Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.3.14.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.16437	0.893
27DAP/17DAP	1.17319	0.859
39DAP/27DAP	0.77233	0.512
41DAP/39DAP	0.89637	0.59
42DAP/41DAP	0.97471	1
43DAP/42DAP	1.24002	0.755
47DAP/43DAP	0.88229	0.603
52DAP/47DAP	0.91523	0.675
57DAP/52DAP	1.00306	0.983

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.32728	0.016
17DAP/reference	1.09221	0.041
27DAP/reference	1.10694	0.384
39DAP/reference	1.16243	0.093
41DAP/reference	1.12952	0.241
42DAP/reference	1.16718	0.089
43DAP/reference	0.98195	0.728
47DAP/reference	1.07068	0.275
52DAP/reference	1.13705	0.065
57DAP/reference	1.1311	0.147

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.1536	0.176
27DAP/17DAP	0.8343	0.295
39DAP/27DAP	0.6898	0.036
41DAP/39DAP	1.0901	0.484
42DAP/41DAP	0.94538	0.538
43DAP/42DAP	0.77848	0.036
47DAP/43DAP	0.96081	0.787
52DAP/47DAP	1.00913	1
57DAP/52DAP	0.70575	0.115
57DAP/7DAP	0.55155	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00892	1
17DAP/reference	0.88135	0.108
27DAP/reference	0.90716	0.013
39DAP/reference	0.94121	0.17
41DAP/reference	0.97698	0.375
42DAP/reference	0.88947	0.073
43DAP/reference	0.92465	0.086
47DAP/reference	1.05734	1
52DAP/reference	0.83654	0.014
57DAP/reference	0.82162	0.02

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.35012	0.139
17DAP/reference	1.28593	0.015
27DAP/reference	1.47962	0.015
39DAP/reference	1.37795	0.109
41DAP/reference	1.18283	0.204
42DAP/reference	1.21089	0.045
43DAP/reference	1.23399	0.146
47DAP/reference	1.2117	0.041
52DAP/reference	1.1239	0.417
57DAP/reference	0.9737	0.519

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93902	0.183
17DAP/reference	1.28902	0.294
27DAP/reference	0.92444	0.113
39DAP/reference	0.994	0.643
41DAP/reference	0.96547	0.512
42DAP/reference	1.03383	0.816
43DAP/reference	1.06518	0.91
47DAP/reference	1.13062	0.82
52DAP/reference	0.995	0.763
57DAP/reference	1.60707	0.016

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.58155	0.89
26DAP/20DAP	0.9991	1
34DAP/26DAP	1.09328	1
51DAP/34DAP	1.04239	0.854
52DAP/51DAP	1.05039	0.616
53DAP/52DAP	0.78432	0.159
55DAP/53DAP	0.63264	0.023
57DAP/55DAP	1.41402	0.424
62DAP/57DAP	1.12715	0.868
68DAP/62DAP	0.83586	0.101
68DAP/14DAP	0.93963	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.33641	0.021

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.84031	0.301
Mature Green Tomato/Ripe Tomato	2.71469	0.015
Immature Eggplant/Mature Eggplant	0.72661	0.064
Ripe Pepper/Ripe Tomato	2.65715	0.256
Mature Eggplant/Ripe Tomato	5.06553	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	N/A	N/A
3-2/M82	1.06578
4-1-1/M82	N/A	N/A
4-1/M82	0.75225
4-3-2/M82	1.52791	0.262
4-3/M82	N/A	N/A
5-3/M82	N/A	N/A
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	1.23259
7-2/M82	N/A	N/A
9-3-2/M82	1.8181

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.89014	0.247
IL2-6/WTpooled	1.29482	0.584
IL7-5/WTpooled	0.7365	1
IL7-3/WTpooled	0.91758	0.418
IL12-4/WTpooled	1.09305	0.891
IL1-4/WTpooled	1.0898	1
WT/WTpooled	1.08826	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	1.00302	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.90525	1
DC3000/delta hrp 6h	1.11206	1
DC3000/delta hrp 12h	2.35274	1
DC3000/delta hrp 24h	0.50176	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.5862	0.026
DC3000 delta B/DC3000 delta AB	0.59929	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.85936	1
Exp 36h	0.88085	0.471
Exp 60h	0.86813	0.754

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01335	1
Var 0h	2.8042	0.936
Var 12h I row2-row1	0.77297	0.344
Var 12h NI row2-row1	1.00843	1
Var 36h I row2-row1	0.84306	1
Var 36h NI row2-row1	1.34087	0.253
Var 60h I row2-row1	0.92251	0.582
Var 60h NI row2-row1	1.19381	0.904
Time course 0hI-0hNI	0.97658	0.879
Time course 12hI-12hNI	1.0271	0.747
Time course 36hI-36hNI	0.96344	0.396
Time course 60hI-60hNI	0.23329	0.006

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)	1.07346	0.397
transgenic ySAMdc/azygous control (breaker)	1.16978	0.178
transgenic ySAMdc/azygous control (red)	1.09272	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.91786	0.052

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.92897	0.228

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	3.41521	0.083
Manapal/WT (break)	3.65045	0.123
Manapal/WT (red)	3.35547	0.142