Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.4.8.14

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.72134	0.153
27DAP/17DAP	0.48727	0.031
39DAP/27DAP	1.02718	1
41DAP/39DAP	1.08575	1
42DAP/41DAP	1.09744	0.825
43DAP/42DAP	0.75241	0.721
47DAP/43DAP	1.12914	0.769
52DAP/47DAP	1.1275	0.798
57DAP/52DAP	1.14252	0.969

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.50766	0.007
17DAP/reference	0.32316	0.007
27DAP/reference	0.34384	0.011
39DAP/reference	0.53124	0.02
41DAP/reference	0.31729	0.008
42DAP/reference	0.3883	0.001
43DAP/reference	0.48175	0.013
47DAP/reference	0.47789	0.001
52DAP/reference	0.48233	0.021
57DAP/reference	0.6501	0.013

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.14335	0.03
27DAP/17DAP	0.96347	0.878
39DAP/27DAP	1.36472	0.548
41DAP/39DAP	0.78864	0.142
42DAP/41DAP	0.93665	0.545
43DAP/42DAP	0.90757	0.336
47DAP/43DAP	1.34319	0.54
52DAP/47DAP	1.28556	0.696
57DAP/52DAP	0.91182	0.617
57DAP/7DAP	0.40825	0.143

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.80236	0.071
17DAP/reference	0.63684	0.011
27DAP/reference	0.74263	0.019
39DAP/reference	0.82293	0.083
41DAP/reference	0.83675	0.111
42DAP/reference	0.80615	0.055
43DAP/reference	0.7728	0.018
47DAP/reference	0.5391	0.057
52DAP/reference	0.77897	0.012
57DAP/reference	0.84142	0.114

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.16949	0.038
17DAP/reference	0.53073	0.014
27DAP/reference	0.50514	0.009
39DAP/reference	0.41926	0.016
41DAP/reference	0.7392	0.044
42DAP/reference	0.42876	0.011
43DAP/reference	0.55835	0.005
47DAP/reference	0.48297	0.011
52DAP/reference	0.33654	0.003
57DAP/reference	0.52674	0.003

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.39004	0.433
17DAP/reference	0.65416	0.15
27DAP/reference	0.71183	0.044
39DAP/reference	0.6911	0.054
41DAP/reference	0.81658	0.167
42DAP/reference	1.04129	0.848
43DAP/reference	0.8129	0.237
47DAP/reference	0.35913	0.004
52DAP/reference	0.86527	0.36
57DAP/reference	0.61945	0.025

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.7044	0.945
26DAP/20DAP	0.83836	1
34DAP/26DAP	0.81977	0.666
51DAP/34DAP	1.90701
52DAP/51DAP	0.83099	1
53DAP/52DAP	1.9836	0.068
55DAP/53DAP	1.06589	0.925
57DAP/55DAP	0.83207	0.452
62DAP/57DAP	0.90025	0.994
68DAP/62DAP	1.0981	0.84
68DAP/14DAP	1.01603	0.87

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.01694	0.696

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.54299	0.149
Immature Eggplant/Mature Eggplant	1.37847	0.05
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	N/A	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	N/A	N/A
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	0.92078
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	N/A	N/A
6-2/M82	N/A	N/A
6-3/M82	0.74984
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	1.18705

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.5756
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	0.2379
IL7-3/WTpooled	0.79517
IL12-4/WTpooled	0.73863	1
IL1-4/WTpooled	0.76428
WT/WTpooled	1.13887	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	0.84556	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	3.03369
DC3000/delta hrp 6h	1.26901	0.672
DC3000/delta hrp 12h	0.51741	1
DC3000/delta hrp 24h	2.4767

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.7312	0.042
DC3000 delta B/DC3000 delta AB	1.46663	0.09

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.92218	1
Exp 36h	0.67122	0.623
Exp 60h	0.73013	0.522

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

hybridization	ratio	FDR (corrected p value)
self-self	1.07509	1
Var 0h	1.07146	0.98
Var 12h I row2-row1	1.68428	0.58
Var 12h NI row2-row1	0.97413	1
Var 36h I row2-row1	0.58838	0.575
Var 36h NI row2-row1	0.64001	0.432
Var 60h I row2-row1	1.20468	0.271
Var 60h NI row2-row1	1.02962
Time course 0hI-0hNI	0.88856	0.205
Time course 12hI-12hNI	0.87396	0.081
Time course 36hI-36hNI	0.81293	0.166
Time course 60hI-60hNI	0.68663	0.011

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)	1.27944	0.863
transgenic ySAMdc/azygous control (breaker)	1.32357	0.248
transgenic ySAMdc/azygous control (red)	1.00755	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.93209	0.136

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.12376	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.05763	0.105
Manapal/WT (break)	1.1817	1
Manapal/WT (red)	1.70057	0.413