Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.2.8.1

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.67825	0.148
27DAP/17DAP	1.48917	0.552
39DAP/27DAP	2.00704	0.229
41DAP/39DAP	1.48275	0.32
42DAP/41DAP	2.22344	0.018
43DAP/42DAP	1.28047	0.885
47DAP/43DAP	1.69847	0.213
52DAP/47DAP	1.09879	0.898
57DAP/52DAP	1.06483	0.98

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.80653	0.092
17DAP/reference	0.99412	0.858
27DAP/reference	0.97417	0.623
39DAP/reference	0.88965	0.141
41DAP/reference	0.94136	0.434
42DAP/reference	0.92131	0.099
43DAP/reference	1.12892	0.202
47DAP/reference	0.93531	0.258
52DAP/reference	1.00204	0.73
57DAP/reference	1.04907	0.682

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.22394	0.699
27DAP/17DAP	0.93336	0.854
39DAP/27DAP	1.5286	0.071
41DAP/39DAP	0.66261	0.013
42DAP/41DAP	1.40437	0.155
43DAP/42DAP	2.55374	0.014
47DAP/43DAP	1.27724	0.084
52DAP/47DAP	1.40999	0.249
57DAP/52DAP	1.05238	0.892
57DAP/7DAP	2.71316	0.23

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.09701	0.98
17DAP/reference	0.94579	0.295
27DAP/reference	1.06369	0.974
39DAP/reference	0.64901	0.014
41DAP/reference	0.82517	0.082
42DAP/reference	1.0349	1
43DAP/reference	1.18051	0.053
47DAP/reference	0.97631	0.671
52DAP/reference	1.11702	0.941
57DAP/reference	0.90957	0.191

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97227	0.688
17DAP/reference	0.8504	0.208
27DAP/reference	0.81654	0.037
39DAP/reference	0.92788	0.265
41DAP/reference	1.03281	1
42DAP/reference	0.98347	0.594
43DAP/reference	1.16094	0.279
47DAP/reference	1.10456	0.675
52DAP/reference	0.97118	0.5
57DAP/reference	1.06584	0.98

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.12977	0.575
17DAP/reference	0.98224	0.709
27DAP/reference	1.12835	0.51
39DAP/reference	0.86553	0.111
41DAP/reference	1.00464	0.618
42DAP/reference	1.09866	0.635
43DAP/reference	0.88821	0.319
47DAP/reference	0.9173	0.325
52DAP/reference	1.10016	0.888
57DAP/reference	0.93437	0.402

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.10302	0.966
26DAP/20DAP	0.95661	1
34DAP/26DAP	1.25021	0.304
51DAP/34DAP	1.06658	0.949
52DAP/51DAP	1.25043	0.708
53DAP/52DAP	1.24878	0.623
55DAP/53DAP	1.22738	0.813
57DAP/55DAP	1.37566	0.935
62DAP/57DAP	1.36364	0.622
68DAP/62DAP	1.20612	0.866
68DAP/14DAP	1.33756

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	9.79879	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.09206	0.017
Immature Eggplant/Mature Eggplant	N/A	N/A
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	N/A	N/A
1-1-2/M82	2.03458
12-2/M82	N/A	N/A
12-4/M82	2.16309
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	1.38222	0.84
4-1-1/M82	N/A	N/A
4-1/M82	1.32648
4-3-2/M82	1.35013	0.508
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	0.95169
7-2/M82	N/A	N/A
9-3-2/M82	2.14077	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.16102	0.277
IL2-6/WTpooled	1.0801	0.659
IL7-5/WTpooled	0.68349	1
IL7-3/WTpooled	0.79029	0.418
IL12-4/WTpooled	0.90501	1
IL1-4/WTpooled	1.53435	0.426
WT/WTpooled	0.95453	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	0.91387	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.91497	1
DC3000/delta hrp 6h	1.24209	1
DC3000/delta hrp 12h	0.96775	1
DC3000/delta hrp 24h	0.52702

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	N/A
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	0.70984	0.265
Exp 36h	0.81288	0.82
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	1.04853	1
Var 0h	0.93845	1
Var 12h I row2-row1	1.29822	0.196
Var 12h NI row2-row1	1.02883	1
Var 36h I row2-row1	0.9009	0.575
Var 36h NI row2-row1	0.71982	0.253
Var 60h I row2-row1	1.1089	0.562
Var 60h NI row2-row1	1.19889	0.904
Time course 0hI-0hNI	0.97492	0.898
Time course 12hI-12hNI	1.11959	0.137
Time course 36hI-36hNI	1.05696	0.453
Time course 60hI-60hNI	1.02646	0.673

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)	0.99264	0.931
transgenic ySAMdc/azygous control (breaker)	1.31015	0.248
transgenic ySAMdc/azygous control (red)	1.01923	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.98746	0.486

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.26273	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.31266	0.105
Manapal/WT (break)	1.45925	0.183
Manapal/WT (red)	2.25294	0.133