Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.1.9.4

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.66245	0.071
27DAP/17DAP	0.94217	0.879
39DAP/27DAP	1.33211	0.412
41DAP/39DAP	0.76996	0.245
42DAP/41DAP	1.03874	0.978
43DAP/42DAP	1.12726	1
47DAP/43DAP	0.84017	0.504
52DAP/47DAP	0.93097	0.721
57DAP/52DAP	0.96499	0.957

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03555	0.96
17DAP/reference	0.87349	0.074
27DAP/reference	0.93514	0.369
39DAP/reference	0.98361	0.72
41DAP/reference	0.96218	0.667
42DAP/reference	1.38767	0.001
43DAP/reference	1.09573	0.089
47DAP/reference	1.12307	0.078
52DAP/reference	0.91845	0.283
57DAP/reference	1.09191	0.27

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.00686	0.801
27DAP/17DAP	1.03615	0.988
39DAP/27DAP	0.93363	0.514
41DAP/39DAP	0.97204	0.968
42DAP/41DAP	0.97944	0.774
43DAP/42DAP	1.02665	1
47DAP/43DAP	1.0031	0.985
52DAP/47DAP	1.04876	0.979
57DAP/52DAP	1.45168	0.067
57DAP/7DAP	1.55732	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92555	0.326
17DAP/reference	0.97877	0.389
27DAP/reference	1.28964	0.014
39DAP/reference	1.01297	1
41DAP/reference	1.10213	0.336
42DAP/reference	1.0833	0.132
43DAP/reference	0.93733	0.175
47DAP/reference	1.63911	0.047
52DAP/reference	0.94406	0.278
57DAP/reference	0.92093	0.118

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04318	0.852
17DAP/reference	0.93377	0.239
27DAP/reference	1.21617	0.303
39DAP/reference	1.05381	0.602
41DAP/reference	1.10223	0.439
42DAP/reference	1.04874	0.68
43DAP/reference	1.20219	0.503
47DAP/reference	1.25481	0.087
52DAP/reference	0.82954	0.093
57DAP/reference	0.83573	0.079

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.85988	0.059
17DAP/reference	0.91583	0.281
27DAP/reference	0.87709	0.044
39DAP/reference	0.93327	0.122
41DAP/reference	0.97126	0.371
42DAP/reference	1.10152	0.356
43DAP/reference	1.06138	0.973
47DAP/reference	1.3127	0.031
52DAP/reference	1.17829	0.132
57DAP/reference	0.95977	0.516

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.85957	0.89
26DAP/20DAP	1.17247	0.818
34DAP/26DAP	2.11323	0.542
51DAP/34DAP	0.93663	0.681
52DAP/51DAP	1.89894	0.044
53DAP/52DAP	0.65159	0.06
55DAP/53DAP	0.66963	0.022
57DAP/55DAP	0.81803	0.42
62DAP/57DAP	1.74374	0.723
68DAP/62DAP	1.3697	0.813
68DAP/14DAP	1.0509	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.77507	0.186

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.03644	0.417
Mature Green Tomato/Ripe Tomato	0.58008	0.04
Immature Eggplant/Mature Eggplant	2.02873	0.05
Ripe Pepper/Ripe Tomato	0.3183	0.224
Mature Eggplant/Ripe Tomato	1.15571	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.29755	0.536
1-1-2/M82	1.36929	1
12-2/M82	0.76059	0.955
12-4/M82	1.04014	1
1-3/M82	2.98203	0.255
2-1-1/M82	1.40589	0.457
2-1/M82	1.21189	1
2-6/M82	1.33112	0.505
3-2/M82	1.46336
4-1-1/M82	1.06561	1
4-1/M82	0.92428
4-3-2/M82	N/A	N/A
4-3/M82	1.8874	1
5-3/M82	1.23106	0.572
6-2/M82	2.98574	0.253
6-3/M82	0.93822	1
7-1/M82	1.03181	1
7-2/M82	1.82247	0.318
9-3-2/M82	1.14638

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.86708	0.247
IL2-6/WTpooled	1.33178	0.419
IL7-5/WTpooled	0.85832	1
IL7-3/WTpooled	1.11884	1
IL12-4/WTpooled	1.00119	1
IL1-4/WTpooled	0.9781	1
WT/WTpooled	0.99789	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	1.26138	0.309

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.97956	1
DC3000/delta hrp 6h	1.11504	1
DC3000/delta hrp 12h	0.91579	1
DC3000/delta hrp 24h	1.87888	0.03

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.12036	0.183
DC3000 delta B/DC3000 delta AB	1.17743	0.372

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.13253	1
Exp 36h	1.03801	0.943
Exp 60h	1.21248	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	1.03664	1
Var 0h	0.9519	1
Var 12h I row2-row1	1.04744	0.544
Var 12h NI row2-row1	1.06876	0.649
Var 36h I row2-row1	1.08135	1
Var 36h NI row2-row1	0.88599	0.584
Var 60h I row2-row1	0.77372	0.582
Var 60h NI row2-row1	0.96196	1
Time course 0hI-0hNI	0.92981	0.497
Time course 12hI-12hNI	1.13575	0.275
Time course 36hI-36hNI	1.56606	0.005
Time course 60hI-60hNI	1.67294	0.011

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)	0.72639	0.26
transgenic ySAMdc/azygous control (breaker)	0.95665	0.49
transgenic ySAMdc/azygous control (red)	0.96689	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.27802	0.13

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.95296	0.431

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.03659	0.09
Manapal/WT (break)	0.91236	0.333
Manapal/WT (red)	0.677	0.181