Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.2.17.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.41742	0.463
27DAP/17DAP	1.09013	0.92
39DAP/27DAP	1.27707	0.693
41DAP/39DAP	1.26854	0.591
42DAP/41DAP	3.51566	0.016
43DAP/42DAP	1.52978	0.69
47DAP/43DAP	1.00944	0.972
52DAP/47DAP	0.64403	0.218
57DAP/52DAP	0.94008	0.936

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.13075	0.218
17DAP/reference	1.41729	0.02
27DAP/reference	0.98261	0.694
39DAP/reference	1.21289	0.083
41DAP/reference	1.67736	0.017
42DAP/reference	1.37341	0.001
43DAP/reference	1.18704	0.064
47DAP/reference	1.56281	0.001
52DAP/reference	1.14578	0.498
57DAP/reference	1.10206	0.802

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.95102	0.56
27DAP/17DAP	1.02528	0.976
39DAP/27DAP	1.04336	0.623
41DAP/39DAP	0.88087	0.333
42DAP/41DAP	1.14979	0.365
43DAP/42DAP	1.24474	0.016
47DAP/43DAP	0.94462	0.606
52DAP/47DAP	1.0826	0.713
57DAP/52DAP	0.91849	0.176
57DAP/7DAP	1.25308	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.24761	0.064
17DAP/reference	1.19285	0.147
27DAP/reference	0.88433	0.033
39DAP/reference	0.79875	0.02
41DAP/reference	0.9252	0.311
42DAP/reference	0.79148	0.063
43DAP/reference	0.9738	0.459
47DAP/reference	1.04273	1
52DAP/reference	1.07146	0.375
57DAP/reference	0.89399	0.183

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.09598	0.559
17DAP/reference	1.43024	0.022
27DAP/reference	1.39515	0.029
39DAP/reference	1.31134	0.014
41DAP/reference	1.13309	0.416
42DAP/reference	1.4005	0.01
43DAP/reference	1.57549	0.072
47DAP/reference	1.39028	0.008
52DAP/reference	1.28993	0.011
57DAP/reference	1.66858	0.011

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00099	0.699
17DAP/reference	1.17677	0.294
27DAP/reference	1.05836	0.695
39DAP/reference	0.818	0.058
41DAP/reference	1.04467	0.984
42DAP/reference	0.91069	0.22
43DAP/reference	1.11489	0.79
47DAP/reference	1.39512	0.115
52DAP/reference	0.78559	0.144
57DAP/reference	0.92524	0.299

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.30044	1
26DAP/20DAP	0.89965	0.512
34DAP/26DAP	0.96415	0.92
51DAP/34DAP	0.97397	0.785
52DAP/51DAP	1.04522	0.783
53DAP/52DAP	1.0366	0.921
55DAP/53DAP	1.12622	0.429
57DAP/55DAP	0.86916	0.423
62DAP/57DAP	1.09664	0.723
68DAP/62DAP	1.03907	0.936
68DAP/14DAP	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.99405	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.19765	0.017
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.03749
Mature Eggplant/Ripe Tomato	0.19833

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	N/A	N/A
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	3.4102
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	N/A	N/A
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	1.36968
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.92348	1
IL12-4/WTpooled	1.86422	0.42
IL1-4/WTpooled	0.94253	1
WT/WTpooled	1.0363	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	1.27164	0.222

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	N/A	N/A
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	0.8571	1
DC3000/delta hrp 24h	N/A	N/A

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.84613	0.037
DC3000 delta B/DC3000 delta AB	0.98992	1

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	N/A	N/A
Exp 60h	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
self-self	0.96898	1
Var 0h	1.31114	0.98
Var 12h I row2-row1	1.04511	0.613
Var 12h NI row2-row1	0.92192	0.713
Var 36h I row2-row1	0.95713	1
Var 36h NI row2-row1	0.90098	0.584
Var 60h I row2-row1	1.13408	0.562
Var 60h NI row2-row1	0.97933	1
Time course 0hI-0hNI	1.10499	0.662
Time course 12hI-12hNI	1.01878	0.836
Time course 36hI-36hNI	0.93435	0.084
Time course 60hI-60hNI	0.96651	0.646

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)	N/A	N/A
transgenic ySAMdc/azygous control (breaker)	1.00495	1
transgenic ySAMdc/azygous control (red)	1.17911	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	N/A	N/A

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)	0.84512	1
Manapal/WT (red)	1.0908	0.863