Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.3.19.4

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.0889	0.739
27DAP/17DAP	0.98384	0.984
39DAP/27DAP	0.75144	0.392
41DAP/39DAP	1.25801	0.282
42DAP/41DAP	1.10754	0.941
43DAP/42DAP	1.02709	1
47DAP/43DAP	1.34802	0.542
52DAP/47DAP	0.74682	0.41
57DAP/52DAP	1.05097	0.996

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.28921	0.071
17DAP/reference	1.22654
27DAP/reference	1.16022	0.205
39DAP/reference	1.22647	0.186
41DAP/reference	1.3936	0.013
42DAP/reference	1.42371	0.001
43DAP/reference	1.03854	0.928
47DAP/reference	1.35971	0.001
52DAP/reference	N/A	N/A
57DAP/reference	1.15408	0.529

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.96469	0.629
27DAP/17DAP	0.99586	0.969
39DAP/27DAP	1.07763	0.56
41DAP/39DAP	1.15344	0.623
42DAP/41DAP	0.96742	0.715
43DAP/42DAP	1.02256	0.746
47DAP/43DAP	0.98387	0.933
52DAP/47DAP	0.99973	0.979
57DAP/52DAP	0.95348	0.608
57DAP/7DAP	0.97837	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97896	0.326
17DAP/reference	0.97668	0.039
27DAP/reference	0.94779	0.094
39DAP/reference	1.04579	0.186
41DAP/reference	1.05369	0.27
42DAP/reference	1.02869	0.308
43DAP/reference	0.97607	0.252
47DAP/reference	0.98459	0.504
52DAP/reference	1.02627	0.526
57DAP/reference	0.97859	0.17

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.21767	0.17
17DAP/reference	1.37103	0.012
27DAP/reference	1.35885	0.041
39DAP/reference	1.54005	0.011
41DAP/reference	1.51887	0.005
42DAP/reference	1.52655	0.008
43DAP/reference	1.10301	0.575
47DAP/reference	1.35748	0.011
52DAP/reference	1.51803	0.006
57DAP/reference	1.53746	0.009

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97584	0.127
17DAP/reference	1.00117	1
27DAP/reference	1.03309	0.284
39DAP/reference	0.97755	0.43
41DAP/reference	1.01402	0.754
42DAP/reference	0.99552	0.816
43DAP/reference	1.12375	0.555
47DAP/reference	0.92656	0.069
52DAP/reference	1.02121	0.928
57DAP/reference	1.13259	0.132

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.10837	0.966
26DAP/20DAP	0.77686	0.317
34DAP/26DAP	1.01186	1
51DAP/34DAP	1.08884	0.416
52DAP/51DAP	1.02048	0.873
53DAP/52DAP	0.96296	0.83
55DAP/53DAP	1.13737	0.576
57DAP/55DAP	1.15599	0.376
62DAP/57DAP	1.0892	1
68DAP/62DAP	0.9593	0.7
68DAP/14DAP	0.85057	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.82363	0.122

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.87145	0.017
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.91246	1
Mature Eggplant/Ripe Tomato	1.264

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.1567	0.409
1-1-2/M82	0.91221	1
12-2/M82	1.07987	1
12-4/M82	0.95807	1
1-3/M82	0.88456	0.378
2-1-1/M82	1.09498	0.764
2-1/M82	1.10346	1
2-6/M82	0.94715	1
3-2/M82	1.08112
4-1-1/M82	0.9107	1
4-1/M82	0.83581	1
4-3-2/M82	0.89078	1
4-3/M82	0.95939	1
5-3/M82	1.04276	0.496
6-2/M82	1.11953	1
6-3/M82	1.08521	1
7-1/M82	1.09369	1
7-2/M82	0.98799	1
9-3-2/M82	0.85801	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.98997	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.04024
IL12-4/WTpooled	1.25664	0.737
IL1-4/WTpooled	1.08956	1
WT/WTpooled	1.01188	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	0.69758	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.95996	1
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	1.08205	1
DC3000/delta hrp 24h	1.14009	0.516

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.80402	0.088
DC3000 delta B/DC3000 delta AB	0.95544	0.619

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.09994	1
Exp 36h	N/A	N/A
Exp 60h	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
self-self	0.96883	1
Var 0h	1.30506	0.782
Var 12h I row2-row1	0.83603	0.338
Var 12h NI row2-row1	0.70286	0.315
Var 36h I row2-row1	1.02757	1
Var 36h NI row2-row1	1.39877	0.482
Var 60h I row2-row1	1.01668	1
Var 60h NI row2-row1	1.1666	0.904
Time course 0hI-0hNI	0.74934	0.044
Time course 12hI-12hNI	1.03332	0.811
Time course 36hI-36hNI	0.8193	0.084
Time course 60hI-60hNI	0.33515	0.006

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)	0.89316	0.567
transgenic ySAMdc/azygous control (breaker)	0.99239	1
transgenic ySAMdc/azygous control (red)	0.79152	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.81712	0.049

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.67372	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	N/A	N/A
Manapal/WT (break)	N/A	N/A
Manapal/WT (red)	1.10954	1