Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.4.4.3

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.18511	0.912
27DAP/17DAP	1.26074	0.738
39DAP/27DAP	1.15709	0.915
41DAP/39DAP	1.2029	0.392
42DAP/41DAP	0.86582	0.774
43DAP/42DAP	0.82984	0.589
47DAP/43DAP	1.10927	0.618
52DAP/47DAP	1.02554	0.982
57DAP/52DAP	1.37033	0.55

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.27409	0.023
17DAP/reference	0.95767	0.567
27DAP/reference	1.02699	0.794
39DAP/reference	1.06126	0.534
41DAP/reference	0.98646	0.814
42DAP/reference	0.99876	0.608
43DAP/reference	0.93183	0.273
47DAP/reference	1.05584	0.353
52DAP/reference	1.11476	0.033
57DAP/reference	1.07239	0.332

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.91776	0.526
27DAP/17DAP	0.96035	0.887
39DAP/27DAP	1.05111	0.672
41DAP/39DAP	0.95664	0.91
42DAP/41DAP	1.12267	0.601
43DAP/42DAP	0.98223	0.831
47DAP/43DAP	1.09294	0.92
52DAP/47DAP	0.78121	0.243
57DAP/52DAP	0.86046	0.331
57DAP/7DAP	0.7635

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.10685	0.325
17DAP/reference	1.10923	0.525
27DAP/reference	1.2154	0.197
39DAP/reference	1.04132	0.74
41DAP/reference	1.12552	0.35
42DAP/reference	1.50049	0.037
43DAP/reference	0.8834	0.139
47DAP/reference	1.10537	0.571
52DAP/reference	0.96387	0.363
57DAP/reference	0.85399	0.054

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.0914	0.055
17DAP/reference	0.85399	0.056
27DAP/reference	1.17068	0.217
39DAP/reference	1.1402	0.62
41DAP/reference	0.94309	0.364
42DAP/reference	0.96722	0.482
43DAP/reference	1.21326	0.297
47DAP/reference	1.12542	0.321
52DAP/reference	0.90564	0.239
57DAP/reference	0.83124	0.04

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.34091	0.027
17DAP/reference	1.17043	0.376
27DAP/reference	1.15455	0.156
39DAP/reference	1.04907	1
41DAP/reference	1.22256	0.04
42DAP/reference	1.16356	0.086
43DAP/reference	1.29236	0.04
47DAP/reference	1.12691	0.066
52DAP/reference	1.04238	0.851
57DAP/reference	1.28708	0.044

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.96971	1
26DAP/20DAP	1.23675	0.642
34DAP/26DAP	1.20324	1
51DAP/34DAP	0.78626	0.07
52DAP/51DAP	0.94155	1
53DAP/52DAP	0.68315	0.061
55DAP/53DAP	0.60329	0.017
57DAP/55DAP	1.35148	0.301
62DAP/57DAP	1.40091	0.158
68DAP/62DAP	0.76657	0.464
68DAP/14DAP	1.11556	0.85

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.7196	0.02

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.07934	0.666
Mature Green Tomato/Ripe Tomato	0.91159	0.522
Immature Eggplant/Mature Eggplant	1.63909	0.05
Ripe Pepper/Ripe Tomato	0.88382	0.293
Mature Eggplant/Ripe Tomato	0.99464	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.07465	1
1-1-2/M82	0.90812
12-2/M82	1.12017	1
12-4/M82	1.07121	1
1-3/M82	0.82466
2-1-1/M82	0.93383	1
2-1/M82	1.40771	1
2-6/M82	1.12496	0.505
3-2/M82	N/A	N/A
4-1-1/M82	1.43573	0.968
4-1/M82	1.3835
4-3-2/M82	N/A	N/A
4-3/M82	1.5195	1
5-3/M82	1.1567	1
6-2/M82	1.08531	1
6-3/M82	1.05533	1
7-1/M82	1.3621	0.598
7-2/M82	1.09	1
9-3-2/M82	1.16906	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.94458	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.87974	0.31
IL12-4/WTpooled	1.02405	0.891
IL1-4/WTpooled	1.11111
WT/WTpooled	0.94873	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	1.55735	0.309

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.16562	0.715
DC3000/delta hrp 6h	0.86852	0.942
DC3000/delta hrp 12h	1.10382	1
DC3000/delta hrp 24h	1.09713	0.673

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	2.00176
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	1.16688	1
Exp 36h	1.44713	0.489
Exp 60h	1.50216	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	N/A	N/A
Var 0h	0.97377	1
Var 12h I row2-row1	N/A	N/A
Var 12h NI row2-row1	N/A	N/A
Var 36h I row2-row1	N/A	N/A
Var 36h NI row2-row1	N/A	N/A
Var 60h I row2-row1	N/A	N/A
Var 60h NI row2-row1	N/A	N/A
Time course 0hI-0hNI	N/A	N/A
Time course 12hI-12hNI	N/A	N/A
Time course 36hI-36hNI	N/A	N/A
Time course 60hI-60hNI	N/A	N/A

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)	0.83885	0.295
transgenic ySAMdc/azygous control (breaker)	0.96097	1
transgenic ySAMdc/azygous control (red)	0.98955	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.00984	0.723

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.84898	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.97513	1
Manapal/WT (break)	0.62681	0.297
Manapal/WT (red)	1.02142	1