Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.4.19.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.97259	0.752
27DAP/17DAP	0.91481	0.922
39DAP/27DAP	0.82223	0.564
41DAP/39DAP	1.26546	0.715
42DAP/41DAP	0.89993	1
43DAP/42DAP	1.00958	0.937
47DAP/43DAP	1.3016	0.68
52DAP/47DAP	1.23312	0.772
57DAP/52DAP	1.57111	0.918

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.25076	0.013
17DAP/reference	0.9547	0.321
27DAP/reference	1.02352	0.863
39DAP/reference	1.01248	0.734
41DAP/reference	0.98978	0.814
42DAP/reference	1.25306	0.015
43DAP/reference	0.98615	0.745
47DAP/reference	1.11258	0.125
52DAP/reference	1.53473	0.013
57DAP/reference	1.08946	0.511

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.95195	0.455
27DAP/17DAP	1.18503	0.98
39DAP/27DAP	1.11971	0.932
41DAP/39DAP	1.00589	1
42DAP/41DAP	1.14579	0.762
43DAP/42DAP	0.93021	0.665
47DAP/43DAP	1.27918	0.708
52DAP/47DAP	1.18163	1
57DAP/52DAP	1.20019	1
57DAP/7DAP	1.59725	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9501	0.445
17DAP/reference	1.04135	1
27DAP/reference	0.87822	0.117
39DAP/reference	0.92056	0.264
41DAP/reference	0.9578	0.412
42DAP/reference	0.91636	0.262
43DAP/reference	0.995	0.637
47DAP/reference	1.29467	0.36
52DAP/reference	0.99658	0.621
57DAP/reference	0.957	0.367

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02249	1
17DAP/reference	1.19959	0.061
27DAP/reference	1.20923	0.31
39DAP/reference	1.36482	0.059
41DAP/reference	1.78582	0.005
42DAP/reference	1.52349	0.009
43DAP/reference	1.06799	0.929
47DAP/reference	1.15093	0.031
52DAP/reference	1.15976	0.085
57DAP/reference	1.03574	0.887

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04193	1
17DAP/reference	0.8856	0.205
27DAP/reference	0.85494	0.133
39DAP/reference	0.87909	0.05
41DAP/reference	0.96837	0.56
42DAP/reference	1.07706	0.836
43DAP/reference	1.22145	0.314
47DAP/reference	1.27374	0.309
52DAP/reference	0.98754	0.718
57DAP/reference	2.27054	0.005

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.05597	1
26DAP/20DAP	0.95064	1
34DAP/26DAP	1.36932	0.819
51DAP/34DAP	1.02093	0.957
52DAP/51DAP	1.28827	0.261
53DAP/52DAP	0.78614	0.226
55DAP/53DAP	1.15337	0.964
57DAP/55DAP	0.9541	0.804
62DAP/57DAP	0.95947	0.871
68DAP/62DAP	1.32277	0.557
68DAP/14DAP	1.09692	0.889

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.91062	0.635

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.95375	0.658
Mature Green Tomato/Ripe Tomato	N/A	N/A
Immature Eggplant/Mature Eggplant	1.63139	0.05
Ripe Pepper/Ripe Tomato	0.90732	1
Mature Eggplant/Ripe Tomato	0.45378

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	N/A	N/A
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	N/A	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	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	N/A	N/A
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.96278	1
IL2-6/WTpooled	0.86992
IL7-5/WTpooled	1.07938	0.792
IL7-3/WTpooled	1.21375	1
IL12-4/WTpooled	0.85362	1
IL1-4/WTpooled	1.00062	1
WT/WTpooled	1.16221	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	0.90423

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	N/A	N/A
DC3000/delta hrp 6h	0.83669	0.95
DC3000/delta hrp 12h	1.11364	1
DC3000/delta hrp 24h	1.01962	1

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.44214
DC3000 delta B/DC3000 delta AB	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.05111	1
Exp 36h	1.04432	1
Exp 60h	1.16062	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.1462	1
Var 0h	N/A	N/A
Var 12h I row2-row1	5.34987	0.196
Var 12h NI row2-row1	0.41435	1
Var 36h I row2-row1	1.21851	0.601
Var 36h NI row2-row1	N/A	N/A
Var 60h I row2-row1	0.99072	1
Var 60h NI row2-row1	1.52625
Time course 0hI-0hNI	0.92747	0.799
Time course 12hI-12hNI	0.89187	0.646
Time course 36hI-36hNI	1.03714	0.975
Time course 60hI-60hNI	7.3701	0.115

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)	1.20356	0.431
transgenic ySAMdc/azygous control (breaker)	0.4516	0.142
transgenic ySAMdc/azygous control (red)	1.11422	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.042	0.17

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.60357	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.1689	0.096
Manapal/WT (break)	1.29424	1
Manapal/WT (red)	N/A	N/A