Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.2.2.14

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	2.42355	0.046
27DAP/17DAP	0.96523	0.923
39DAP/27DAP	1.2275	0.789
41DAP/39DAP	0.50508	0.041
42DAP/41DAP	1.1112	0.971
43DAP/42DAP	0.89268	0.77
47DAP/43DAP	2.19387	0.156
52DAP/47DAP	1.2743	0.559
57DAP/52DAP	1.57817	0.669

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.70402	0.068
17DAP/reference	1.12234	0.843
27DAP/reference	1.699	0.014
39DAP/reference	1.27216	0.277
41DAP/reference	1.04174	1
42DAP/reference	0.76778	0.009
43DAP/reference	0.80794	0.054
47DAP/reference	2.36589	0.002
52DAP/reference	2.65087	0.011
57DAP/reference	2.57499	0.008

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.37843	0.058
27DAP/17DAP	1.11186	0.576
39DAP/27DAP	0.85147	0.231
41DAP/39DAP	1.03119	0.793
42DAP/41DAP	0.87194	0.259
43DAP/42DAP	1.01458	0.788
47DAP/43DAP	0.92375	0.418
52DAP/47DAP	1.6947	0.081
57DAP/52DAP	1.78847	0.057
57DAP/7DAP	2.39831	0.23

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.08169	0.511
17DAP/reference	0.94356	0.338
27DAP/reference	1.03105	0.804
39DAP/reference	1.77423	0.006
41DAP/reference	0.86339	0.16
42DAP/reference	1.49862	0.007
43DAP/reference	1.70579	0.006
47DAP/reference	1.09284	1
52DAP/reference	0.94353	0.332
57DAP/reference	1.18815	0.07

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.64915	0.013
17DAP/reference	0.89504	0.176
27DAP/reference	0.85347	0.173
39DAP/reference	0.89942	0.129
41DAP/reference	0.6176	0.01
42DAP/reference	0.94355	0.289
43DAP/reference	0.55853	0.007
47DAP/reference	0.84043	0.097
52DAP/reference	0.68614	0.007
57DAP/reference	0.51225	0.002

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.68935	0.022
17DAP/reference	0.83665	0.107
27DAP/reference	0.99605	0.763
39DAP/reference	1.32437	0.029
41DAP/reference	1.24186	0.15
42DAP/reference	1.06708	0.5
43DAP/reference	1.039	0.738
47DAP/reference	0.76236	0.063
52DAP/reference	1.30761	0.705
57DAP/reference	3.20516	0.011

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.87789	0.566
26DAP/20DAP	0.91354	1
34DAP/26DAP	0.80261	0.381
51DAP/34DAP	0.9282	0.498
52DAP/51DAP	0.64913	0.151
53DAP/52DAP	1.03316	0.901
55DAP/53DAP	0.66869	0.02
57DAP/55DAP	1.09613	0.975
62DAP/57DAP	3.72206
68DAP/62DAP	0.54	0.579
68DAP/14DAP	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	2.7741	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.74032	0.206
Mature Green Tomato/Ripe Tomato	0.95562	0.774
Immature Eggplant/Mature Eggplant	1.57446	0.05
Ripe Pepper/Ripe Tomato	0.78698	0.293
Mature Eggplant/Ripe Tomato	0.73066	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.84822	0.605
1-1-2/M82	1.08537
12-2/M82	0.75281
12-4/M82	1.04753	1
1-3/M82	2.33433	0.248
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	1.17717	0.695
3-2/M82	0.87551
4-1-1/M82	1.4108	0.876
4-1/M82	1.56926	0.512
4-3-2/M82	1.53621	0.508
4-3/M82	0.99538	1
5-3/M82	0.78704	0.642
6-2/M82	0.92458	0.497
6-3/M82	1.02411	1
7-1/M82	1.1518	0.741
7-2/M82	1.142	0.324
9-3-2/M82	1.49223	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.68609	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.98678
IL12-4/WTpooled	0.79365	0.71
IL1-4/WTpooled	1.1135
WT/WTpooled	0.91646	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	0.98959	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.97139	1
DC3000/delta hrp 6h	0.97806	0.95
DC3000/delta hrp 12h	1.33639	1
DC3000/delta hrp 24h	0.53416	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.62249	0.028
DC3000 delta B/DC3000 delta AB	0.42113	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.98687	1
Exp 36h	0.74817	0.504
Exp 60h	0.69968	0.259

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

hybridization	ratio	FDR (corrected p value)
self-self	0.9915	1
Var 0h	0.90789	0.933
Var 12h I row2-row1	0.68187	0.338
Var 12h NI row2-row1	1.01981	1
Var 36h I row2-row1	0.89575	0.805
Var 36h NI row2-row1	1.23252	1
Var 60h I row2-row1	1.27038	0.543
Var 60h NI row2-row1	1.00329	1
Time course 0hI-0hNI	0.96644	0.827
Time course 12hI-12hNI	0.87029	0.238
Time course 36hI-36hNI	0.77775	0.023
Time course 60hI-60hNI	0.15679	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)	1.08192	0.748
transgenic ySAMdc/azygous control (breaker)	0.35946	0.131
transgenic ySAMdc/azygous control (red)	1.24459	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	2.05669	0.061

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.96042	0.431

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.90919	1
Manapal/WT (break)	0.99782	1
Manapal/WT (red)	0.89934	0.315