Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.3.20.5

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.6895	0.028
27DAP/17DAP	1.07816	0.885
39DAP/27DAP	1.11988	0.755
41DAP/39DAP	0.97646	0.886
42DAP/41DAP	0.73885	0.774
43DAP/42DAP	0.90741	0.741
47DAP/43DAP	0.87352	0.591
52DAP/47DAP	1.02631	0.98
57DAP/52DAP	1.0393	0.977

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.70522	0.007
17DAP/reference	1.09078	0.787
27DAP/reference	0.83891	0.023
39DAP/reference	0.86682	0.103
41DAP/reference	0.84753	0.085
42DAP/reference	1.00329	0.707
43DAP/reference	0.93709	0.36
47DAP/reference	0.85629	0.014
52DAP/reference	0.71861	0.015
57DAP/reference	0.90856	0.138

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.48291	0.032
27DAP/17DAP	2.01473	0.044
39DAP/27DAP	0.53271	0.04
41DAP/39DAP	1.582	0.469
42DAP/41DAP	0.90816	0.461
43DAP/42DAP	1.798	0.049
47DAP/43DAP	1.13285	0.678
52DAP/47DAP	0.65092	0.078
57DAP/52DAP	2.06406	0.056
57DAP/7DAP	0.57006	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.22064	0.418
17DAP/reference	0.88215	0.108
27DAP/reference	0.7538	0.013
39DAP/reference	0.81295	0.043
41DAP/reference	0.84621	0.139
42DAP/reference	0.66592	0.01
43DAP/reference	0.9348	0.334
47DAP/reference	1.50179	0.224
52DAP/reference	0.96367	0.435
57DAP/reference	1.00675	0.694

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.70124	0.042
17DAP/reference	1.47461	0.05
27DAP/reference	1.4239	0.021
39DAP/reference	1.2733	0.112
41DAP/reference	1.31147	0.029
42DAP/reference	1.56917	0.008
43DAP/reference	0.87436	0.147
47DAP/reference	1.10064	0.212
52DAP/reference	1.02216	0.988
57DAP/reference	0.74088	0.02

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.86144	0.112
17DAP/reference	1.03836	0.833
27DAP/reference	0.87069	0.119
39DAP/reference	0.81697	0.025
41DAP/reference	0.93281	0.107
42DAP/reference	0.78884	0.025
43DAP/reference	0.83868	0.179
47DAP/reference	0.77645	0.005
52DAP/reference	0.70544	0.131
57DAP/reference	0.80013	0.087

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.13842	0.966
26DAP/20DAP	3.54674	0.097
34DAP/26DAP	0.63218	0.079
51DAP/34DAP	1.22854	0.105
52DAP/51DAP	1.03859	0.939
53DAP/52DAP	1.08587	0.797
55DAP/53DAP	0.99996	0.876
57DAP/55DAP	2.07561	0.086
62DAP/57DAP	0.65139	0.01
68DAP/62DAP	1.81001	0.033
68DAP/14DAP	3.11008	0.021

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.15099	0.527

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.1234	0.666
Mature Green Tomato/Ripe Tomato	1.68219	0.016
Immature Eggplant/Mature Eggplant	0.86556	0.329
Ripe Pepper/Ripe Tomato	1.51323	1
Mature Eggplant/Ripe Tomato	2.15142	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.67242	0.536
1-1-2/M82	0.85698	0.754
12-2/M82	0.60069
12-4/M82	0.86487	0.619
1-3/M82	2.67196
2-1-1/M82	0.75668
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	0.82127
4-1/M82	0.90191	1
4-3-2/M82	0.86302	0.698
4-3/M82	0.87214	0.72
5-3/M82	0.97279	1
6-2/M82	2.50793	1
6-3/M82	1.23039	1
7-1/M82	1.57469
7-2/M82	N/A	N/A
9-3-2/M82	0.85873

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.90808
IL7-5/WTpooled	1.02556
IL7-3/WTpooled	1.14483	1
IL12-4/WTpooled	1.14217	0.785
IL1-4/WTpooled	1.5522	1
WT/WTpooled	0.93073	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	0.79591	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.06662	0.875
DC3000/delta hrp 6h	0.79047	0.942
DC3000/delta hrp 12h	0.889	1
DC3000/delta hrp 24h	1.91098	0.022

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.79572	0.151
DC3000 delta B/DC3000 delta AB	1.10916	0.453

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.98861	1
Exp 36h	1.38987	1
Exp 60h	0.95999	0.855

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00838	1
Var 0h	N/A	N/A
Var 12h I row2-row1	1.1965	0.692
Var 12h NI row2-row1	1.16687	1
Var 36h I row2-row1	1.33491	1
Var 36h NI row2-row1	0.99199	1
Var 60h I row2-row1	0.77935	0.285
Var 60h NI row2-row1	1.42558	0.904
Time course 0hI-0hNI	0.98202	0.942
Time course 12hI-12hNI	0.97751	0.87
Time course 36hI-36hNI	0.81796	0.045
Time course 60hI-60hNI	0.71352	0.007

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)	1.07586	0.511
transgenic ySAMdc/azygous control (breaker)	0.69526	0.137
transgenic ySAMdc/azygous control (red)	0.95093	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.08008	0.587

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.87913	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.90869	1
Manapal/WT (break)	1.33066	0.183
Manapal/WT (red)	0.84033	0.503