Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.1.8.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.36926	0.124
27DAP/17DAP	1.34748	0.624
39DAP/27DAP	1.62522	0.262
41DAP/39DAP	0.99956	0.949
42DAP/41DAP	1.62393	0.12
43DAP/42DAP	1.50389	0.096
47DAP/43DAP	2.9234	0.156
52DAP/47DAP	0.90831	0.712
57DAP/52DAP	1.42983	0.92

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.48826	0.024
17DAP/reference	0.58575	0.008
27DAP/reference	0.71834	0.012
39DAP/reference	1.14758	0.628
41DAP/reference	0.78595	0.114
42DAP/reference	1.33618	0.007
43DAP/reference	3.01764	0.006
47DAP/reference	3.6671	0.001
52DAP/reference	3.31951	0.007
57DAP/reference	3.19827	0.008

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.5059	0.036
27DAP/17DAP	1.02405	0.96
39DAP/27DAP	1.75095	0.046
41DAP/39DAP	0.70883	0.083
42DAP/41DAP	1.68829	0.002
43DAP/42DAP	2.01503	0.013
47DAP/43DAP	1.46314	0.012
52DAP/47DAP	0.81267	0.329
57DAP/52DAP	1.01679	1
57DAP/7DAP	1.84342	0.22

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93677	0.445
17DAP/reference	1.09665	0.361
27DAP/reference	1.03311	0.8
39DAP/reference	1.11297	0.601
41DAP/reference	1.23442	0.26
42DAP/reference	1.08237	0.686
43DAP/reference	1.27686	0.008
47DAP/reference	1.01135	1
52DAP/reference	1.28931	0.026
57DAP/reference	1.34609	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.43656	0.006
17DAP/reference	0.41337	0.003
27DAP/reference	0.63895	0.018
39DAP/reference	0.786	0.014
41DAP/reference	0.64994	0.012
42DAP/reference	0.74425	0.018
43DAP/reference	0.72264	0.021
47DAP/reference	0.99292	0.643
52DAP/reference	0.65334	0.004
57DAP/reference	0.62925	0.003

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.64971	0.059
17DAP/reference	0.58184	0.115
27DAP/reference	0.89193	0.23
39DAP/reference	1.09542	0.773
41DAP/reference	1.01413	0.754
42DAP/reference	1.37892	0.013
43DAP/reference	2.05872	0.006
47DAP/reference	3.34691	0.004
52DAP/reference	3.03094	0.029
57DAP/reference	3.28454	0.007

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.11194	0.966
26DAP/20DAP	0.96165	1
34DAP/26DAP	1.06688	1
51DAP/34DAP	2.58706	0.024
52DAP/51DAP	0.58658	0.151
53DAP/52DAP	4.55495	0.019
55DAP/53DAP	1.2088	0.29
57DAP/55DAP	1.05763	0.969
62DAP/57DAP	0.63324	0.088
68DAP/62DAP	1.00763	0.914
68DAP/14DAP	2.55627	0.018

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.21288	0.466

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.33265	0.073
Mature Green Tomato/Ripe Tomato	0.12316	0.017
Immature Eggplant/Mature Eggplant	0.95715	0.72
Ripe Pepper/Ripe Tomato	0.42467	0.224
Mature Eggplant/Ripe Tomato	0.18743	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.15683	0.742
1-1-2/M82	1.52367	1
12-2/M82	0.94593	0.955
12-4/M82	1.14887	1
1-3/M82	2.05664	0.26
2-1-1/M82	0.92442	0.465
2-1/M82	0.94337	0.74
2-6/M82	0.99117	1
3-2/M82	1.11537	0.717
4-1-1/M82	1.27339	1
4-1/M82	1.44711	1
4-3-2/M82	1.17153	0.508
4-3/M82	0.97169	1
5-3/M82	0.97085	0.642
6-2/M82	N/A	N/A
6-3/M82	0.9515	1
7-1/M82	1.10076	1
7-2/M82	1.34284	0.385
9-3-2/M82	1.7202	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.7243	0.247
IL2-6/WTpooled	0.93021	1
IL7-5/WTpooled	0.93779	1
IL7-3/WTpooled	0.67152	0.298
IL12-4/WTpooled	0.82137	0.71
IL1-4/WTpooled	1.02891	1
WT/WTpooled	0.96308	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	1.16685	0.309

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.99528	1
DC3000/delta hrp 6h	1.27748	1
DC3000/delta hrp 12h	1.22088	1
DC3000/delta hrp 24h	0.78878	0.062

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.38908
DC3000 delta B/DC3000 delta AB	0.9191	0.745

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
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	1.00986	1
Var 0h	2.36546	0.98
Var 12h I row2-row1	1.0109	0.736
Var 12h NI row2-row1	1.02459	1
Var 36h I row2-row1	1.27177	0.41
Var 36h NI row2-row1	0.82974	1
Var 60h I row2-row1	0.81665	0.582
Var 60h NI row2-row1	0.86308	0.866
Time course 0hI-0hNI	1.09419	0.227
Time course 12hI-12hNI	0.95388	0.698
Time course 36hI-36hNI	0.98303	0.601
Time course 60hI-60hNI	1.21638	0.013

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)	1.03927	0.654
transgenic ySAMdc/azygous control (breaker)	0.74192	0.173
transgenic ySAMdc/azygous control (red)	1.16817	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.01088	0.656

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.67031	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.06653	1
Manapal/WT (break)	1.06956	1
Manapal/WT (red)	0.94414	0.607