Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.2.4.21

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.54263	0.019
27DAP/17DAP	1.09978	0.849
39DAP/27DAP	1.30733	0.22
41DAP/39DAP	1.31324	0.904
42DAP/41DAP	1.27048	0.792
43DAP/42DAP	1.23292	0.861
47DAP/43DAP	1.01765	1
52DAP/47DAP	0.9757	0.87
57DAP/52DAP	1.16289	0.962

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.15186	0.5
17DAP/reference	1.00436	0.843
27DAP/reference	0.80395	0.152
39DAP/reference	0.83805	0.042
41DAP/reference	0.95714	0.814
42DAP/reference	1.12644	0.103
43DAP/reference	0.52911	0.211
47DAP/reference	1.30125	0.024
52DAP/reference	0.65178	0.026
57DAP/reference	N/A	N/A

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.73958	0.041
27DAP/17DAP	1.06835	0.805
39DAP/27DAP	1.07109	0.553
41DAP/39DAP	1.18085	0.514
42DAP/41DAP	0.86851	0.236
43DAP/42DAP	0.99362	0.991
47DAP/43DAP	1.03947	0.822
52DAP/47DAP	0.94286	0.797
57DAP/52DAP	0.83677	0.131
57DAP/7DAP	0.87199	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.64122	0.038
17DAP/reference	1.36509	0.035
27DAP/reference	1.17053	0.107
39DAP/reference	1.233	0.069
41DAP/reference	1.2334	0.104
42DAP/reference	1.25952	0.037
43DAP/reference	1.13303	0.148
47DAP/reference	1.18061	0.165
52DAP/reference	1.15188	0.247
57DAP/reference	1.04885	0.331

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.14534	0.098
17DAP/reference	1.02524	0.892
27DAP/reference	1.04357	0.822
39DAP/reference	1.16022	0.978
41DAP/reference	0.90186	0.16
42DAP/reference	0.8448	0.02
43DAP/reference	1.02457	0.846
47DAP/reference	1.01657	1
52DAP/reference	0.84101	0.037
57DAP/reference	1.20847	0.131

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.6079	0.024
17DAP/reference	1.07774	0.767
27DAP/reference	0.95663	0.416
39DAP/reference	1.07851	0.318
41DAP/reference	1.09671	0.343
42DAP/reference	1.06757	0.848
43DAP/reference	1.14995	0.531
47DAP/reference	0.90805	0.04
52DAP/reference	1.10373	0.664
57DAP/reference	0.74835	0.046

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.14299	0.735
26DAP/20DAP	1.43695	0.147
34DAP/26DAP	0.6161	0.067
51DAP/34DAP	1.04059	0.759
52DAP/51DAP	1.02152	0.848
53DAP/52DAP	0.95552	0.811
55DAP/53DAP	1.10003	0.468
57DAP/55DAP	1.16519	0.682
62DAP/57DAP	N/A	N/A
68DAP/62DAP	1.0257	1
68DAP/14DAP	1.37083

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.96347	0.493

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.31071	0.058
Mature Green Tomato/Ripe Tomato	0.91406	0.611
Immature Eggplant/Mature Eggplant	1.23304	0.058
Ripe Pepper/Ripe Tomato	0.74273	0.224
Mature Eggplant/Ripe Tomato	1.15867	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.16755	0.591
1-1-2/M82	1.30336	1
12-2/M82	0.65969
12-4/M82	1.22576	1
1-3/M82	1.29839	1
2-1-1/M82	1.34489	0.764
2-1/M82	0.95809	1
2-6/M82	1.09875	0.594
3-2/M82	1.09595
4-1-1/M82	1.13266	1
4-1/M82	1.10728	1
4-3-2/M82	1.45953	0.284
4-3/M82	1.06193	1
5-3/M82	1.19261	1
6-2/M82	1.31492	1
6-3/M82	1.05435	1
7-1/M82	0.8476	0.44
7-2/M82	1.02908	1
9-3-2/M82	1.42961	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.88105	1
IL2-6/WTpooled	0.92471	1
IL7-5/WTpooled	0.9994
IL7-3/WTpooled	1.19061	1
IL12-4/WTpooled	1.20846	0.513
IL1-4/WTpooled	0.87077	0.699
WT/WTpooled	0.98965	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	0.98963	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.09252	0.921
DC3000/delta hrp 6h	0.86141	0.95
DC3000/delta hrp 12h	1.07244	1
DC3000/delta hrp 24h	0.80968	0.05

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.00584	0.556
DC3000 delta B/DC3000 delta AB	1.2325	0.177

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.93799	1
Exp 36h	1.22881	1
Exp 60h	0.95178	0.855

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99856	1
Var 0h	1.34939	0.936
Var 12h I row2-row1	1.32321	0.235
Var 12h NI row2-row1	0.95161	0.82
Var 36h I row2-row1	0.92647	1
Var 36h NI row2-row1	0.85151	0.478
Var 60h I row2-row1	1.10476	1
Var 60h NI row2-row1	1.00268	1
Time course 0hI-0hNI	1.07847	0.867
Time course 12hI-12hNI	0.96552	0.815
Time course 36hI-36hNI	1.09639	0.513
Time course 60hI-60hNI	2.31145	0.009

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)	0.81883	0.289
transgenic ySAMdc/azygous control (breaker)	0.86732	0.251
transgenic ySAMdc/azygous control (red)	1.08429	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.09146	0.125

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.97907	0.789

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.28439	0.14
Manapal/WT (break)	1.32641	0.14
Manapal/WT (red)	0.9073	0.274