Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.4.14.7

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.93542	0.586
27DAP/17DAP	1.08609	0.859
39DAP/27DAP	0.94925	0.583
41DAP/39DAP	1.71008	0.334
42DAP/41DAP	0.86864	1
43DAP/42DAP	0.88932	0.759
47DAP/43DAP	1.10239	0.842
52DAP/47DAP	1.39159	0.493
57DAP/52DAP	0.85609	0.7

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.06842	0.788
17DAP/reference	1.12899	0.148
27DAP/reference	0.8933	0.295
39DAP/reference	1.06081	0.453
41DAP/reference	1.50402	0.024
42DAP/reference	1.15329	0.041
43DAP/reference	1.0319	0.787
47DAP/reference	0.9526	0.3
52DAP/reference	0.91786	0.275
57DAP/reference	0.93822	0.377

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.96215	0.644
27DAP/17DAP	0.95505	0.878
39DAP/27DAP	1.00173	1
41DAP/39DAP	0.93285	0.713
42DAP/41DAP	0.97897	0.764
43DAP/42DAP	1.03576	0.699
47DAP/43DAP	1.07308	0.822
52DAP/47DAP	1.07756	0.804
57DAP/52DAP	0.99851	0.892
57DAP/7DAP	1.02031	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.37797	0.027
17DAP/reference	1.94518	0.006
27DAP/reference	1.50889	0.008
39DAP/reference	1.19929	0.008
41DAP/reference	1.36952	0.019
42DAP/reference	1.17155	0.174
43DAP/reference	1.22311	0.132
47DAP/reference	1.17031	0.345
52DAP/reference	1.15636	0.375
57DAP/reference	1.04727	0.907

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.38093	0.041
17DAP/reference	1.2098	0.038
27DAP/reference	1.31789	0.082
39DAP/reference	1.26011	0.109
41DAP/reference	1.55507	0.024
42DAP/reference	1.20278	0.162
43DAP/reference	1.07278	0.713
47DAP/reference	1.58362	0.01
52DAP/reference	1.36147	0.016
57DAP/reference	1.53051	0.011

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.94226	0.02
17DAP/reference	1.41026	0.189
27DAP/reference	1.37483	0.041
39DAP/reference	1.3047	0.057
41DAP/reference	1.23471	0.025
42DAP/reference	1.06894	0.566
43DAP/reference	1.05919	0.744
47DAP/reference	0.94964	0.371
52DAP/reference	0.972	0.663
57DAP/reference	0.75633	0.019

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.87609	1
26DAP/20DAP	0.90412	0.512
34DAP/26DAP	1.31615	0.027
51DAP/34DAP	0.98549	0.873
52DAP/51DAP	0.99529	1
53DAP/52DAP	1.0821	0.688
55DAP/53DAP	1.0428	0.855
57DAP/55DAP	1.19152	0.793
62DAP/57DAP	0.9614	0.994
68DAP/62DAP	0.79068	0.429
68DAP/14DAP	0.57137	0.121

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.9114	0.443

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.15461	0.051
Mature Green Tomato/Ripe Tomato	1.0707	0.69
Immature Eggplant/Mature Eggplant	12.7722	0.05
Ripe Pepper/Ripe Tomato	5.29417	1
Mature Eggplant/Ripe Tomato	1.26519	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.04197	0.526
1-1-2/M82	0.87094	1
12-2/M82	1.1064	1
12-4/M82	0.99451	1
1-3/M82	0.93453	1
2-1-1/M82	1.24866
2-1/M82	1.13385	1
2-6/M82	1.06774
3-2/M82	1.00211	1
4-1-1/M82	0.93112	1
4-1/M82	0.79807	1
4-3-2/M82	0.8565	0.698
4-3/M82	1.01891	1
5-3/M82	1.01314	1
6-2/M82	1.03447
6-3/M82	0.90086
7-1/M82	0.96482	0.803
7-2/M82	1.16694	0.385
9-3-2/M82	0.99223	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.91549	0.243
IL2-6/WTpooled	0.91319	0.473
IL7-5/WTpooled	0.71281	1
IL7-3/WTpooled	0.9337	0.418
IL12-4/WTpooled	0.97611	1
IL1-4/WTpooled	1.00384	1
WT/WTpooled	0.99735	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	1.02104	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.01564	1
DC3000/delta hrp 6h	1.21375	1
DC3000/delta hrp 12h	1.32931	1
DC3000/delta hrp 24h	1.0832	0.535

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.96178	1
DC3000 delta B/DC3000 delta AB	1.01701	0.771

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.32124	1
Exp 36h	1.57422	0.693
Exp 60h	1.19019	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99388	1
Var 0h	2.31068	0.98
Var 12h I row2-row1	1.0743	0.406
Var 12h NI row2-row1	0.95074	0.906
Var 36h I row2-row1	0.87055	0.575
Var 36h NI row2-row1	8.03959	1
Var 60h I row2-row1	1.37513	1
Var 60h NI row2-row1	1.19565	0.904
Time course 0hI-0hNI	1.03542	0.852
Time course 12hI-12hNI	1.04326	0.741
Time course 36hI-36hNI	0.95454	0.255
Time course 60hI-60hNI	1.06534	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)	0.87082	0.428
transgenic ySAMdc/azygous control (breaker)	0.66966	0.251
transgenic ySAMdc/azygous control (red)	1.15613	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.14124	0.142

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.99984	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	7.76737	0.105
Manapal/WT (break)	1.62652	0.381
Manapal/WT (red)	0.88656	0.424