Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.1.20.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.17868	0.725
27DAP/17DAP	0.50724	0.03
39DAP/27DAP	1.23712	0.893
41DAP/39DAP	1.03277	1
42DAP/41DAP	1.71376	0.047
43DAP/42DAP	0.74559	0.744
47DAP/43DAP	1.39283	0.889
52DAP/47DAP	0.81965	0.554
57DAP/52DAP	0.52461	0.692

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.86511	0.032
17DAP/reference	1.07638	0.112
27DAP/reference	0.99977	0.885
39DAP/reference	1.04887	0.474
41DAP/reference	1.14202	0.032
42DAP/reference	0.9043	0.023
43DAP/reference	1.01233	1
47DAP/reference	0.89798	0.021
52DAP/reference	0.93306	0.23
57DAP/reference	0.83203	0.013

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.87363	0.211
27DAP/17DAP	1.12124	0.768
39DAP/27DAP	1.29115	0.236
41DAP/39DAP	1.13525	1
42DAP/41DAP	0.74096	0.007
43DAP/42DAP	1.12844	0.554
47DAP/43DAP	0.92924	0.743
52DAP/47DAP	1.38559	0.232
57DAP/52DAP	1.15033	0.402
57DAP/7DAP	2.49134	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.83468	0.08
17DAP/reference	1.01399	1
27DAP/reference	0.93637	0.071
39DAP/reference	0.98215	0.411
41DAP/reference	0.90576	0.09
42DAP/reference	0.95271	0.338
43DAP/reference	0.91611	0.095
47DAP/reference	0.90509	0.101
52DAP/reference	0.81128	0.02
57DAP/reference	0.92835	0.156

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99639	0.884
17DAP/reference	0.84315	0.011
27DAP/reference	0.83936	0.087
39DAP/reference	0.86287	0.022
41DAP/reference	0.85193	0.089
42DAP/reference	0.8139	0.016
43DAP/reference	1.05748	0.641
47DAP/reference	0.87983	0.054
52DAP/reference	0.9811	0.351
57DAP/reference	1.05094	0.848

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92143	0.061
17DAP/reference	0.95305	0.452
27DAP/reference	1.01044	0.934
39DAP/reference	0.90045	0.022
41DAP/reference	0.99485	0.754
42DAP/reference	0.9573	0.552
43DAP/reference	0.85857	0.165
47DAP/reference	0.87323	0.139
52DAP/reference	0.98302	0.732
57DAP/reference	0.86264	0.184

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.90611	0.585
26DAP/20DAP	0.99704	1
34DAP/26DAP	1.04979	1
51DAP/34DAP	0.84645	0.201
52DAP/51DAP	0.86477	1
53DAP/52DAP	1.02262	0.91
55DAP/53DAP	1.24174	0.126
57DAP/55DAP	0.78907	0.271
62DAP/57DAP	1.18954	0.081
68DAP/62DAP	0.98221	0.863
68DAP/14DAP	0.90962	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.79211	0.358

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.51342
Mature Green Tomato/Ripe Tomato	N/A	N/A
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	0.54092

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.9632	0.944
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	1.20448
1-3/M82	0.63624
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	0.94017	1
3-2/M82	1.14074
4-1-1/M82	0.67463
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	1.13136
5-3/M82	0.94281	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	0.83232	0.527
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.58911	0.243
IL2-6/WTpooled	0.80469	0.473
IL7-5/WTpooled	1.08515	1
IL7-3/WTpooled	0.85983	0.418
IL12-4/WTpooled	0.54105	0.554
IL1-4/WTpooled	0.64911	0.415
WT/WTpooled	0.94288	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	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.03226	0.921
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	1.21865	1
DC3000/delta hrp 24h	1.00925	1

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	2.1323
DC3000 delta B/DC3000 delta AB	N/A	N/A

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

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

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

hybridization	ratio	FDR (corrected p value)
self-self	1.0376	1
Var 0h	N/A	N/A
Var 12h I row2-row1	1.17648	0.406
Var 12h NI row2-row1	0.62224	0.546
Var 36h I row2-row1	0.85363	1
Var 36h NI row2-row1	1.15994	1
Var 60h I row2-row1	1.2105	0.543
Var 60h NI row2-row1	1.29138	0.904
Time course 0hI-0hNI	1.05897	0.799
Time course 12hI-12hNI	0.94929	0.759
Time course 36hI-36hNI	0.85926	0.236
Time course 60hI-60hNI	1.07633	0.16

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)	1.17102	0.294
transgenic ySAMdc/azygous control (breaker)	1.27051	0.248
transgenic ySAMdc/azygous control (red)	0.9711	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.00234	1

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.29496	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.4828	0.172
Manapal/WT (break)	1.00849	1
Manapal/WT (red)	0.76341	0.36