Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.1.19.19

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.83944	0.339
27DAP/17DAP	0.96597	0.945
39DAP/27DAP	1.08981	0.922
41DAP/39DAP	0.8052	0.32
42DAP/41DAP	0.9512	1
43DAP/42DAP	1.17108	0.957
47DAP/43DAP	1.16314	0.542
52DAP/47DAP	0.9989	0.662
57DAP/52DAP	0.9697	0.938

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94711	0.293
17DAP/reference	0.84433	0.169
27DAP/reference	1.12454	0.435
39DAP/reference	1.27618	0.07
41DAP/reference	1.24584	0.025
42DAP/reference	0.98042	0.337
43DAP/reference	1.01361	1
47DAP/reference	0.99319	0.602
52DAP/reference	1.16846	0.031
57DAP/reference	1.22469	0.052

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.8558	0.26
27DAP/17DAP	1.06494	0.976
39DAP/27DAP	0.92119	0.437
41DAP/39DAP	1.01342	1
42DAP/41DAP	0.88646	0.391
43DAP/42DAP	1.07192	0.513
47DAP/43DAP	1.15808	0.681
52DAP/47DAP	1.26137	0.458
57DAP/52DAP	1.07678	0.874
57DAP/7DAP	0.79871	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.74063	0.108
17DAP/reference	0.8743	0.082
27DAP/reference	1.12401	0.197
39DAP/reference	0.72696	0.021
41DAP/reference	0.90351	0.223
42DAP/reference	1.19093	0.076
43DAP/reference	0.92186	0.175
47DAP/reference	0.7698	0.101
52DAP/reference	0.96528	0.435
57DAP/reference	0.84075	0.02

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01296	0.979
17DAP/reference	0.86991	0.153
27DAP/reference	1.14748	0.212
39DAP/reference	1.03612	0.868
41DAP/reference	1.1062	0.657
42DAP/reference	1.07109	0.649
43DAP/reference	1.52729	0.065
47DAP/reference	1.16235	0.033
52DAP/reference	1.15394	0.05
57DAP/reference	1.00068	0.789

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.80155	0.077
17DAP/reference	0.93998	0.305
27DAP/reference	1.02755	0.883
39DAP/reference	0.96801	0.464
41DAP/reference	1.20584	0.058
42DAP/reference	1.02329	0.73
43DAP/reference	0.87859	0.197
47DAP/reference	0.94824	0.325
52DAP/reference	1.26548	0.664
57DAP/reference	1.13648	0.394

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.84533	0.966
26DAP/20DAP	2.03129	0.187
34DAP/26DAP	1.09703	1
51DAP/34DAP	0.80147	0.555
52DAP/51DAP	1.33899	0.123
53DAP/52DAP	0.7287	0.21
55DAP/53DAP	1.721	0.722
57DAP/55DAP	0.89121	0.694
62DAP/57DAP	3.0821	0.723
68DAP/62DAP	1.13047	1
68DAP/14DAP	1.13161	0.558

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.85302	0.065

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.50336	0.058
Mature Green Tomato/Ripe Tomato	2.89311	0.026
Immature Eggplant/Mature Eggplant	1.74016	0.05
Ripe Pepper/Ripe Tomato	1.63625
Mature Eggplant/Ripe Tomato	2.68308	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	N/A	N/A
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	1.82292
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
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	0.84777	1
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.69879	0.243
IL2-6/WTpooled	1.022	0.788
IL7-5/WTpooled	1.37956	0.75
IL7-3/WTpooled	0.64551	0.293
IL12-4/WTpooled	1.00898	1
IL1-4/WTpooled	0.8219	0.562
WT/WTpooled	0.91126	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	1.08141	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.99626	1
DC3000/delta hrp 6h	1.06985	1
DC3000/delta hrp 12h	1.07087	1
DC3000/delta hrp 24h	0.81512	0.148

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.05018	0.068
DC3000 delta B/DC3000 delta AB	1.34824	0.215

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.99087	1
Exp 36h	0.89825	0.82
Exp 60h	0.958	0.855

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00183	1
Var 0h	0.39695
Var 12h I row2-row1	1.01497	0.795
Var 12h NI row2-row1	1.17774	0.649
Var 36h I row2-row1	1.13788	0.742
Var 36h NI row2-row1	1.11615	0.482
Var 60h I row2-row1	0.98182
Var 60h NI row2-row1	1.22001	0.904
Time course 0hI-0hNI	1.05306	0.852
Time course 12hI-12hNI	0.88225	0.264
Time course 36hI-36hNI	0.90542	0.36
Time course 60hI-60hNI	0.71618	0.047

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)	1.32546	0.261
transgenic ySAMdc/azygous control (breaker)	0.9351	0.49
transgenic ySAMdc/azygous control (red)	1.09332	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.0743	0.086

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.22621	0.237

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.75802	1
Manapal/WT (break)	N/A	N/A
Manapal/WT (red)	0.53886	0.181