Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.2.2.17

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.16786	0.681
27DAP/17DAP	0.44302	0.029
39DAP/27DAP	0.61874	0.382
41DAP/39DAP	0.54097	0.047
42DAP/41DAP	0.58648	0.397
43DAP/42DAP	1.42666	0.368
47DAP/43DAP	0.39818	0.049
52DAP/47DAP	1.43749	0.376
57DAP/52DAP	1.28187	0.892

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.79206	0.121
17DAP/reference	0.51066	0.008
27DAP/reference	0.4939	0.014
39DAP/reference	0.438	0.01
41DAP/reference	0.33169	0.008
42DAP/reference	0.35101	0.001
43DAP/reference	0.41639	0.015
47DAP/reference	0.35653	0.001
52DAP/reference	0.4455	0.021
57DAP/reference	0.51667	0.008

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	2.06658	0.036
27DAP/17DAP	0.72814	0.218
39DAP/27DAP	0.36964	0.028
41DAP/39DAP	1.45173	0.046
42DAP/41DAP	0.78704	0.017
43DAP/42DAP	0.66241	0.022
47DAP/43DAP	0.98847	0.939
52DAP/47DAP	0.98787	0.93
57DAP/52DAP	0.99145	0.823
57DAP/7DAP	0.55984	0.186

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.23942	0.119
17DAP/reference	0.84191	0.094
27DAP/reference	0.45335	0.01
39DAP/reference	0.43971	0.011
41DAP/reference	0.40507	0.009
42DAP/reference	0.42702	0.01
43DAP/reference	0.34356	0.01
47DAP/reference	0.2705	0.026
52DAP/reference	0.40061	0.009
57DAP/reference	0.39849	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.42734	0.007
17DAP/reference	0.46471	0.008
27DAP/reference	0.65422	0.062
39DAP/reference	0.42463	0.011
41DAP/reference	0.4172	0.005
42DAP/reference	0.36814	0.01
43DAP/reference	0.26416	0.002
47DAP/reference	0.31378	0.007
52DAP/reference	0.25549	0.003
57DAP/reference	0.18447	0.002

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.0171	0.015
17DAP/reference	2.00035	0.105
27DAP/reference	1.32121	0.054
39DAP/reference	0.941	0.43
41DAP/reference	0.77126	0.058
42DAP/reference	0.50919	0.016
43DAP/reference	0.53335	0.025
47DAP/reference	0.34084	0.004
52DAP/reference	0.32215	0.047
57DAP/reference	1.34192	0.47

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.16866	0.966
26DAP/20DAP	1.0228	1
34DAP/26DAP	0.79337	0.122
51DAP/34DAP	0.46824	0.057
52DAP/51DAP	1.0049	1
53DAP/52DAP	0.85461	0.25
55DAP/53DAP	1.00829	0.852
57DAP/55DAP	0.9841	0.819
62DAP/57DAP	1.8182	0.185
68DAP/62DAP	0.80969	0.037
68DAP/14DAP	0.91523	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.37445	0.02

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	3.42162	0.058
Mature Green Tomato/Ripe Tomato	18.729	0.016
Immature Eggplant/Mature Eggplant	0.40367	0.062
Ripe Pepper/Ripe Tomato	112.009	1
Mature Eggplant/Ripe Tomato	58.903	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.97102
12-2/M82	N/A	N/A
12-4/M82	0.72298	0.619
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	1.19359
4-1-1/M82	N/A	N/A
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	2.53519	1
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	1.10208
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.38976
IL2-6/WTpooled	0.65892	0.358
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.28635	1
IL12-4/WTpooled	0.95112	1
IL1-4/WTpooled	N/A	N/A
WT/WTpooled	1.0137	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	1.08169	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.84982
DC3000/delta hrp 6h	0.84182	0.95
DC3000/delta hrp 12h	1.20036	1
DC3000/delta hrp 24h	0.95986	0.861

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.78709	0.024
DC3000 delta B/DC3000 delta AB	0.66988	0.024

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.9757	1
Exp 36h	0.88515	0.749
Exp 60h	0.82292	0.586

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99218	1
Var 0h	0.86666	1
Var 12h I row2-row1	0.95988	0.77
Var 12h NI row2-row1	1.01232	1
Var 36h I row2-row1	1.05446	1
Var 36h NI row2-row1	0.97193	0.743
Var 60h I row2-row1	1.68665	0.562
Var 60h NI row2-row1	1.0832	0.904
Time course 0hI-0hNI	0.97182	0.829
Time course 12hI-12hNI	1.02297	0.786
Time course 36hI-36hNI	1.02812	0.401
Time course 60hI-60hNI	0.36565	0.015

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)	1.1739	0.699
transgenic ySAMdc/azygous control (breaker)	3.19341	0.166
transgenic ySAMdc/azygous control (red)	1.04187	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.46296	0.073

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.49016	0.237

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	26.6464	0.087
Manapal/WT (break)	14.8057	0.126
Manapal/WT (red)	2.44809	1