Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.2.20.4

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.40539	0.964
27DAP/17DAP	1.35643	0.755
39DAP/27DAP	0.93781	0.67
41DAP/39DAP	1.33382	0.498
42DAP/41DAP	0.73535	0.774
43DAP/42DAP	0.89401	0.613
47DAP/43DAP	1.0162	0.949
52DAP/47DAP	1.00823	0.903
57DAP/52DAP	0.99322	0.983

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.10942	0.46
17DAP/reference	0.97384	0.737
27DAP/reference	0.95347	0.514
39DAP/reference	1.43716	0.023
41DAP/reference	1.3475	0.03
42DAP/reference	0.96541	0.44
43DAP/reference	0.87828	0.708
47DAP/reference	0.71754	0.012
52DAP/reference	1.14701	0.695
57DAP/reference	N/A	N/A

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.14247	0.605
27DAP/17DAP	0.96582	0.887
39DAP/27DAP	0.9317	0.594
41DAP/39DAP	1.33753	0.565
42DAP/41DAP	0.83923	0.151
43DAP/42DAP	1.52314	0.273
47DAP/43DAP	0.98132	0.933
52DAP/47DAP	1.14268	0.649
57DAP/52DAP	1.44762	0.476
57DAP/7DAP	1.93496	0.249

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91415	0.326
17DAP/reference	0.99176	0.599
27DAP/reference	1.03052	0.551
39DAP/reference	0.98048	0.552
41DAP/reference	1.0002	0.811
42DAP/reference	1.02608	0.713
43DAP/reference	0.87763	0.047
47DAP/reference	0.86887	0.168
52DAP/reference	0.96512	0.398
57DAP/reference	0.91889	0.215

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.85795	0.197
17DAP/reference	0.82204	0.086
27DAP/reference	0.78346	0.111
39DAP/reference	0.79707	0.105
41DAP/reference	0.79152	0.08
42DAP/reference	1.3479	0.61
43DAP/reference	1.63459	0.055
47DAP/reference	2.86221
52DAP/reference	0.92452	0.22
57DAP/reference	1.07584	0.908

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96362	0.455
17DAP/reference	0.94986	0.47
27DAP/reference	0.959	0.376
39DAP/reference	0.82666	0.022
41DAP/reference	0.86205	0.107
42DAP/reference	1.03157	0.923
43DAP/reference	1.07449	1
47DAP/reference	1.15065	0.68
52DAP/reference	0.87434	0.211
57DAP/reference	1.23743	0.939

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.82893	0.566
26DAP/20DAP	0.738	0.512
34DAP/26DAP	1.16728	1
51DAP/34DAP	0.88169	0.579
52DAP/51DAP	1.67186	0.176
53DAP/52DAP	0.94166	0.882
55DAP/53DAP	1.20969	0.813
57DAP/55DAP	0.80742	0.3
62DAP/57DAP	0.95389	0.871
68DAP/62DAP	1.54269	0.018
68DAP/14DAP	1.63978	0.067

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.05801	0.737

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.02296	1
Immature Eggplant/Mature Eggplant	1.44834
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	N/A	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.03752	1
1-1-2/M82	1.03459	1
12-2/M82	1.17551
12-4/M82	1.23003	0.611
1-3/M82	0.68124	0.378
2-1-1/M82	0.74949
2-1/M82	N/A	N/A
2-6/M82	0.90663	1
3-2/M82	0.79586
4-1-1/M82	0.92752	1
4-1/M82	N/A	N/A
4-3-2/M82	0.96884	1
4-3/M82	N/A	N/A
5-3/M82	1.00437	1
6-2/M82	0.83249
6-3/M82	1.00398	1
7-1/M82	N/A	N/A
7-2/M82	0.94224	0.881
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.94243	1
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	1.21762
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	1.57963
IL1-4/WTpooled	0.92409	0.834
WT/WTpooled	0.98344	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	1.5432	0.479

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.98424	1
DC3000/delta hrp 6h	1.12391	1
DC3000/delta hrp 12h	0.98499	1
DC3000/delta hrp 24h	1.05131	0.535

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.02428
DC3000 delta B/DC3000 delta AB	1.19955	0.225

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.91768	1
Exp 36h	N/A	N/A
Exp 60h	0.72334	0.259

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

hybridization	ratio	FDR (corrected p value)
self-self	0.97869	1
Var 0h	N/A	N/A
Var 12h I row2-row1	1.09461	0.22
Var 12h NI row2-row1	1.06757	1
Var 36h I row2-row1	0.86936	0.202
Var 36h NI row2-row1	1.65007	1
Var 60h I row2-row1	1.09221	0.562
Var 60h NI row2-row1	0.79956	0.904
Time course 0hI-0hNI	0.85003	0.3
Time course 12hI-12hNI	1.0208	0.827
Time course 36hI-36hNI	0.94735	0.411
Time course 60hI-60hNI	0.72096	0.011

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)	1.01399	0.798
transgenic ySAMdc/azygous control (breaker)	1.1765	1
transgenic ySAMdc/azygous control (red)	1.12399	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.01622	0.372

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.24835	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.7512	0.172
Manapal/WT (break)	N/A	N/A
Manapal/WT (red)	0.60224	0.184