Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.3.9.8

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.15205	0.014
27DAP/17DAP	0.62761	0.139
39DAP/27DAP	0.76884	0.397
41DAP/39DAP	1.3792	0.243
42DAP/41DAP	1.14304	0.873
43DAP/42DAP	0.99165	0.932
47DAP/43DAP	0.99688	0.949
52DAP/47DAP	0.89628	0.612
57DAP/52DAP	1.10182	0.902

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.19018	0.01
17DAP/reference	0.30045	0.007
27DAP/reference	0.39822	0.012
39DAP/reference	0.47254	0.013
41DAP/reference	0.33827	0.008
42DAP/reference	0.47219	0.001
43DAP/reference	0.46917	0.013
47DAP/reference	0.44871	0.001
52DAP/reference	0.43276	0.014
57DAP/reference	0.58884	0.007

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.21723	0.017
27DAP/17DAP	0.72119	0.58
39DAP/27DAP	1.06736	0.718
41DAP/39DAP	1.04214	1
42DAP/41DAP	1.03342	0.947
43DAP/42DAP	1.00231	1
47DAP/43DAP	1.15465	0.111
52DAP/47DAP	1.13166	0.779
57DAP/52DAP	1.17546	0.438
57DAP/7DAP	0.92899	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.07556	0.024
17DAP/reference	1.15945	0.244
27DAP/reference	0.82568	0.058
39DAP/reference	1.28532	0.016
41DAP/reference	1.31735	0.207
42DAP/reference	1.18372	0.037
43DAP/reference	0.83316	0.139
47DAP/reference	0.68732	0.079
52DAP/reference	0.74866	0.02
57DAP/reference	0.71049	0.022

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.17199	0.043
17DAP/reference	0.20638	0.003
27DAP/reference	0.31467	0.007
39DAP/reference	0.44684	0.011
41DAP/reference	0.61183	0.015
42DAP/reference	0.53003	0.016
43DAP/reference	0.47591	0.008
47DAP/reference	0.58363	0.011
52DAP/reference	0.34069	0.003
57DAP/reference	0.29303	0.002

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	3.02151	0.039
17DAP/reference	0.6235	0.139
27DAP/reference	0.95562	0.49
39DAP/reference	0.93216	0.393
41DAP/reference	0.6824	0.03
42DAP/reference	0.71342	0.071
43DAP/reference	0.66419	0.035
47DAP/reference	0.34492	0.004
52DAP/reference	0.84198	0.327
57DAP/reference	0.77732	0.083

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.19794	0.966
26DAP/20DAP	1.02126	1
34DAP/26DAP	0.85686	0.364
51DAP/34DAP	0.9438	0.571
52DAP/51DAP	0.89521	0.151
53DAP/52DAP	1.53442	0.129
55DAP/53DAP	0.7788	0.022
57DAP/55DAP	1.01552	0.955
62DAP/57DAP	0.79055	0.162
68DAP/62DAP	1.16415	0.405
68DAP/14DAP	0.83371	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.54157	0.021

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	9.48262
Mature Green Tomato/Ripe Tomato	0.38564
Immature Eggplant/Mature Eggplant	0.96082	0.545
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	38.5826	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	1.03404
12-2/M82	N/A	N/A
12-4/M82	0.82377
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	1.032	0.452
3-2/M82	0.8599
4-1-1/M82	0.75916
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	0.97879	1
6-2/M82	0.91787
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	1.06099
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.1823	0.493
IL2-6/WTpooled	1.02193	1
IL7-5/WTpooled	1.31485
IL7-3/WTpooled	1.03098	1
IL12-4/WTpooled	1.09865	0.673
IL1-4/WTpooled	0.89734	0.457
WT/WTpooled	1.03333	0.818

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	0.74559	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.03119	0.921
DC3000/delta hrp 6h	1.24907	1
DC3000/delta hrp 12h	0.42071	1
DC3000/delta hrp 24h	7.57322	0.023

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.00777	0.648
DC3000 delta B/DC3000 delta AB	1.06447	0.528

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.86277	1
Exp 36h	0.80426	0.749
Exp 60h	0.71376	0.454

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

hybridization	ratio	FDR (corrected p value)
self-self	1.1251	1
Var 0h	0.94286	1
Var 12h I row2-row1	1.54999	0.613
Var 12h NI row2-row1	1.01758	0.906
Var 36h I row2-row1	0.90296	1
Var 36h NI row2-row1	1.2807	1
Var 60h I row2-row1	0.88841	0.582
Var 60h NI row2-row1	0.95723	1
Time course 0hI-0hNI	0.78816	0.047
Time course 12hI-12hNI	0.94491	0.646
Time course 36hI-36hNI	0.96606	0.433
Time course 60hI-60hNI	1.84449	0.008

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)	1.09019	0.455
transgenic ySAMdc/azygous control (breaker)	0.84345	0.49
transgenic ySAMdc/azygous control (red)	1.012	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.0328	0.273

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.08223	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.13676	1
Manapal/WT (break)	0.7283	1
Manapal/WT (red)	1.37893	1