Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.2.11.17

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.02722	0.83
27DAP/17DAP	1.41769	0.793
39DAP/27DAP	1.14441	0.985
41DAP/39DAP	1.47891	0.342
42DAP/41DAP	0.85954	1
43DAP/42DAP	1.23281	0.831
47DAP/43DAP	0.90794	0.687
52DAP/47DAP	0.70115	0.331
57DAP/52DAP	1.45304	0.96

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9716	0.489
17DAP/reference	1.11509	0.161
27DAP/reference	0.94395	0.457
39DAP/reference	1.0026	0.975
41DAP/reference	1.22399	0.02
42DAP/reference	0.85121	0.045
43DAP/reference	0.98176	0.728
47DAP/reference	0.86336	0.042
52DAP/reference	0.80658	0.065
57DAP/reference	0.74658	0.016

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.94262	0.613
27DAP/17DAP	1.19266	0.9
39DAP/27DAP	0.89439	0.556
41DAP/39DAP	1.06421	0.876
42DAP/41DAP	1.06874	0.936
43DAP/42DAP	1.27245	0.585
47DAP/43DAP	1.11626	0.997
52DAP/47DAP	1.21649	0.73
57DAP/52DAP	1.47629	0.168
57DAP/7DAP	1.15054

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93463	0.326
17DAP/reference	1.19686	0.054
27DAP/reference	1.07535	0.301
39DAP/reference	0.88894	0.17
41DAP/reference	0.93338	0.412
42DAP/reference	0.83356	0.136
43DAP/reference	0.82909	0.151
47DAP/reference	1.04386	1
52DAP/reference	0.88324	0.097
57DAP/reference	1.21562	0.04

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.06856	0.874
17DAP/reference	0.82022	0.143
27DAP/reference	1.02627	0.79
39DAP/reference	0.99172	0.586
41DAP/reference	0.85324	0.023
42DAP/reference	0.87942	0.073
43DAP/reference	1.1544	0.347
47DAP/reference	0.99956	0.749
52DAP/reference	0.87924	0.121
57DAP/reference	1.02196	0.834

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92334	0.249
17DAP/reference	1.14103	0.248
27DAP/reference	1.35796	0.031
39DAP/reference	1.09938	0.108
41DAP/reference	1.0433	0.84
42DAP/reference	1.10018	0.68
43DAP/reference	0.80623	0.056
47DAP/reference	0.9591	0.465
52DAP/reference	1.1524	0.42
57DAP/reference	1.10649	0.939

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.74357	0.966
26DAP/20DAP	1.08041
34DAP/26DAP	0.79751	0.539
51DAP/34DAP	0.9086	0.537
52DAP/51DAP	N/A	N/A
53DAP/52DAP	1.08043	0.895
55DAP/53DAP	1.44942	0.939
57DAP/55DAP	1.05029	0.923
62DAP/57DAP	1.00733	1
68DAP/62DAP	0.99781	0.939
68DAP/14DAP	0.38249	0.016

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.04756	1

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.82819
Immature Eggplant/Mature Eggplant	0.09754
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	N/A	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	N/A	N/A
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	0.60803
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	N/A	N/A
5-3/M82	1.14368	0.496
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.09805	0.788
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.98298	1
IL12-4/WTpooled	1.05818	0.557
IL1-4/WTpooled	0.99673	1
WT/WTpooled	1.10788	0.855

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	1.07434	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.08404
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	1.04974	1
DC3000/delta hrp 24h	1.00467	1

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	1.02909	1
Exp 36h	N/A	N/A
Exp 60h	1.0764	0.283

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

hybridization	ratio	FDR (corrected p value)
self-self	1.04094	1
Var 0h	0.94217	1
Var 12h I row2-row1	3.43001	0.506
Var 12h NI row2-row1	1.0465	1
Var 36h I row2-row1	0.81733
Var 36h NI row2-row1	0.78909	0.645
Var 60h I row2-row1	1.03168
Var 60h NI row2-row1	0.96948	1
Time course 0hI-0hNI	0.97139	0.873
Time course 12hI-12hNI	1.10394	0.347
Time course 36hI-36hNI	0.9521	0.312
Time course 60hI-60hNI	0.92961	0.161

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)	1.11996	0.431
transgenic ySAMdc/azygous control (breaker)	1.04364	1
transgenic ySAMdc/azygous control (red)	1.05875	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.96114	0.196

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.72955	0.237

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)	1.06278	1
Manapal/WT (red)	0.84967	0.188