Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.2.2.2

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.10921	0.827
27DAP/17DAP	1.03616	1
39DAP/27DAP	1.3897	0.232
41DAP/39DAP	0.7322	0.103
42DAP/41DAP	1.05979	0.999
43DAP/42DAP	0.92772	0.874
47DAP/43DAP	0.62769	0.083
52DAP/47DAP	0.85955	0.612
57DAP/52DAP	0.88138	0.827

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.45279	0.034
17DAP/reference	1.14726	0.457
27DAP/reference	0.9756	0.668
39DAP/reference	1.37909	0.106
41DAP/reference	1.11386	0.516
42DAP/reference	1.47249	0.001
43DAP/reference	1.13507	0.217
47DAP/reference	1.06726	0.391
52DAP/reference	0.91648	0.267
57DAP/reference	1.04482	0.853

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.16394	0.305
27DAP/17DAP	0.94582	0.748
39DAP/27DAP	0.81765	0.044
41DAP/39DAP	1.56213	0.612
42DAP/41DAP	0.95787	0.662
43DAP/42DAP	1.00904	0.83
47DAP/43DAP	0.98351	0.923
52DAP/47DAP	0.88112	0.254
57DAP/52DAP	0.87877	0.424
57DAP/7DAP	0.78921	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.9073	0.024
17DAP/reference	1.34357	0.006
27DAP/reference	1.33672	0.011
39DAP/reference	1.81316	0.005
41DAP/reference	1.47382	0.01
42DAP/reference	1.72547	0.007
43DAP/reference	1.64351	0.008
47DAP/reference	1.8277	0.014
52DAP/reference	1.63834	0.007
57DAP/reference	1.37345	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.0517	0.979
17DAP/reference	1.72451	0.009
27DAP/reference	1.8354	0.013
39DAP/reference	1.69897	0.011
41DAP/reference	1.70174	0.005
42DAP/reference	1.8596	0.007
43DAP/reference	1.45994	0.059
47DAP/reference	1.87706	0.008
52DAP/reference	1.2555	0.036
57DAP/reference	1.00882	0.649

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.26465	0.036
17DAP/reference	1.35333	0.215
27DAP/reference	1.04222	0.487
39DAP/reference	1.24189	0.014
41DAP/reference	1.33276	0.034
42DAP/reference	1.53892	0.036
43DAP/reference	1.64287	0.056
47DAP/reference	1.20395	0.372
52DAP/reference	0.96178	0.623
57DAP/reference	1.20923	0.531

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.01775	1
26DAP/20DAP	1.28898	1
34DAP/26DAP	1.91688	1
51DAP/34DAP	1.00342	0.967
52DAP/51DAP	0.80251	1
53DAP/52DAP	0.64104	0.049
55DAP/53DAP	0.73766	0.098
57DAP/55DAP	1.63195	0.301
62DAP/57DAP	0.8278	0.28
68DAP/62DAP	1.27814	0.166
68DAP/14DAP	1.36821	0.119

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.44306	0.023

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.82712	0.279
Mature Green Tomato/Ripe Tomato	2.39449	0.028
Immature Eggplant/Mature Eggplant	2.12746	0.05
Ripe Pepper/Ripe Tomato	1.01645	1
Mature Eggplant/Ripe Tomato	0.63604	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.0607	0.742
1-1-2/M82	1.07921	1
12-2/M82	0.83351	0.464
12-4/M82	1.03006	1
1-3/M82	1.33811	0.479
2-1-1/M82	0.89005	0.784
2-1/M82	0.8441	0.325
2-6/M82	1.15069	0.452
3-2/M82	0.9211
4-1-1/M82	0.9587	1
4-1/M82	1.22688
4-3-2/M82	1.67603	0.241
4-3/M82	1.26229	0.268
5-3/M82	1.11352	1
6-2/M82	N/A	N/A
6-3/M82	0.96201	1
7-1/M82	1.07211	1
7-2/M82	1.11363	1
9-3-2/M82	1.27428

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.65955	0.321
IL2-6/WTpooled	0.72345	0.473
IL7-5/WTpooled	1.23714	0.792
IL7-3/WTpooled	0.88842	0.418
IL12-4/WTpooled	1.1037	0.516
IL1-4/WTpooled	1.56976	0.426
WT/WTpooled	0.95541	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	1.02117	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.03845	0.921
DC3000/delta hrp 6h	1.0349	1
DC3000/delta hrp 12h	1.04942	1
DC3000/delta hrp 24h	0.95602	0.711

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.04531	0.441
DC3000 delta B/DC3000 delta AB	1.02466	0.687

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.96286	1
Exp 36h	1.08832	1
Exp 60h	1.00696	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98427	1
Var 0h	1.04086	0.98
Var 12h I row2-row1	1.08585	0.654
Var 12h NI row2-row1	1.00238	1
Var 36h I row2-row1	1.02394	1
Var 36h NI row2-row1	1.02721	1
Var 60h I row2-row1	0.66137
Var 60h NI row2-row1	0.89112	0.351
Time course 0hI-0hNI	1.03108	0.852
Time course 12hI-12hNI	0.97457	0.802
Time course 36hI-36hNI	0.98897	0.632
Time course 60hI-60hNI	1.02641	1

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)	0.95085	0.338
transgenic ySAMdc/azygous control (breaker)	0.95626	1
transgenic ySAMdc/azygous control (red)	1.10786	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.06376	0.089

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.64862	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.79636	0.172
Manapal/WT (break)	0.82897	1
Manapal/WT (red)	0.76043	0.181