Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-3.3.14.3

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.20874	0.561
27DAP/17DAP	1.05359	1
39DAP/27DAP	1.00445	0.84
41DAP/39DAP	1.31839	0.303
42DAP/41DAP	1.217	0.802
43DAP/42DAP	0.79511	0.631
47DAP/43DAP	0.99978	0.934
52DAP/47DAP	1.28929	0.451
57DAP/52DAP	0.82067	0.737

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99624	0.727
17DAP/reference	1.04764	0.306
27DAP/reference	0.96601	0.525
39DAP/reference	0.91229	0.292
41DAP/reference	1.08693	0.047
42DAP/reference	0.93746	0.054
43DAP/reference	1.02086	0.73
47DAP/reference	0.89283	0.032
52DAP/reference	0.84617	0.099
57DAP/reference	0.84011	0.04

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.93241	0.454
27DAP/17DAP	0.95433	0.854
39DAP/27DAP	0.99159	0.964
41DAP/39DAP	0.9927	1
42DAP/41DAP	1.10777	0.601
43DAP/42DAP	1.11318	0.192
47DAP/43DAP	1.0285	0.951
52DAP/47DAP	1.00069	0.979
57DAP/52DAP	0.94513	0.352
57DAP/7DAP	1.19364	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92165	0.122
17DAP/reference	0.90143	0.056
27DAP/reference	0.93848	0.055
39DAP/reference	0.87303	0.011
41DAP/reference	0.83005	0.023
42DAP/reference	0.80982	0.011
43DAP/reference	0.88123	0.061
47DAP/reference	0.88805	0.128
52DAP/reference	0.8872	0.15
57DAP/reference	0.87411	0.011

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.23741	0.111
17DAP/reference	1.18302	0.11
27DAP/reference	0.98237	0.501
39DAP/reference	0.94798	0.339
41DAP/reference	0.85834	0.067
42DAP/reference	0.8909	0.098
43DAP/reference	1.15583	0.117
47DAP/reference	0.91575	0.133
52DAP/reference	1.04831	0.596
57DAP/reference	1.23629	0.166

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95861	0.158
17DAP/reference	1.05642	0.503
27DAP/reference	0.92792	0.047
39DAP/reference	0.89495	0.019
41DAP/reference	0.94165	0.148
42DAP/reference	0.89304	0.22
43DAP/reference	0.85951	0.125
47DAP/reference	0.92408	0.161
52DAP/reference	0.85682	0.137
57DAP/reference	0.59875	0.017

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.25612	0.021
26DAP/20DAP	1.05922	0.77
34DAP/26DAP	1.02015	1
51DAP/34DAP	0.84134	0.097
52DAP/51DAP	1.05792	0.588
53DAP/52DAP	1.00115	1
55DAP/53DAP	1.1865	0.562
57DAP/55DAP	0.81924	0.194
62DAP/57DAP	1.2406	0.35
68DAP/62DAP	0.99878	0.81
68DAP/14DAP	0.80425	0.09

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.68966	0.048

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.51283	0.063
Mature Green Tomato/Ripe Tomato	0.86717	0.256
Immature Eggplant/Mature Eggplant	0.95963	0.72
Ripe Pepper/Ripe Tomato	0.49476	0.224
Mature Eggplant/Ripe Tomato	0.56824	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.82043	N/A
1-1-2/M82	0.8626	0.804
12-2/M82	N/A	N/A
12-4/M82	0.97909	1
1-3/M82	0.80401	0.378
2-1-1/M82	1.22785	0.342
2-1/M82	N/A	N/A
2-6/M82	1.11867	N/A
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	0.91289	1
4-3-2/M82	0.93513	1
4-3/M82	N/A	N/A
5-3/M82	1.03684	1
6-2/M82	N/A	N/A
6-3/M82	0.54232	N/A
7-1/M82	0.95436	N/A
7-2/M82	0.94465	0.881
9-3-2/M82	0.84348	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	0.35545	0.71
IL1-4/WTpooled	1.08418	1
WT/WTpooled	0.94537	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	0.93599	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.98989	1
DC3000/delta hrp 6h	0.92913	0.95
DC3000/delta hrp 12h	1.00243	1
DC3000/delta hrp 24h	1.10308	0.383

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.29735	0.11
DC3000 delta B/DC3000 delta AB	1.10914	0.42

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.97396	1
Exp 36h	1.39961	0.326
Exp 60h	1.3666	0.283

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98061	1
Var 0h	0.47576	1
Var 12h I row2-row1	1.07679	0.544
Var 12h NI row2-row1	0.88958	0.713
Var 36h I row2-row1	1.02936	1
Var 36h NI row2-row1	1.00401	1
Var 60h I row2-row1	1.27483	0.562
Var 60h NI row2-row1	1.03734	1
Time course 0hI-0hNI	1.02851	0.867
Time course 12hI-12hNI	1.02521	0.816
Time course 36hI-36hNI	0.95999	0.494
Time course 60hI-60hNI	1.22133	0.022

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)	0.94599	0.454
transgenic ySAMdc/azygous control (breaker)	0.86279	0.142
transgenic ySAMdc/azygous control (red)	0.85576	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.98089	0.651

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	2.03139	0.229

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.80527	0.172
Manapal/WT (break)	0.95478	1
Manapal/WT (red)	1.01194	1