Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.2.14.8

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.86442	0.389
27DAP/17DAP	0.74215	0.298
39DAP/27DAP	1.03097	0.857
41DAP/39DAP	0.79299	0.267
42DAP/41DAP	0.99814	1
43DAP/42DAP	1.11306	1
47DAP/43DAP	0.6527	0.115
52DAP/47DAP	1.30259	0.649
57DAP/52DAP	1.02883	1

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.49821	0.015
17DAP/reference	1.10054	0.355
27DAP/reference	0.95617	0.385
39DAP/reference	0.94447	0.704
41DAP/reference	0.93452	0.341
42DAP/reference	1.35732	0.001
43DAP/reference	0.92889	0.377
47DAP/reference	0.91845	0.09
52DAP/reference	0.8454	0.215
57DAP/reference	1.0657	0.127

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.78534	0.036
27DAP/17DAP	1.11676	0.423
39DAP/27DAP	0.72139	0.035
41DAP/39DAP	1.17922	0.407
42DAP/41DAP	1.01389	1
43DAP/42DAP	0.89885	0.246
47DAP/43DAP	1.10541	0.389
52DAP/47DAP	0.82162	0.28
57DAP/52DAP	0.90594	0.371
57DAP/7DAP	0.59513	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.54758
17DAP/reference	1.33661	0.008
27DAP/reference	1.36642	0.014
39DAP/reference	1.2062	0.01
41DAP/reference	1.22811	0.011
42DAP/reference	1.28948	0.016
43DAP/reference	1.20561	0.007
47DAP/reference	1.27401	0.042
52DAP/reference	1.57167	0.007
57DAP/reference	1.4264	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.05295	0.495
17DAP/reference	1.38985	0.032
27DAP/reference	1.37466	0.111
39DAP/reference	1.3458	0.022
41DAP/reference	1.32097	0.009
42DAP/reference	1.28087	0.045
43DAP/reference	1.17331	0.54
47DAP/reference	1.27096	0.054
52DAP/reference	1.06184	0.988
57DAP/reference	0.99571	0.754

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.62235	0.015
17DAP/reference	1.44613	0.115
27DAP/reference	1.19025	0.027
39DAP/reference	1.29	0.004
41DAP/reference	1.41477	0.008
42DAP/reference	1.64768	0.007
43DAP/reference	1.49555	0.033
47DAP/reference	0.95745	0.371
52DAP/reference	1.15056	0.198
57DAP/reference	1.39994	0.029

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.45884	0.966
26DAP/20DAP	1.01514	1
34DAP/26DAP	1.05951	1
51DAP/34DAP	0.7474	0.08
52DAP/51DAP	0.87633	1
53DAP/52DAP	1.01192	0.944
55DAP/53DAP	0.93825	0.675
57DAP/55DAP	1.22693	0.05
62DAP/57DAP	1.22358	0.069
68DAP/62DAP	0.90871	0.668
68DAP/14DAP	1.16903	0.161

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.52106	0.021

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.00347	0.059
Mature Green Tomato/Ripe Tomato	3.65333	0.015
Immature Eggplant/Mature Eggplant	0.61032	0.062
Ripe Pepper/Ripe Tomato	1.37491	1
Mature Eggplant/Ripe Tomato	2.88638	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.9126	0.944
1-1-2/M82	1.22231	1
12-2/M82	N/A	N/A
12-4/M82	1.07063	1
1-3/M82	1.80808
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	1.43646
3-2/M82	0.95964
4-1-1/M82	1.04401
4-1/M82	0.61252
4-3-2/M82	2.46327
4-3/M82	0.93333	1
5-3/M82	1.39492	0.455
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	1.19061	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.27623	0.277
IL2-6/WTpooled	1.01456	0.788
IL7-5/WTpooled	1.06208	1
IL7-3/WTpooled	1.08255	1
IL12-4/WTpooled	0.86632	0.71
IL1-4/WTpooled	0.96876	0.834
WT/WTpooled	0.94065	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	1.15842	1

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	1.10418	1
DC3000/delta hrp 12h	1.43353	1
DC3000/delta hrp 24h	0.54388	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.62987	0.041
DC3000 delta B/DC3000 delta AB	0.6098	0.021

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.93554	1
Exp 36h	0.73944	0.539
Exp 60h	0.50512	0.257

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99628	1
Var 0h	1.12246
Var 12h I row2-row1	0.77362	0.31
Var 12h NI row2-row1	0.91711	0.82
Var 36h I row2-row1	0.86638	0.805
Var 36h NI row2-row1	0.93151	0.645
Var 60h I row2-row1	1.79794	0.562
Var 60h NI row2-row1	0.97604	1
Time course 0hI-0hNI	0.94938	0.631
Time course 12hI-12hNI	0.96381	0.695
Time course 36hI-36hNI	0.80732	0.077
Time course 60hI-60hNI	0.31661	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)	0.98846	0.789
transgenic ySAMdc/azygous control (breaker)	1.76743	0.172
transgenic ySAMdc/azygous control (red)	1.30498	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.81694	0.105

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.10459	0.233

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.39918	0.09
Manapal/WT (break)	1.90931	0.14
Manapal/WT (red)	2.32539	0.15