Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.4.3.21

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.88304	0.511
27DAP/17DAP	0.76674	0.359
39DAP/27DAP	1.64808	0.476
41DAP/39DAP	0.97058	0.785
42DAP/41DAP	1.22167	0.938
43DAP/42DAP	0.92568	0.867
47DAP/43DAP	0.38063	0.049
52DAP/47DAP	1.17721	0.596
57DAP/52DAP	0.99553	0.983

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87622	0.205
17DAP/reference	0.72475	0.022
27DAP/reference	0.87716	0.304
39DAP/reference	0.65888	0.023
41DAP/reference	0.56751	0.014
42DAP/reference	0.79626	0.002
43DAP/reference	0.8354	0.259
47DAP/reference	0.73828	0.023
52DAP/reference	0.65008	0.024
57DAP/reference	0.81752	0.02

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.13757	0.547
27DAP/17DAP	0.74332	0.218
39DAP/27DAP	0.9442	0.668
41DAP/39DAP	2.33317	0.005
42DAP/41DAP	0.72789	0.023
43DAP/42DAP	0.64675	0.022
47DAP/43DAP	1.09654	0.572
52DAP/47DAP	0.82337	0.237
57DAP/52DAP	0.80931	0.399
57DAP/7DAP	1.4566	0.249

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.276	0.119
17DAP/reference	1.10945	0.971
27DAP/reference	0.83236	0.058
39DAP/reference	0.86598	0.146
41DAP/reference	0.66223	0.013
42DAP/reference	0.85	0.086
43DAP/reference	0.85633	0.139
47DAP/reference	0.77573	0.101
52DAP/reference	1.01667	0.802
57DAP/reference	0.89209	0.077

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.55434	0.012
17DAP/reference	0.60779	0.027
27DAP/reference	0.7822	0.129
39DAP/reference	0.83895	0.126
41DAP/reference	0.85166	0.057
42DAP/reference	0.95189	0.392
43DAP/reference	0.85158	0.191
47DAP/reference	1.21348	0.24
52DAP/reference	0.54073	0.004
57DAP/reference	0.86722	0.18

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.57421	0.021
17DAP/reference	1.36943	0.163
27DAP/reference	1.00829	0.805
39DAP/reference	0.84052	0.02
41DAP/reference	0.84997	0.293
42DAP/reference	0.69135	0.028
43DAP/reference	0.70933	0.028
47DAP/reference	0.48973	0.005
52DAP/reference	0.47008	0.047
57DAP/reference	0.88384	0.095

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.27033	0.56
26DAP/20DAP	1.3493	0.305
34DAP/26DAP	0.97838	0.972
51DAP/34DAP	2.13506	0.032
52DAP/51DAP	0.70403	0.151
53DAP/52DAP	1.2581	0.108
55DAP/53DAP	0.4975	0.016
57DAP/55DAP	0.92283	0.691
62DAP/57DAP	0.92336	0.871
68DAP/62DAP	1.15226	0.85
68DAP/14DAP	1.98115	0.032

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.37516	0.019

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.52917	0.11
Mature Green Tomato/Ripe Tomato	2.14634	0.015
Immature Eggplant/Mature Eggplant	1.2849	0.096
Ripe Pepper/Ripe Tomato	12.4507	0.256
Mature Eggplant/Ripe Tomato	6.4903	0.268

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.76365	0.613
1-1-2/M82	1.10208	1
12-2/M82	1.34215	1
12-4/M82	1.08369	1
1-3/M82	1.56388	0.277
2-1-1/M82	1.01444
2-1/M82	1.2392
2-6/M82	1.19335
3-2/M82	3.11516	0.426
4-1-1/M82	2.44593
4-1/M82	N/A	N/A
4-3-2/M82	2.78491
4-3/M82	0.98374
5-3/M82	2.01418	0.496
6-2/M82	7.88448	0.235
6-3/M82	0.90244	1
7-1/M82	0.50655	0.509
7-2/M82	1.27081	0.385
9-3-2/M82	1.80528

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.02039	1
IL2-6/WTpooled	0.94722	1
IL7-5/WTpooled	0.92475	0.483
IL7-3/WTpooled	1.04478	1
IL12-4/WTpooled	0.87545	1
IL1-4/WTpooled	0.84176	0.444
WT/WTpooled	0.9529	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	1.14061	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.00642	0.921
DC3000/delta hrp 6h	0.84175	0.95
DC3000/delta hrp 12h	0.32018
DC3000/delta hrp 24h	1.04057	0.633

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.80406	0.036
DC3000 delta B/DC3000 delta AB	0.78094	0.043

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.02682	1
Exp 36h	0.96999	0.879
Exp 60h	1.20095	0.283

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98776	1
Var 0h	1.1245	0.782
Var 12h I row2-row1	0.87981	0.418
Var 12h NI row2-row1	1.2043	0.649
Var 36h I row2-row1	1.133	0.368
Var 36h NI row2-row1	0.73963	0.549
Var 60h I row2-row1	0.94777	0.952
Var 60h NI row2-row1	1.01429	1
Time course 0hI-0hNI	1.02146	1
Time course 12hI-12hNI	1.01257	0.9
Time course 36hI-36hNI	1.5844	0.004
Time course 60hI-60hNI	2.39663	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)	0.57112	0.229
transgenic ySAMdc/azygous control (breaker)	1.12864	1
transgenic ySAMdc/azygous control (red)	1.20146	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.93892	0.444

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.961	0.239

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	7.44619	0.087
Manapal/WT (break)	1.94985	0.381
Manapal/WT (red)	0.9406	0.607