Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.4.17.1

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.98157	0.801
27DAP/17DAP	1.06389	0.905
39DAP/27DAP	1.73104	0.101
41DAP/39DAP	1.35474	0.359
42DAP/41DAP	2.14376	0.024
43DAP/42DAP	1.48157	0.121
47DAP/43DAP	1.40467	0.394
52DAP/47DAP	1.04497	0.821
57DAP/52DAP	1.12197	0.927

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.79684	0.058
17DAP/reference	0.85706	0.097
27DAP/reference	0.99795	0.61
39DAP/reference	1.13205	0.377
41DAP/reference	0.84143	0.065
42DAP/reference	1.46707	0.001
43DAP/reference	1.39935	0.014
47DAP/reference	1.59671	0.003
52DAP/reference	0.97244	0.475
57DAP/reference	1.14959	0.159

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.09438	0.812
27DAP/17DAP	0.93534	0.821
39DAP/27DAP	1.35361	0.11
41DAP/39DAP	1.01604	1
42DAP/41DAP	1.33275	0.007
43DAP/42DAP	1.09784	0.413
47DAP/43DAP	1.24861	0.262
52DAP/47DAP	1.00716	1
57DAP/52DAP	0.9394	0.498
57DAP/7DAP	1.5429	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.31483	0.051
17DAP/reference	1.3154	0.032
27DAP/reference	1.48133	0.008
39DAP/reference	1.44291	0.006
41DAP/reference	1.9069	0.01
42DAP/reference	1.77268	0.008
43DAP/reference	1.47422	0.006
47DAP/reference	1.38527	0.018
52DAP/reference	2.12469	0.007
57DAP/reference	1.56841	0.005

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92716	0.412
17DAP/reference	0.91264	0.23
27DAP/reference	0.92561	0.327
39DAP/reference	0.97316	0.416
41DAP/reference	1.1922	0.172
42DAP/reference	1.2308	0.084
43DAP/reference	1.20596	0.304
47DAP/reference	1.78529	0.008
52DAP/reference	0.87731	0.072
57DAP/reference	1.23805	0.078

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.1249	0.218
17DAP/reference	1.01739	1
27DAP/reference	1.14378	0.115
39DAP/reference	1.27494	0.012
41DAP/reference	1.4655	0.01
42DAP/reference	1.24094	0.059
43DAP/reference	1.43977	0.022
47DAP/reference	1.34394	0.017
52DAP/reference	1.50471	0.052
57DAP/reference	1.30766	0.031

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.37251	0.786
26DAP/20DAP	0.69524	0.317
34DAP/26DAP	1.04054	1
51DAP/34DAP	3.28935	0.021
52DAP/51DAP	0.92903	1
53DAP/52DAP	0.73885	0.113
55DAP/53DAP	0.85417	0.091
57DAP/55DAP	1.29707	0.626
62DAP/57DAP	0.90714	0.681
68DAP/62DAP	2.18475	0.038
68DAP/14DAP	2.05703	0.025

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.81156	0.079

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.61054	0.157
Mature Green Tomato/Ripe Tomato	0.16755	0.017
Immature Eggplant/Mature Eggplant	4.35707	0.05
Ripe Pepper/Ripe Tomato	0.43965	0.224
Mature Eggplant/Ripe Tomato	0.06187	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.19949	0.742
1-1-2/M82	1.51928	1
12-2/M82	1.39889	1
12-4/M82	2.75698	1
1-3/M82	0.88038	0.441
2-1-1/M82	1.00664	1
2-1/M82	0.62107
2-6/M82	1.30502	0.329
3-2/M82	1.42896	0.388
4-1-1/M82	1.44932	1
4-1/M82	2.71414	0.466
4-3-2/M82	N/A	N/A
4-3/M82	3.72862	0.268
5-3/M82	0.80329	1
6-2/M82	1.07009	1
6-3/M82	1.3409	1
7-1/M82	0.53058
7-2/M82	0.93732	1
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.20778	0.659
IL7-5/WTpooled	0.33496
IL7-3/WTpooled	0.54137	0.298
IL12-4/WTpooled	0.93465	1
IL1-4/WTpooled	N/A	N/A
WT/WTpooled	0.89318	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	1.22832	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.04116	0.921
DC3000/delta hrp 6h	2.27045	1
DC3000/delta hrp 12h	1.1479	1
DC3000/delta hrp 24h	1.04415	0.797

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.50956	0.076
DC3000 delta B/DC3000 delta AB	1.43957	0.146

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.56063	0.254
Exp 36h	1.88823	0.349
Exp 60h	2.38304	0.215

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

hybridization	ratio	FDR (corrected p value)
self-self	0.97714	1
Var 0h	1.76809	0.936
Var 12h I row2-row1	1.13017	0.187
Var 12h NI row2-row1	1.24604	0.649
Var 36h I row2-row1	1.55146	0.305
Var 36h NI row2-row1	0.89498	1
Var 60h I row2-row1	0.86663	0.832
Var 60h NI row2-row1	1.18674	1
Time course 0hI-0hNI	1.0133	1
Time course 12hI-12hNI	0.9078	0.228
Time course 36hI-36hNI	1.33381	0.031
Time course 60hI-60hNI	1.81467	0.008

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)	1.68647	0.277
transgenic ySAMdc/azygous control (breaker)	0.19966	0.142
transgenic ySAMdc/azygous control (red)	1.08864	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.88927	0.255

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.89478	0.14
Manapal/WT (break)	1.45633	1
Manapal/WT (red)	0.79781	0.36