Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.3.16.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.12418	0.786
27DAP/17DAP	0.89769	0.766
39DAP/27DAP	1.24595	0.363
41DAP/39DAP	0.89829	0.566
42DAP/41DAP	1.2516	0.877
43DAP/42DAP	0.97057	0.912
47DAP/43DAP	1.17285	0.825
52DAP/47DAP	0.92581	0.769
57DAP/52DAP	0.99606	0.976

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90422	0.154
17DAP/reference	0.95967	0.503
27DAP/reference	1.0749	0.365
39DAP/reference	1.04153	0.524
41DAP/reference	0.93885	0.201
42DAP/reference	0.89807	0.041
43DAP/reference	0.93734	0.377
47DAP/reference	0.96677	0.322
52DAP/reference	0.85037	0.105
57DAP/reference	0.84473	0.065

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.14434	0.961
27DAP/17DAP	0.92319	0.782
39DAP/27DAP	0.89063	0.367
41DAP/39DAP	1.01672	1
42DAP/41DAP	0.92914	0.515
43DAP/42DAP	0.98174	0.801
47DAP/43DAP	0.96006	0.877
52DAP/47DAP	1.11973	0.689
57DAP/52DAP	0.88817	0.424
57DAP/7DAP	0.97796	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92789	0.361
17DAP/reference	1.08184	0.477
27DAP/reference	0.98511	0.53
39DAP/reference	0.84445	0.146
41DAP/reference	0.94768	0.326
42DAP/reference	0.63893	0.013
43DAP/reference	0.95979	0.305
47DAP/reference	1.11816	0.121
52DAP/reference	0.9682	0.435
57DAP/reference	1.05294	0.654

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.0164	0.894
17DAP/reference	1.04231	0.961
27DAP/reference	0.90249	0.327
39DAP/reference	0.96692	0.455
41DAP/reference	0.9038	0.169
42DAP/reference	0.92573	0.108
43DAP/reference	1.13996	0.662
47DAP/reference	1.03292	0.513
52DAP/reference	1.02637	1
57DAP/reference	0.92407	0.278

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98921	0.653
17DAP/reference	0.93654	0.364
27DAP/reference	0.94121	0.442
39DAP/reference	1.29823	0.022
41DAP/reference	0.97361	0.56
42DAP/reference	1.11207	0.566
43DAP/reference	0.9199	0.281
47DAP/reference	1.16027	0.03
52DAP/reference	0.88021	0.262
57DAP/reference	0.96706	0.491

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.99403	1
26DAP/20DAP	0.86338	0.512
34DAP/26DAP	0.86484	0.682
51DAP/34DAP	0.79528	0.436
52DAP/51DAP	0.91816	1
53DAP/52DAP	1.06351	0.868
55DAP/53DAP	1.26637	0.434
57DAP/55DAP	1.0244	0.96
62DAP/57DAP	1.23959	0.902
68DAP/62DAP	0.90517	0.769
68DAP/14DAP	1.11742	0.714

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.00158	0.665

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.02441	1
Immature Eggplant/Mature Eggplant	0.864
Ripe Pepper/Ripe Tomato	0.52453
Mature Eggplant/Ripe Tomato	1.5214

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.08119	1
1-1-2/M82	1.21442	1
12-2/M82	1.12978
12-4/M82	1.1821	1
1-3/M82	0.554
2-1-1/M82	0.71991
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	N/A	N/A
4-3-2/M82	1.30924
4-3/M82	N/A	N/A
5-3/M82	1.13686	1
6-2/M82	0.63184
6-3/M82	0.84565
7-1/M82	N/A	N/A
7-2/M82	0.98367	1
9-3-2/M82	0.97785	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.87126	0.348
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.91787	0.418
IL12-4/WTpooled	1.01438	0.891
IL1-4/WTpooled	0.97286	0.699
WT/WTpooled	1.01098	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	0.85753	0.497

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.02263	0.921
DC3000/delta hrp 6h	0.8049	0.95
DC3000/delta hrp 12h	1.09568	1
DC3000/delta hrp 24h	1.03742	0.673

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	N/A	N/A
Exp 36h	1.3737	0.409
Exp 60h	0.99215	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.06332	1
Var 0h	0.94048	1
Var 12h I row2-row1	1.1214	0.176
Var 12h NI row2-row1	1.14251	0.649
Var 36h I row2-row1	0.79953	0.805
Var 36h NI row2-row1	0.89775	0.645
Var 60h I row2-row1	1.00946	1
Var 60h NI row2-row1	0.80056	0.932
Time course 0hI-0hNI	1.06667	0.63
Time course 12hI-12hNI	0.96505	0.687
Time course 36hI-36hNI	0.89903	0.108
Time course 60hI-60hNI	0.96787	0.646

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)	1.01167	0.612
transgenic ySAMdc/azygous control (breaker)	1.0266	1
transgenic ySAMdc/azygous control (red)	1.07207	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.98026	0.122

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.07155	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.72155	0.172
Manapal/WT (break)	0.87247	0.299
Manapal/WT (red)	0.62213	0.181