Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.3.8.13

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.79145	0.419
27DAP/17DAP	1.56562	0.815
39DAP/27DAP	1.13724	1
41DAP/39DAP	1.72024	0.037
42DAP/41DAP	1.12232	0.903
43DAP/42DAP	0.81696	0.776
47DAP/43DAP	0.77921	0.496
52DAP/47DAP	0.54804	0.299
57DAP/52DAP	0.79821	0.759

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.81233	0.083
17DAP/reference	0.91647	0.342
27DAP/reference	0.85611	0.106
39DAP/reference	0.8555	0.078
41DAP/reference	0.90715	0.434
42DAP/reference	0.91155	0.088
43DAP/reference	0.90455	0.18
47DAP/reference	1.07442	0.593
52DAP/reference	0.88354	0.096
57DAP/reference	1.02816	0.901

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.36389	0.069
27DAP/17DAP	1.21332	0.253
39DAP/27DAP	0.83362	0.094
41DAP/39DAP	0.99094	0.98
42DAP/41DAP	0.97484	0.777
43DAP/42DAP	0.8248	0.026
47DAP/43DAP	1.04491	0.853
52DAP/47DAP	1.13113	0.645
57DAP/52DAP	0.97557	0.685
57DAP/7DAP	0.92272	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98046	0.445
17DAP/reference	1.2281	0.102
27DAP/reference	1.15637	0.16
39DAP/reference	0.94278	0.126
41DAP/reference	0.92872	0.298
42DAP/reference	0.88482	0.1
43DAP/reference	0.89353	0.192
47DAP/reference	1.07693	0.618
52DAP/reference	1.00199	1
57DAP/reference	0.88912	0.057

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93353	0.306
17DAP/reference	0.72723	0.007
27DAP/reference	0.78304	0.036
39DAP/reference	0.82756	0.077
41DAP/reference	0.80017	0.11
42DAP/reference	0.79568	0.05
43DAP/reference	1.01986	1
47DAP/reference	1.08104	0.377
52DAP/reference	0.86245	0.131
57DAP/reference	0.91891	0.068

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.06018	0.202
17DAP/reference	0.93756	0.499
27DAP/reference	1.00109	0.843
39DAP/reference	1.01171	1
41DAP/reference	0.92384	0.293
42DAP/reference	1.01501	1
43DAP/reference	0.77576	0.106
47DAP/reference	0.83756	0.054
52DAP/reference	0.89733	0.415
57DAP/reference	0.76562	0.016

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.7388	0.355
26DAP/20DAP	0.93271	1
34DAP/26DAP	1.0655	1
51DAP/34DAP	1.03758	0.759
52DAP/51DAP	0.99449	1
53DAP/52DAP	1.06465	0.83
55DAP/53DAP	0.96379	0.761
57DAP/55DAP	0.98258	0.902
62DAP/57DAP	0.88606	0.681
68DAP/62DAP	1.15874	0.919
68DAP/14DAP	1.3699	0.558

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.0613	0.821

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.01035	1
Mature Green Tomato/Ripe Tomato	N/A	N/A
Immature Eggplant/Mature Eggplant	14.4949	0.05
Ripe Pepper/Ripe Tomato	0.73964	0.293
Mature Eggplant/Ripe Tomato	0.51284	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.21345
1-1-2/M82	0.56405
12-2/M82	1.20422	1
12-4/M82	0.71811	1
1-3/M82	1.24211
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	1.17872
3-2/M82	0.42813
4-1-1/M82	1.30605	0.657
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	1.96058	1
5-3/M82	1.25954	0.415
6-2/M82	0.87984
6-3/M82	0.67359	0.637
7-1/M82	N/A	N/A
7-2/M82	0.62659
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	2.42269
IL7-5/WTpooled	1.9016
IL7-3/WTpooled	1.03193
IL12-4/WTpooled	1.47715	0.785
IL1-4/WTpooled	0.89423	1
WT/WTpooled	0.79858	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	1.21528	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.88339	1
DC3000/delta hrp 6h	1.03915	0.95
DC3000/delta hrp 12h	0.98215	1
DC3000/delta hrp 24h	1.94136	0.05

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.10609	0.121
DC3000 delta B/DC3000 delta AB	1.12393	0.381

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.5018	1
Exp 36h	3.18649	0.693
Exp 60h	1.7207	0.237

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99914	1
Var 0h	1.10236	0.782
Var 12h I row2-row1	1.13758	0.211
Var 12h NI row2-row1	0.93734	0.82
Var 36h I row2-row1	0.96871	1
Var 36h NI row2-row1	1.01947	1
Var 60h I row2-row1	1.04688	0.543
Var 60h NI row2-row1	1.04841	0.904
Time course 0hI-0hNI	1.01738	0.852
Time course 12hI-12hNI	0.95195	0.283
Time course 36hI-36hNI	0.92857	0.284
Time course 60hI-60hNI	0.90954	0.081

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)	1.08979	1
transgenic ySAMdc/azygous control (breaker)	0.66984	0.173
transgenic ySAMdc/azygous control (red)	1.00845	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.11896	0.073

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.95652	1
Manapal/WT (break)	1.05796	1
Manapal/WT (red)	0.51597	0.188