Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-2.2.14.16

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.04406	0.863
27DAP/17DAP	1.041	1
39DAP/27DAP	0.80815	0.378
41DAP/39DAP	1.28069	0.38
42DAP/41DAP	1.25971	0.712
43DAP/42DAP	1.211	0.698
47DAP/43DAP	1.06542	0.965
52DAP/47DAP	1.08649	0.913
57DAP/52DAP	0.88785	0.666

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.10489	0.089
17DAP/reference	0.929	0.393
27DAP/reference	0.97625	0.497
39DAP/reference	0.98484	0.72
41DAP/reference	0.97888	0.667
42DAP/reference	0.95984	0.196
43DAP/reference	1.02487	0.495
47DAP/reference	1.00648	1
52DAP/reference	0.97848	0.35
57DAP/reference	0.92172	0.054

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.99276	0.826
27DAP/17DAP	0.96235	0.854
39DAP/27DAP	1.03574	0.685
41DAP/39DAP	1.00685	1
42DAP/41DAP	1.01089	1
43DAP/42DAP	0.9947	0.991
47DAP/43DAP	1.07218	0.276
52DAP/47DAP	1.01878	0.927
57DAP/52DAP	1.01934	0.933
57DAP/7DAP	1.05458	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99028	0.613
17DAP/reference	0.98163	0.338
27DAP/reference	0.98073	0.303
39DAP/reference	1.00793	0.865
41DAP/reference	1.01027	0.891
42DAP/reference	0.97679	0.415
43DAP/reference	0.99646	0.727
47DAP/reference	0.934	0.293
52DAP/reference	1.02034	0.636
57DAP/reference	0.92741	0.011

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04646	0.495
17DAP/reference	1.02283	0.406
27DAP/reference	1.01953	0.961
39DAP/reference	0.9654	0.348
41DAP/reference	0.94167	0.268
42DAP/reference	0.94404	0.121
43DAP/reference	0.97959	0.62
47DAP/reference	0.91779	0.053
52DAP/reference	0.98217	0.407
57DAP/reference	1.06163	0.353

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03253	0.518
17DAP/reference	0.9706	0.462
27DAP/reference	1.0248	0.373
39DAP/reference	0.96031	0.222
41DAP/reference	1.03311	0.537
42DAP/reference	1.02738	0.68
43DAP/reference	0.9703	0.294
47DAP/reference	0.96215	0.145
52DAP/reference	0.96083	0.464
57DAP/reference	0.85307	0.042

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.94651	1
26DAP/20DAP	0.96054	1
34DAP/26DAP	0.98574	1
51DAP/34DAP	1.06173	0.445
52DAP/51DAP	1.06488	0.492
53DAP/52DAP	0.99377	0.978
55DAP/53DAP	1.01081	1
57DAP/55DAP	1.0739	0.61
62DAP/57DAP	0.98873	1
68DAP/62DAP	0.93756	0.579
68DAP/14DAP	1.11354	0.311

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.85892	0.072

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.61616	0.141
Mature Green Tomato/Ripe Tomato	0.8801	0.317
Immature Eggplant/Mature Eggplant	0.79046	0.063
Ripe Pepper/Ripe Tomato	4.48802	0.258
Mature Eggplant/Ripe Tomato	1.99298	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.05833	0.877
1-1-2/M82	0.87382	0.958
12-2/M82	1.11996	N/A
12-4/M82	0.90316	1
1-3/M82	0.99856	1
2-1-1/M82	0.93185	N/A
2-1/M82	N/A	N/A
2-6/M82	1.09401	0.695
3-2/M82	0.99588	N/A
4-1-1/M82	N/A	N/A
4-1/M82	1.03891	1
4-3-2/M82	0.98556	1
4-3/M82	N/A	N/A
5-3/M82	0.97612	1
6-2/M82	N/A	N/A
6-3/M82	1.33141	N/A
7-1/M82	N/A	N/A
7-2/M82	1.05002	0.318
9-3-2/M82	0.85196	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.05087	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.1693	1
IL12-4/WTpooled	1.1291	0.673
IL1-4/WTpooled	0.92105	0.699
WT/WTpooled	1.031	0.785

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	0.8768	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.93549	1
DC3000/delta hrp 6h	0.77659	0.808
DC3000/delta hrp 12h	0.97133	1
DC3000/delta hrp 24h	1.2497	0.347

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.04796	0.313
DC3000 delta B/DC3000 delta AB	0.91161	0.203

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.7865	0.328
Exp 36h	0.53087	0.406
Exp 60h	0.54889	0.249

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

hybridization	ratio	FDR (corrected p value)
self-self	1.02254	1
Var 0h	0.77794	0.933
Var 12h I row2-row1	0.95005	0.467
Var 12h NI row2-row1	0.97276	0.906
Var 36h I row2-row1	0.98187	1
Var 36h NI row2-row1	1.14623	1
Var 60h I row2-row1	1.47804	0.562
Var 60h NI row2-row1	1.05127	0.904
Time course 0hI-0hNI	0.94386	0.452
Time course 12hI-12hNI	1.00892	0.88
Time course 36hI-36hNI	0.92088	0.159
Time course 60hI-60hNI	0.57508	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)	1.03333	1
transgenic ySAMdc/azygous control (breaker)	0.79567	0.251
transgenic ySAMdc/azygous control (red)	1.21289	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.99863	0.858

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.17234	0.239

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	2.32024	0.093
Manapal/WT (break)	1.92953	0.14
Manapal/WT (red)	1.55637	0.142