Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.1.2.9

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.11803	0.615
27DAP/17DAP	0.86278	0.658
39DAP/27DAP	1.26578	0.44
41DAP/39DAP	0.91835	0.63
42DAP/41DAP	1.08682	1
43DAP/42DAP	0.89408	0.721
47DAP/43DAP	0.91077	0.663
52DAP/47DAP	1.49483	0.396
57DAP/52DAP	0.84364	0.622

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01275	1
17DAP/reference	0.80483	0.007
27DAP/reference	1.02525	0.953
39DAP/reference	0.92759	0.184
41DAP/reference	0.85302	0.039
42DAP/reference	1.18447	0.008
43DAP/reference	1.0894	0.031
47DAP/reference	1.12524	0.233
52DAP/reference	1.17882	0.371
57DAP/reference	1.62089	0.008

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.18692	0.29
27DAP/17DAP	1.11073	0.55
39DAP/27DAP	0.79747	0.069
41DAP/39DAP	1.1009	0.214
42DAP/41DAP	0.89446	0.178
43DAP/42DAP	0.86145	0.025
47DAP/43DAP	1.00293	1
52DAP/47DAP	0.88316	0.378
57DAP/52DAP	0.97017	0.732
57DAP/7DAP	1.08626	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01156	1
17DAP/reference	0.92314	0.049
27DAP/reference	0.90597	0.024
39DAP/reference	0.93805	0.031
41DAP/reference	0.9738	0.469
42DAP/reference	1.01544	1
43DAP/reference	1.2266	0.027
47DAP/reference	1.27395	0.298
52DAP/reference	0.99957	0.802
57DAP/reference	1.05955	0.25

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.85683	0.093
17DAP/reference	0.87055	0.063
27DAP/reference	1.24492	0.182
39DAP/reference	1.41758	0.063
41DAP/reference	1.84472	0.005
42DAP/reference	1.43928	0.008
43DAP/reference	0.97346	0.468
47DAP/reference	1.21026	0.011
52DAP/reference	1.16681	0.036
57DAP/reference	1.10846	0.737

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.89898	0.169
17DAP/reference	0.96808	0.601
27DAP/reference	0.96011	0.27
39DAP/reference	0.86255	0.133
41DAP/reference	0.91659	0.185
42DAP/reference	1.28412	0.391
43DAP/reference	1.2787	0.439
47DAP/reference	1.27286	0.207
52DAP/reference	0.98973	0.763
57DAP/reference	2.70817	0.015

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.06373	0.966
26DAP/20DAP	0.8794
34DAP/26DAP	0.97382	0.998
51DAP/34DAP	0.86048	0.328
52DAP/51DAP	1.10581	0.522
53DAP/52DAP	0.96642	0.83
55DAP/53DAP	1.00907	0.951
57DAP/55DAP	1.06371	1
62DAP/57DAP	1.2141	0.445
68DAP/62DAP	2.48293	0.05
68DAP/14DAP	3.66512	0.016

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	2.22229	0.017

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.73451	0.058
Mature Green Tomato/Ripe Tomato	1.67193	0.048
Immature Eggplant/Mature Eggplant	0.73048	0.159
Ripe Pepper/Ripe Tomato	0.15056	0.224
Mature Eggplant/Ripe Tomato	0.11885	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.11574	1
1-1-2/M82	1.22794
12-2/M82	1.42846	0.448
12-4/M82	1.08689	1
1-3/M82	0.96032	1
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	0.97263	1
3-2/M82	0.74161
4-1-1/M82	1.00142	1
4-1/M82	0.93018
4-3-2/M82	1.06214
4-3/M82	0.82915	0.611
5-3/M82	0.95678	1
6-2/M82	0.88861
6-3/M82	0.97628	1
7-1/M82	0.94477
7-2/M82	0.93788	1
9-3-2/M82	1.09666

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.94919	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.07287	1
IL12-4/WTpooled	0.96043	1
IL1-4/WTpooled	1.03646
WT/WTpooled	1.00442	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	0.97695	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.06172	0.894
DC3000/delta hrp 6h	0.85247	0.95
DC3000/delta hrp 12h	1.14675	1
DC3000/delta hrp 24h	0.86034	0.152

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.1281	0.29
DC3000 delta B/DC3000 delta AB	0.99389	0.961

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.96239	1
Exp 36h	0.77867	0.623
Exp 60h	0.63175	0.266

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

hybridization	ratio	FDR (corrected p value)
self-self	0.97674	1
Var 0h	1.11175	0.98
Var 12h I row2-row1	1.05898	0.613
Var 12h NI row2-row1	0.94605	0.713
Var 36h I row2-row1	1.024	1
Var 36h NI row2-row1	0.81485	0.584
Var 60h I row2-row1	0.98368	1
Var 60h NI row2-row1	0.93016	0.932
Time course 0hI-0hNI	0.94468	0.617
Time course 12hI-12hNI	0.92939	0.216
Time course 36hI-36hNI	1.00435	0.68
Time course 60hI-60hNI	1.09239	0.187

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)	1.13742	0.272
transgenic ySAMdc/azygous control (breaker)	0.36744	0.142
transgenic ySAMdc/azygous control (red)	1.05751	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.08209	0.032

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.73569	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.81678	1
Manapal/WT (break)	0.84063	1
Manapal/WT (red)	0.77625	0.274