Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.3.8.1

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.96979	0.689
27DAP/17DAP	0.97325	0.952
39DAP/27DAP	1.26568	0.354
41DAP/39DAP	0.74584	0.202
42DAP/41DAP	1.08928	0.916
43DAP/42DAP	1.05767	1
47DAP/43DAP	0.78333	0.36
52DAP/47DAP	0.80971	0.528
57DAP/52DAP	1.28627	0.776

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.86774	0.111
17DAP/reference	0.94163	0.368
27DAP/reference	0.93014	0.471
39DAP/reference	0.95445	0.541
41DAP/reference	0.98631	0.814
42DAP/reference	0.85907	0.009
43DAP/reference	1.02601	0.812
47DAP/reference	0.92691	0.207
52DAP/reference	1.01946	1
57DAP/reference	1.02371	0.927

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.21081	0.124
27DAP/17DAP	1.11459	0.826
39DAP/27DAP	0.8249	0.251
41DAP/39DAP	1.24004	0.682
42DAP/41DAP	0.98188	0.791
43DAP/42DAP	0.80199	0.023
47DAP/43DAP	1.03831	0.914
52DAP/47DAP	0.8824	0.338
57DAP/52DAP	0.89714	0.104
57DAP/7DAP	0.90327	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.14468	0.332
17DAP/reference	0.98509	0.518
27DAP/reference	1.01077	0.656
39DAP/reference	0.8721	0.146
41DAP/reference	0.82495	0.116
42DAP/reference	1.02332	0.828
43DAP/reference	1.07641	0.83
47DAP/reference	1.02452	1
52DAP/reference	0.93751	0.332
57DAP/reference	1.04725	0.698

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87742	0.306
17DAP/reference	0.79215	0.059
27DAP/reference	0.91157	0.282
39DAP/reference	0.82223	0.14
41DAP/reference	1.08081	0.737
42DAP/reference	0.93006	0.289
43DAP/reference	0.96117	0.507
47DAP/reference	0.89816	0.24
52DAP/reference	0.87007	0.02
57DAP/reference	0.88404	0.125

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92281	0.335
17DAP/reference	0.87282	0.186
27DAP/reference	1.04767	0.596
39DAP/reference	1.06534	0.189
41DAP/reference	0.85434	0.064
42DAP/reference	0.77747	0.036
43DAP/reference	0.8801	0.165
47DAP/reference	0.90608	0.24
52DAP/reference	0.92745	0.493
57DAP/reference	0.93195	0.424

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.45755	0.966
26DAP/20DAP	1.47578	0.374
34DAP/26DAP	1.19623	1
51DAP/34DAP	0.88799	0.376
52DAP/51DAP	0.72926	0.151
53DAP/52DAP	1.00923	0.854
55DAP/53DAP	0.67438	0.041
57DAP/55DAP	0.84402	0.403
62DAP/57DAP	1.12286	0.393
68DAP/62DAP	1.06425	1
68DAP/14DAP	0.84765	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.67162	0.015

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	8.54417	0.058
Mature Green Tomato/Ripe Tomato	1.70961	0.017
Immature Eggplant/Mature Eggplant	0.39807	0.059
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	1.84455

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.82824	1
12-2/M82	N/A	N/A
12-4/M82	1.02228	1
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	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	2.58415	0.466
4-3-2/M82	1.58225	0.241
4-3/M82	1.10912
5-3/M82	1.14236	0.572
6-2/M82	N/A	N/A
6-3/M82	1.01966
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	1.34735	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.88856	1
IL2-6/WTpooled	1.08729	0.584
IL7-5/WTpooled	0.74012	1
IL7-3/WTpooled	0.93587	1
IL12-4/WTpooled	0.94194	1
IL1-4/WTpooled	0.99985	1
WT/WTpooled	0.94293	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	1.04418	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.10678	0.921
DC3000/delta hrp 6h	1.02444	1
DC3000/delta hrp 12h	1.24123	1
DC3000/delta hrp 24h	0.93358	0.607

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.594
DC3000 delta B/DC3000 delta AB	1.04935	0.535

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.73583	0.242
Exp 36h	1.25532	0.326
Exp 60h	0.91459	0.386

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01328	1
Var 0h	1.17918	0.936
Var 12h I row2-row1	0.86211	0.363
Var 12h NI row2-row1	1.07329	1
Var 36h I row2-row1	1.13483	0.304
Var 36h NI row2-row1	0.83681	0.522
Var 60h I row2-row1	1.01279	1
Var 60h NI row2-row1	0.82622	0.483
Time course 0hI-0hNI	0.91373	0.317
Time course 12hI-12hNI	1.05644	0.536
Time course 36hI-36hNI	1.15932	0.453
Time course 60hI-60hNI	1.07338	0.575

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)	0.92761	0.338
transgenic ySAMdc/azygous control (breaker)	0.8361	0.251
transgenic ySAMdc/azygous control (red)	1.10431	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.01137	0.525

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.89465	0.284

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	N/A	N/A
Manapal/WT (break)	N/A	N/A
Manapal/WT (red)	0.90947	0.607