Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.3.13.17

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.96758	0.77
27DAP/17DAP	1.08019	0.872
39DAP/27DAP	0.94221	0.652
41DAP/39DAP	1.04158	0.929
42DAP/41DAP	1.1176	0.843
43DAP/42DAP	0.84626	0.705
47DAP/43DAP	0.89455	0.671
52DAP/47DAP	1.06782	0.861
57DAP/52DAP	1.01663	0.992

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.06589	0.278
17DAP/reference	1.0394	0.342
27DAP/reference	1.04718	0.365
39DAP/reference	0.99635	0.975
41DAP/reference	0.97128	0.667
42DAP/reference	0.98695	0.305
43DAP/reference	1.01961	0.838
47DAP/reference	0.98685	0.445
52DAP/reference	0.99464	0.668
57DAP/reference	1.06489	0.068

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.03358	0.662
27DAP/17DAP	1.02292	0.924
39DAP/27DAP	0.99868	1
41DAP/39DAP	1.05028	0.773
42DAP/41DAP	1.01623	0.872
43DAP/42DAP	0.99026	0.902
47DAP/43DAP	1.00158	0.973
52DAP/47DAP	0.95652	0.694
57DAP/52DAP	1.00013	0.926
57DAP/7DAP	1.02121	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92724	0.361
17DAP/reference	1.01455	1
27DAP/reference	0.9671	0.402
39DAP/reference	1.22954	0.126
41DAP/reference	1.09847	0.43
42DAP/reference	1.05581	0.889
43DAP/reference	0.97026	0.305
47DAP/reference	1.06593	1
52DAP/reference	0.92183	0.232
57DAP/reference	1.19885	0.232

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97976	0.607
17DAP/reference	1.00056	0.873
27DAP/reference	1.00111	0.79
39DAP/reference	1.01117	0.978
41DAP/reference	0.9847	0.472
42DAP/reference	0.98606	0.594
43DAP/reference	1.00935	0.875
47DAP/reference	0.98335	0.379
52DAP/reference	0.96124	0.072
57DAP/reference	1.00259	0.916

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99117	0.653
17DAP/reference	1.05948	0.65
27DAP/reference	0.87768	0.092
39DAP/reference	0.87269	0.111
41DAP/reference	1.02894	1
42DAP/reference	0.89996	0.287
43DAP/reference	0.96751	0.523
47DAP/reference	0.9974	0.708
52DAP/reference	0.71264	0.16
57DAP/reference	0.95069	0.229

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.00501	0.966
26DAP/20DAP	0.9762	1
34DAP/26DAP	1.01404	1
51DAP/34DAP	1.0108	0.962
52DAP/51DAP	0.97061	1
53DAP/52DAP	1.11143	0.537
55DAP/53DAP	1.0567	0.782
57DAP/55DAP	0.94467	0.76
62DAP/57DAP	0.90759	0.28
68DAP/62DAP	1.1313	0.253
68DAP/14DAP	1.09103	0.594

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.01647	0.954

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.48817	0.101
Mature Green Tomato/Ripe Tomato	N/A	N/A
Immature Eggplant/Mature Eggplant	1.20629	0.363
Ripe Pepper/Ripe Tomato	0.93399	1
Mature Eggplant/Ripe Tomato	0.72585	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.05195	1
1-1-2/M82	1.03282	1
12-2/M82	0.94481	0.955
12-4/M82	0.93043	1
1-3/M82	0.93605	0.501
2-1-1/M82	0.99167	1
2-1/M82	1.39108	1
2-6/M82	0.98754	1
3-2/M82	1.05383	0.967
4-1-1/M82	1.03593	1
4-1/M82	1.06731	0.853
4-3-2/M82	0.99038	1
4-3/M82	0.95612	0.72
5-3/M82	0.99369	1
6-2/M82	1.00968	1
6-3/M82	0.99533	1
7-1/M82	0.99	1
7-2/M82	0.94721	0.881
9-3-2/M82	0.98452	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.88315	0.348
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.00624	1
IL12-4/WTpooled	0.92985	1
IL1-4/WTpooled	1.17319	0.426
WT/WTpooled	0.97504	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	1.42513	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.01431	0.921
DC3000/delta hrp 6h	0.82142	0.95
DC3000/delta hrp 12h	0.91757	1
DC3000/delta hrp 24h	1.07557	0.553

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.01442	1
DC3000 delta B/DC3000 delta AB	1.04394	0.528

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.03159	1
Exp 36h	1.33967	1
Exp 60h	1.96832	0.283

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98596	1
Var 0h	0.98467	1
Var 12h I row2-row1	1.14541	0.272
Var 12h NI row2-row1	1.08048	1
Var 36h I row2-row1	0.88718	0.805
Var 36h NI row2-row1	1.02055	1
Var 60h I row2-row1	1.16194	0.562
Var 60h NI row2-row1	1.07101	0.904
Time course 0hI-0hNI	1.01233	1
Time course 12hI-12hNI	1.06246	0.599
Time course 36hI-36hNI	1.08409	0.316
Time course 60hI-60hNI	1.1247	0.06

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)	0.97573	0.409
transgenic ySAMdc/azygous control (breaker)	0.91308	0.49
transgenic ySAMdc/azygous control (red)	1.24192	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.97144	0.077

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.88947	0.308

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.80838	0.172
Manapal/WT (break)	0.93914	1
Manapal/WT (red)	0.91756	0.424