Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.4.1.16

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.75625	0.131
27DAP/17DAP	0.84563	0.677
39DAP/27DAP	0.78115	0.315
41DAP/39DAP	1.04944	0.866
42DAP/41DAP	1.30702	0.681
43DAP/42DAP	0.98908	0.934
47DAP/43DAP	0.94245	0.71
52DAP/47DAP	1.29544	0.608
57DAP/52DAP	0.98021	0.971

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.10188	0.04
17DAP/reference	1.15614	0.015
27DAP/reference	1.00419	1
39DAP/reference	0.98812	0.816
41DAP/reference	1.05515	0.338
42DAP/reference	0.91035	0.03
43DAP/reference	0.94307	0.555
47DAP/reference	0.89528	0.06
52DAP/reference	0.87429	0.125
57DAP/reference	0.80239	0.024

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.14271	0.642
27DAP/17DAP	1.09389	0.872
39DAP/27DAP	0.82248	0.291
41DAP/39DAP	1.25528	0.674
42DAP/41DAP	0.78265	0.119
43DAP/42DAP	0.94778	0.558
47DAP/43DAP	1.10807	0.601
52DAP/47DAP	1.13606	0.589
57DAP/52DAP	1.1443	0.745
57DAP/7DAP	1.98179	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.12914	0.185
17DAP/reference	0.96963	0.389
27DAP/reference	1.04006	0.8
39DAP/reference	0.87627	0.126
41DAP/reference	1.05227	0.949
42DAP/reference	0.97662	0.506
43DAP/reference	1.05441	0.694
47DAP/reference	0.92093	0.128
52DAP/reference	1.07619	0.13
57DAP/reference	1.12562	0.331

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.14682	0.114
17DAP/reference	1.02944	0.756
27DAP/reference	1.006	0.711
39DAP/reference	0.95511	0.381
41DAP/reference	0.94125	0.242
42DAP/reference	0.81069	0.019
43DAP/reference	0.9509	0.459
47DAP/reference	0.83777	0.017
52DAP/reference	0.82827	0.02
57DAP/reference	0.86516	0.208

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.20824	0.251
17DAP/reference	1.14193	0.456
27DAP/reference	1.07163	0.596
39DAP/reference	0.93347	0.299
41DAP/reference	0.85166	0.237
42DAP/reference	0.95154	0.552
43DAP/reference	0.94767	0.432
47DAP/reference	1.1546	0.034
52DAP/reference	1.62088	0.443
57DAP/reference	0.95511	0.387

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.43891	0.678
26DAP/20DAP	1.07014	0.806
34DAP/26DAP	0.96209	0.917
51DAP/34DAP	1.46765	0.387
52DAP/51DAP	0.97741	1
53DAP/52DAP	1.06751	0.819
55DAP/53DAP	0.90753	0.35
57DAP/55DAP	1.04023	0.875
62DAP/57DAP	1.23211	0.217
68DAP/62DAP	0.72441	0.345
68DAP/14DAP	0.78045	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.73227	0.175

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.05824	0.176
Mature Green Tomato/Ripe Tomato	1.97764	0.024
Immature Eggplant/Mature Eggplant	0.73505	0.075
Ripe Pepper/Ripe Tomato	1.74329	1
Mature Eggplant/Ripe Tomato	4.05536	0.268

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.02053
1-1-2/M82	0.99156	1
12-2/M82	0.86413
12-4/M82	1.15354	1
1-3/M82	N/A	N/A
2-1-1/M82	0.96615
2-1/M82	1.19108
2-6/M82	1.22531
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	N/A	N/A
4-3/M82	0.96268
5-3/M82	1.18957	0.572
6-2/M82	N/A	N/A
6-3/M82	0.84146
7-1/M82	N/A	N/A
7-2/M82	1.09049
9-3-2/M82	1.00564

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.93279	0.321
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	0.63442
IL1-4/WTpooled	2.25947	1
WT/WTpooled	0.91645	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	1.05744	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.98181	1
DC3000/delta hrp 6h	1.04834	1
DC3000/delta hrp 12h	1.07649	1
DC3000/delta hrp 24h	0.80956	0.065

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.47791	0.042
DC3000 delta B/DC3000 delta AB	0.49158	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.94179	1
Exp 36h	0.70954	0.397
Exp 60h	0.54935	0.253

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

hybridization	ratio	FDR (corrected p value)
self-self	0.94653
Var 0h	2.35226	0.98
Var 12h I row2-row1	0.81242	0.344
Var 12h NI row2-row1	1.08873	1
Var 36h I row2-row1	1.06583	1
Var 36h NI row2-row1	1.2085	1
Var 60h I row2-row1	0.91329
Var 60h NI row2-row1	0.94021	0.977
Time course 0hI-0hNI	0.97276	0.801
Time course 12hI-12hNI	0.94584	0.661
Time course 36hI-36hNI	0.94062	0.225
Time course 60hI-60hNI	0.54031	0.006

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)	0.99116	0.862
transgenic ySAMdc/azygous control (breaker)	1.01527	1
transgenic ySAMdc/azygous control (red)	0.99065	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.0154	0.687

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.93884	0.239

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.13913	0.105
Manapal/WT (break)	1.9023	0.13
Manapal/WT (red)	1.32133	0.413