Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.1.4.19

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.18587	0.656
27DAP/17DAP	0.8707	0.679
39DAP/27DAP	1.35426	0.426
41DAP/39DAP	0.57542	0.046
42DAP/41DAP	0.97673	1
43DAP/42DAP	1.10877	1
47DAP/43DAP	0.87561	0.58
52DAP/47DAP	0.96763	0.859
57DAP/52DAP	1.28928	0.907

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87268	0.08
17DAP/reference	0.84859	0.18
27DAP/reference	0.87625	0.068
39DAP/reference	0.69227	0.009
41DAP/reference	0.69728	0.065
42DAP/reference	0.80728	0.001
43DAP/reference	0.74451
47DAP/reference	0.70584	0.055
52DAP/reference	0.79727	0.03
57DAP/reference	0.96449

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.05558	0.728
27DAP/17DAP	0.8385	0.158
39DAP/27DAP	0.84813	0.058
41DAP/39DAP	1.08821	0.849
42DAP/41DAP	0.96574	0.721
43DAP/42DAP	0.62943	0.022
47DAP/43DAP	0.97803	0.886
52DAP/47DAP	0.93313	0.777
57DAP/52DAP	0.85283	0.43
57DAP/7DAP	0.71551	0.181

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.69796	0.036
17DAP/reference	1.72899	0.006
27DAP/reference	1.57277	0.01
39DAP/reference	1.74049	0.005
41DAP/reference	1.50421	0.026
42DAP/reference	1.51159	0.009
43DAP/reference	1.30753	0.012
47DAP/reference	0.96473	0.671
52DAP/reference	1.34276	0.025
57DAP/reference	1.34848	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04379	0.812
17DAP/reference	0.97746	0.626
27DAP/reference	0.96446	0.483
39DAP/reference	1.21222	0.556
41DAP/reference	1.23296	0.149
42DAP/reference	0.82247	0.067
43DAP/reference	0.89682	0.257
47DAP/reference	0.85626	0.058
52DAP/reference	0.96954	0.469
57DAP/reference	0.95367	0.488

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.28747	0.303
17DAP/reference	1.02931	0.825
27DAP/reference	1.29137	0.096
39DAP/reference	1.16928	0.245
41DAP/reference	1.19671	0.089
42DAP/reference	1.15932	0.333
43DAP/reference	1.14116	0.381
47DAP/reference	0.73098	0.011
52DAP/reference	1.10791	0.89
57DAP/reference	1.50139	0.083

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.09784	0.966
26DAP/20DAP	0.801	1
34DAP/26DAP	0.90622	0.763
51DAP/34DAP	1.40793	0.719
52DAP/51DAP	2.13983	0.033
53DAP/52DAP	1.1268	0.697
55DAP/53DAP	0.85732	0.619
57DAP/55DAP	1.28563
62DAP/57DAP	0.99245	1
68DAP/62DAP	1.12313	0.872
68DAP/14DAP	1.23246	0.161

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.9602	0.081

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	2.00831	0.016
Immature Eggplant/Mature Eggplant	0.80782	0.084
Ripe Pepper/Ripe Tomato	0.23036	0.224
Mature Eggplant/Ripe Tomato	1.91174	0.268

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	0.5007
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	1.8367
5-3/M82	1.09111
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	1.13211	1
IL2-6/WTpooled	1.20272	0.409
IL7-5/WTpooled	1.18214	1
IL7-3/WTpooled	1.0012	1
IL12-4/WTpooled	1.05347	0.646
IL1-4/WTpooled	0.96707	1
WT/WTpooled	0.93708	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	1.0678	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.1244	0.921
DC3000/delta hrp 6h	0.87933	0.95
DC3000/delta hrp 12h	1.00023	1
DC3000/delta hrp 24h	0.92927	0.564

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.15747	0.068
DC3000 delta B/DC3000 delta AB	0.97355	0.873

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.99924	1
Exp 36h	0.77847	0.623
Exp 60h	0.60435	0.343

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01998	1
Var 0h	1.20714	0.936
Var 12h I row2-row1	0.81838	0.338
Var 12h NI row2-row1	0.98371	1
Var 36h I row2-row1	1.02271	1
Var 36h NI row2-row1	1.49398	0.482
Var 60h I row2-row1	0.9436	0.832
Var 60h NI row2-row1	1.11027	0.904
Time course 0hI-0hNI	1.03138	0.852
Time course 12hI-12hNI	0.94014	0.402
Time course 36hI-36hNI	0.73021	0.023
Time course 60hI-60hNI	0.14823	0.005

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)	1.12535	0.261
transgenic ySAMdc/azygous control (breaker)	1.06465	1
transgenic ySAMdc/azygous control (red)	1.12604	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.08447	0.495

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.7672	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.63608	0.172
Manapal/WT (break)	1.26618	0.381
Manapal/WT (red)	1.31679	0.413