Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.4.7.17

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.072	0.947
27DAP/17DAP	1.05599	0.883
39DAP/27DAP	0.81728	0.364
41DAP/39DAP	1.29929	0.597
42DAP/41DAP	1.00779	1
43DAP/42DAP	0.99077	0.937
47DAP/43DAP	1.07392	0.909
52DAP/47DAP	1.02593	0.98
57DAP/52DAP	1.04115	1

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.7342	0.013
17DAP/reference	2.47986	0.015
27DAP/reference	1.00868	1
39DAP/reference	0.90816	0.292
41DAP/reference	1.04701	0.855
42DAP/reference	0.67314	0.001
43DAP/reference	0.83705	0.088
47DAP/reference	0.6975	0.002
52DAP/reference	0.76026	0.024
57DAP/reference	0.76789	0.014

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.3333	0.398
27DAP/17DAP	1.1033	0.78
39DAP/27DAP	0.93596	0.622
41DAP/39DAP	1.16509	0.69
42DAP/41DAP	1.11679	0.894
43DAP/42DAP	0.95722	0.684
47DAP/43DAP	1.04826	0.963
52DAP/47DAP	1.09737	0.81
57DAP/52DAP	1.04226	0.926
57DAP/7DAP	1.16766	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.22251	0.625
17DAP/reference	1.02155	0.693
27DAP/reference	1.01183	0.698
39DAP/reference	1.184	0.538
41DAP/reference	0.91149	0.259
42DAP/reference	1.05474	0.534
43DAP/reference	0.90184	0.21
47DAP/reference	0.79932	0.128
52DAP/reference	1.04011	0.832
57DAP/reference	0.91281	0.162

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.44102	0.104
17DAP/reference	4.8231	0.006
27DAP/reference	1.38377	0.2
39DAP/reference	0.79125	0.048
41DAP/reference	0.87694	0.124
42DAP/reference	0.9857	0.534
43DAP/reference	0.93775	0.404
47DAP/reference	0.82775	0.049
52DAP/reference	0.72614	0.008
57DAP/reference	0.64115	0.007

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.51617	1
17DAP/reference	1.68516	0.243
27DAP/reference	1.03886	1
39DAP/reference	1.11591	0.245
41DAP/reference	1.05931	0.867
42DAP/reference	0.94822	0.552
43DAP/reference	0.89326	0.237
47DAP/reference	0.72629	0.004
52DAP/reference	0.87406	0.228
57DAP/reference	0.67252	0.016

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.34136	0.752
26DAP/20DAP	1.15125	0.886
34DAP/26DAP	1.4271	1
51DAP/34DAP	1.20894	0.719
52DAP/51DAP	0.9036	1
53DAP/52DAP	0.97498	0.882
55DAP/53DAP	0.89879	0.489
57DAP/55DAP	0.96529	0.799
62DAP/57DAP	0.97952	0.994
68DAP/62DAP	0.91534	0.81
68DAP/14DAP	0.57568	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.03184	0.696

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	222.461	0.058
Mature Green Tomato/Ripe Tomato	0.87431	0.226
Immature Eggplant/Mature Eggplant	0.09321	0.068
Ripe Pepper/Ripe Tomato	0.52537
Mature Eggplant/Ripe Tomato	N/A	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.17362
1-1-2/M82	1.12929	1
12-2/M82	N/A	N/A
12-4/M82	0.87477	1
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	1.07006
4-1-1/M82	N/A	N/A
4-1/M82	0.95802	0.737
4-3-2/M82	0.8171	1
4-3/M82	N/A	N/A
5-3/M82	N/A	N/A
6-2/M82	N/A	N/A
6-3/M82	0.83939
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	0.90194	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.76958	0.243
IL2-6/WTpooled	1.09229	0.46
IL7-5/WTpooled	0.83195	1
IL7-3/WTpooled	1.09148	0.362
IL12-4/WTpooled	0.94971	0.566
IL1-4/WTpooled	1.04919	1
WT/WTpooled	0.93547	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	1.0172	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.21889	0.715
DC3000/delta hrp 6h	1.95204	1
DC3000/delta hrp 12h	0.73815	1
DC3000/delta hrp 24h	0.99555	0.794

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	N/A
DC3000 delta B/DC3000 delta AB	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.69659	1
Exp 36h	1.17488	1
Exp 60h	0.70904	0.454

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

hybridization	ratio	FDR (corrected p value)
self-self	1.04918	1
Var 0h	0.83938	0.332
Var 12h I row2-row1	1.01995
Var 12h NI row2-row1	1.72943	1
Var 36h I row2-row1	0.93103	1
Var 36h NI row2-row1	1.04028
Var 60h I row2-row1	1.1896	0.562
Var 60h NI row2-row1	1.03204
Time course 0hI-0hNI	1.00448	1
Time course 12hI-12hNI	0.90424	0.435
Time course 36hI-36hNI	0.75565	0.148
Time course 60hI-60hNI	0.72474	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)	1.3914	0.36
transgenic ySAMdc/azygous control (breaker)	2.17555	0.178
transgenic ySAMdc/azygous control (red)	N/A	N/A

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.97923	0.263

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.13632	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.6495	0.307
Manapal/WT (break)	N/A	N/A
Manapal/WT (red)	0.94733	0.728