Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.1.18.10

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.74871	0.128
27DAP/17DAP	1.02909	1
39DAP/27DAP	0.75885	0.298
41DAP/39DAP	1.50702	0.3
42DAP/41DAP	1.25362	0.841
43DAP/42DAP	0.7432	0.705
47DAP/43DAP	0.7504	0.321
52DAP/47DAP	2.17646	0.202
57DAP/52DAP	0.92415	0.912

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.89724	0.109
17DAP/reference	1.00006	0.957
27DAP/reference	0.97361	0.642
39DAP/reference	1.00911	1
41DAP/reference	1.00674	0.91
42DAP/reference	1.10852	0.002
43DAP/reference	1.05038	0.617
47DAP/reference	1.19318	0.007
52DAP/reference	1.12528	0.114
57DAP/reference	1.06819	0.229

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.1847	0.708
27DAP/17DAP	0.72516	0.339
39DAP/27DAP	1.00432	0.953
41DAP/39DAP	0.90404	0.729
42DAP/41DAP	1.00026	0.412
43DAP/42DAP	0.85827	0.367
47DAP/43DAP	0.87442	0.382
52DAP/47DAP	1.14876	0.73
57DAP/52DAP	1.37739	0.405
57DAP/7DAP	1.40351	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04324	0.793
17DAP/reference	1.48688	0.006
27DAP/reference	1.27422	0.015
39DAP/reference	1.31956	0.042
41DAP/reference	1.27673	0.041
42DAP/reference	1.31196	0.03
43DAP/reference	1.1753	0.014
47DAP/reference	1.14255	0.292
52DAP/reference	1.28111	0.018
57DAP/reference	1.4226	0.017

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87758	0.17
17DAP/reference	0.88697	0.223
27DAP/reference	1.04591	0.875
39DAP/reference	0.98195	0.526
41DAP/reference	0.90213	0.115
42DAP/reference	1.00397	1
43DAP/reference	0.90037	0.217
47DAP/reference	0.87598	0.031
52DAP/reference	1.03342	0.988
57DAP/reference	0.95017	0.208

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.07167	0.644
17DAP/reference	0.98574	0.668
27DAP/reference	1.29741	0.027
39DAP/reference	1.17448	0.081
41DAP/reference	1.19497	0.168
42DAP/reference	1.15283	0.258
43DAP/reference	1.27974	0.045
47DAP/reference	1.20237	0.12
52DAP/reference	1.46201	0.074
57DAP/reference	1.18446	0.1

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.1107	0.966
26DAP/20DAP	1.23634	1
34DAP/26DAP	1.4695	1
51DAP/34DAP	1.14902	0.829
52DAP/51DAP	2.15483	0.047
53DAP/52DAP	1.11243	0.901
55DAP/53DAP	1.58323	0.234
57DAP/55DAP	0.58367	0.085
62DAP/57DAP	1.01408	1
68DAP/62DAP	1.35511	0.029
68DAP/14DAP	2.4029	0.019

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.4005	0.027

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.26293	0.062
Mature Green Tomato/Ripe Tomato	0.7602	0.096
Immature Eggplant/Mature Eggplant	1.2475	0.136
Ripe Pepper/Ripe Tomato	2.1583	0.258
Mature Eggplant/Ripe Tomato	1.1237	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.09889	0.877
1-1-2/M82	0.93807	1
12-2/M82	0.98203	1
12-4/M82	0.90013	1
1-3/M82	0.94351	1
2-1-1/M82	0.59508	0.784
2-1/M82	1.02422
2-6/M82	1.00886	1
3-2/M82	0.91924
4-1-1/M82	1.14343	1
4-1/M82	0.57581	0.665
4-3-2/M82	0.87297	0.698
4-3/M82	0.84559	0.578
5-3/M82	0.97074	1
6-2/M82	0.73937	1
6-3/M82	1.00795	1
7-1/M82	1.00507	1
7-2/M82	0.90616	0.881
9-3-2/M82	1.03811

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.54712
IL2-6/WTpooled	0.85934	0.383
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	1.2208
IL1-4/WTpooled	0.8466	1
WT/WTpooled	1.05454	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	0.98501	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.02353	0.921
DC3000/delta hrp 6h	0.87917	0.95
DC3000/delta hrp 12h	1.09177	1
DC3000/delta hrp 24h	0.96972	0.831

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.51834	0.087
DC3000 delta B/DC3000 delta AB	1.79035	0.089

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.07423	1
Exp 36h	1.08955	1
Exp 60h	1.26535	0.283

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

hybridization	ratio	FDR (corrected p value)
self-self	0.8716	1
Var 0h	1.18773	0.936
Var 12h I row2-row1	1.13922	0.613
Var 12h NI row2-row1	1.48797	1
Var 36h I row2-row1	1.61467	0.305
Var 36h NI row2-row1	1.17183	1
Var 60h I row2-row1	0.7686	0.582
Var 60h NI row2-row1	1.37847	0.904
Time course 0hI-0hNI	0.94792	0.833
Time course 12hI-12hNI	1.1034	0.746
Time course 36hI-36hNI	1.62167	0.021
Time course 60hI-60hNI	2.00882	0.01

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)	0.91596	0.33
transgenic ySAMdc/azygous control (breaker)	1.0688	1
transgenic ySAMdc/azygous control (red)	1.01554	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.99687	0.806

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.48066	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.84128	1
Manapal/WT (break)	0.95783	1
Manapal/WT (red)	0.71581	0.216