.10229	1
Var 36h I row2-row1	1.27403	0.489
Var 36h NI row2-row1	0.93656	0.791
Var 60h I row2-row1	0.97296	N/A
Var 60h NI row2-row1	1.11701	0.904
Time course 0hI-0hNI	1.03476	0.833
Time course 12hI-12hNI	0.92789	0.272
Time course 36hI-36hNI	0.90516	0.076
Time course 60hI-60hNI	0.4491	0.005

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)	1.18304	0.294
transgenic ySAMdc/azygous control (breaker)	1.54855	0.248
transgenic ySAMdc/azygous control (red)	1.75653	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.21923	0.239

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.63438	0.084
Manapal/WT (break)	0.69843	1
Manapal/WT (red)	1.7906	0.222