Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.3.3.1

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.28463	0.188
27DAP/17DAP	1.34761	0.761
39DAP/27DAP	0.9288	0.67
41DAP/39DAP	1.0246	0.929
42DAP/41DAP	0.695	0.397
43DAP/42DAP	0.69801	0.639
47DAP/43DAP	0.98935	0.879
52DAP/47DAP	0.99841	0.806
57DAP/52DAP	0.93468	0.912

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.39012	0.027
17DAP/reference	0.97199	0.701
27DAP/reference	2.09057	0.339
39DAP/reference	0.81164	0.298
41DAP/reference	1.02712	0.855
42DAP/reference	0.91429	0.013
43DAP/reference	N/A	N/A
47DAP/reference	0.91176	0.137
52DAP/reference	0.77973	0.028
57DAP/reference	1.81736	0.704

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.96423	0.629
27DAP/17DAP	1.18286	0.212
39DAP/27DAP	0.89865	0.477
41DAP/39DAP	1.07893	0.735
42DAP/41DAP	0.97661	0.764
43DAP/42DAP	0.96554	0.399
47DAP/43DAP	1.00794	0.973
52DAP/47DAP	1.04371	0.835
57DAP/52DAP	0.9229	0.348
57DAP/7DAP	0.86098	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95228	0.361
17DAP/reference	1.09101	0.688
27DAP/reference	1.0155	0.748
39DAP/reference	0.74509	0.016
41DAP/reference	0.97161	0.469
42DAP/reference	0.78488	0.023
43DAP/reference	0.84358	0.029
47DAP/reference	0.84934	0.128
52DAP/reference	0.84445	0.09
57DAP/reference	0.96414	0.426

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.17189	0.203
17DAP/reference	1.01815	0.789
27DAP/reference	1.1362	0.507
39DAP/reference	0.95115	0.195
41DAP/reference	0.98709	0.545
42DAP/reference	0.91952	0.169
43DAP/reference	1.08435	0.462
47DAP/reference	1.05952	0.841
52DAP/reference	1.00845	1
57DAP/reference	0.94958	0.408

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.10891	0.397
17DAP/reference	1.17468	0.496
27DAP/reference	1.22702	0.325
39DAP/reference	0.83744	0.101
41DAP/reference	0.97922	0.618
42DAP/reference	0.78632	0.028
43DAP/reference	0.89257	0.165
47DAP/reference	0.77123	0.008
52DAP/reference	0.9789	0.718
57DAP/reference	0.93548	0.149

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.88981	0.52
26DAP/20DAP	0.96337	1
34DAP/26DAP	0.85812	0.343
51DAP/34DAP	0.776	0.116
52DAP/51DAP	0.88049	1
53DAP/52DAP	0.918	0.64
55DAP/53DAP	0.87279	0.154
57DAP/55DAP	1.07855	0.915
62DAP/57DAP	1.17346	0.081
68DAP/62DAP	1.0855	0.84
68DAP/14DAP	0.98522	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.76386	0.057

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.17219	0.058
Mature Green Tomato/Ripe Tomato	2.59416	0.185
Immature Eggplant/Mature Eggplant	0.94961	0.594
Ripe Pepper/Ripe Tomato	0.98454
Mature Eggplant/Ripe Tomato	6.16415	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.10191	1
1-1-2/M82	0.80565
12-2/M82	1.14822
12-4/M82	0.81275	1
1-3/M82	0.77587
2-1-1/M82	0.83864
2-1/M82	N/A	N/A
2-6/M82	0.98927	1
3-2/M82	1.08995
4-1-1/M82	N/A	N/A
4-1/M82	1.05354
4-3-2/M82	0.61538
4-3/M82	N/A	N/A
5-3/M82	1.01477	1
6-2/M82	N/A	N/A
6-3/M82	1.12088	1
7-1/M82	0.95955
7-2/M82	0.97977
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.0202	1
IL2-6/WTpooled	0.70455
IL7-5/WTpooled	1.29809	1
IL7-3/WTpooled	1.14336	1
IL12-4/WTpooled	1.09438	0.553
IL1-4/WTpooled	1.07758	1
WT/WTpooled	1.11795	0.686

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	0.98686	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.0996	0.914
DC3000/delta hrp 6h	1.06832	1
DC3000/delta hrp 12h	0.98046	1
DC3000/delta hrp 24h	0.92614	0.422

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.88658	0.293
DC3000 delta B/DC3000 delta AB	1.05414	0.748

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.0118	1
Exp 36h	0.91114	0.699
Exp 60h	0.75317	0.257

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98446	1
Var 0h	1.0138	1
Var 12h I row2-row1	0.90977	0.565
Var 12h NI row2-row1	0.90156	0.627
Var 36h I row2-row1	1.12022	1
Var 36h NI row2-row1	1.16496	0.482
Var 60h I row2-row1	1.42559
Var 60h NI row2-row1	0.96287	1
Time course 0hI-0hNI	0.94961	0.699
Time course 12hI-12hNI	0.90679	0.215
Time course 36hI-36hNI	0.8298	0.025
Time course 60hI-60hNI	0.14434	0.006

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)	0.99524	0.931
transgenic ySAMdc/azygous control (breaker)	0.96499	1
transgenic ySAMdc/azygous control (red)	1.05825	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.87473	0.074

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.59388	0.237

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.95395	1
Manapal/WT (break)	1.41517	0.381
Manapal/WT (red)	1.24681	0.222