Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.3.16.16

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.44423	0.034
27DAP/17DAP	0.42355	0.031
39DAP/27DAP	0.53595	0.364
41DAP/39DAP	1.0115	0.911
42DAP/41DAP	0.98506	1
43DAP/42DAP	1.12253	0.956
47DAP/43DAP	0.89144	0.609
52DAP/47DAP	0.68207	0.314
57DAP/52DAP	1.42209	0.935

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.27001	0.006
17DAP/reference	0.91966	0.224
27DAP/reference	0.87894	0.187
39DAP/reference	0.89111	0.188
41DAP/reference	0.95145	0.434
42DAP/reference	0.78352	0.002
43DAP/reference	0.92554	0.093
47DAP/reference	0.79121	0.004
52DAP/reference	0.75292	0.013
57DAP/reference	0.75825	0.011

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.1544	0.016
27DAP/17DAP	0.71346	0.047
39DAP/27DAP	0.67883	0.034
41DAP/39DAP	1.64081	0.012
42DAP/41DAP	0.66776	0.022
43DAP/42DAP	1.02836	1
47DAP/43DAP	1.03709	0.973
52DAP/47DAP	1.0098	0.93
57DAP/52DAP	0.96828	0.726
57DAP/7DAP	0.13867	0.186

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.97502	0.027
17DAP/reference	0.7918	0.019
27DAP/reference	0.69756	0.015
39DAP/reference	0.61547	0.015
41DAP/reference	1.20526	0.314
42DAP/reference	0.64505	0.01
43DAP/reference	0.5567	0.011
47DAP/reference	0.63677	0.04
52DAP/reference	0.5334	0.012
57DAP/reference	0.4574	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.45362	0.038
17DAP/reference	0.87245	0.033
27DAP/reference	0.77427	0.035
39DAP/reference	0.65346	0.01
41DAP/reference	1.03508	1
42DAP/reference	0.70602	0.011
43DAP/reference	0.77476	0.014
47DAP/reference	0.83619	0.097
52DAP/reference	0.67667	0.003
57DAP/reference	0.78808	0.006

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	3.14994	0.021
17DAP/reference	0.90193	0.3
27DAP/reference	0.70526	0.025
39DAP/reference	0.67508	0.014
41DAP/reference	0.70338	0.024
42DAP/reference	0.69436	0.02
43DAP/reference	0.63997	0.018
47DAP/reference	0.76687	0.013
52DAP/reference	0.53486	0.05
57DAP/reference	0.62017	0.016

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.12548	0.966
26DAP/20DAP	0.81112
34DAP/26DAP	0.80791	0.107
51DAP/34DAP	0.91248	0.743
52DAP/51DAP	1.47779	0.77
53DAP/52DAP	1.02126	0.96
55DAP/53DAP	0.80043	0.709
57DAP/55DAP	0.58864	0.04
62DAP/57DAP	1.02258	1
68DAP/62DAP	0.81333	0.152
68DAP/14DAP	0.77932	0.121

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.12822	0.466

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	6.77222	0.021
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.187
Mature Eggplant/Ripe Tomato	5.6146

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.01485
1-1-2/M82	0.78269	0.958
12-2/M82	0.46795
12-4/M82	1.32615	1
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	1.5635
3-2/M82	N/A	N/A
4-1-1/M82	1.16819
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	0.54915	0.642
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	0.96896
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.7563	0.243
IL2-6/WTpooled	1.10672	0.584
IL7-5/WTpooled	0.54569
IL7-3/WTpooled	1.10102	1
IL12-4/WTpooled	0.97942	1
IL1-4/WTpooled	0.86824	0.457
WT/WTpooled	0.998	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	1.24517	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.01226	1
DC3000/delta hrp 6h	0.59787
DC3000/delta hrp 12h	1.05061	1
DC3000/delta hrp 24h	2.69657	0.054

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.86445	0.032
DC3000 delta B/DC3000 delta AB	0.69562

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	0.72713	0.456
Exp 60h	1.33544	0.227

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

hybridization	ratio	FDR (corrected p value)
self-self	1.04041
Var 0h	0.87202	0.933
Var 12h I row2-row1	0.70133	0.196
Var 12h NI row2-row1	3.57232	1
Var 36h I row2-row1	1.01584	1
Var 36h NI row2-row1	0.90315
Var 60h I row2-row1	1.03843	1
Var 60h NI row2-row1	0.65987	1
Time course 0hI-0hNI	1.11951	0.852
Time course 12hI-12hNI	1.06189	0.892
Time course 36hI-36hNI	0.73035	0.101
Time course 60hI-60hNI	0.5989	0.026

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)	1.18281	0.748
transgenic ySAMdc/azygous control (breaker)	0.66745	0.139
transgenic ySAMdc/azygous control (red)	1.13074	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.99324	0.651

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.06109	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.63012	1
Manapal/WT (break)	0.36966	0.299
Manapal/WT (red)	0.47629	0.181