Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.2.9.4

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.86626	0.436
27DAP/17DAP	2.11929	0.103
39DAP/27DAP	2.65613	0.299
41DAP/39DAP	0.89968	0.483
42DAP/41DAP	1.19068	0.832
43DAP/42DAP	0.71606	0.302
47DAP/43DAP	1.45893	0.261
52DAP/47DAP	1.15004	0.639
57DAP/52DAP	0.82906	0.666

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.35747	0.024
17DAP/reference	0.40713	0.007
27DAP/reference	0.47603	0.011
39DAP/reference	0.5473	0.013
41DAP/reference	0.5299	0.01
42DAP/reference	0.534	0.004
43DAP/reference	0.94467	0.594
47DAP/reference	0.56771	0.001
52DAP/reference	0.47855	0.015
57DAP/reference	0.68356	0.013

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.67587	0.131
27DAP/17DAP	1.26763	0.505
39DAP/27DAP	1.87835	0.061
41DAP/39DAP	2.89244	0.007
42DAP/41DAP	0.77298	0.037
43DAP/42DAP	0.41885	0.022
47DAP/43DAP	2.05994	0.011
52DAP/47DAP	0.89977	0.603
57DAP/52DAP	0.88137	0.501
57DAP/7DAP	0.91729

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.79103	0.157
17DAP/reference	0.81718	0.039
27DAP/reference	0.88214	0.055
39DAP/reference	0.75609	0.011
41DAP/reference	0.71333	0.014
42DAP/reference	0.66609	0.01
43DAP/reference	0.73628	0.014
47DAP/reference	0.68816	0.066
52DAP/reference	0.84189	0.031
57DAP/reference	0.88297	0.162

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.40259	0.006
17DAP/reference	0.25887	0.003
27DAP/reference	0.39676	0.006
39DAP/reference	0.4809	0.013
41DAP/reference	0.79103	0.098
42DAP/reference	0.53414	0.014
43DAP/reference	0.83512	0.243
47DAP/reference	0.63879	0.02
52DAP/reference	0.33643	0.004
57DAP/reference	0.68914	0.023

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.69135	0.039
17DAP/reference	0.66119	0.15
27DAP/reference	0.67705	0.031
39DAP/reference	0.68674	0.025
41DAP/reference	0.856	0.148
42DAP/reference	0.73914	0.028
43DAP/reference	0.52998	0.022
47DAP/reference	0.41888	0.017
52DAP/reference	0.96498	0.482
57DAP/reference	0.51966	0.016

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.33022	0.945
26DAP/20DAP	1.43963	0.141
34DAP/26DAP	1.15502	1
51DAP/34DAP	0.73518	0.311
52DAP/51DAP	1.20566	0.733
53DAP/52DAP	1.15081	0.608
55DAP/53DAP	1.1584	0.681
57DAP/55DAP	0.99583	0.902
62DAP/57DAP	0.78293	0.466
68DAP/62DAP	1.587	0.7
68DAP/14DAP	1.5978	0.578

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	2.3537	0.032

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.26725	0.068
Mature Green Tomato/Ripe Tomato	2.15955	0.149
Immature Eggplant/Mature Eggplant	6.0479	0.05
Ripe Pepper/Ripe Tomato	3.65667	0.256
Mature Eggplant/Ripe Tomato	0.57987	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.61433	0.536
1-1-2/M82	1.06954
12-2/M82	1.03014
12-4/M82	0.78139
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	0.72624
3-2/M82	1.57401
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	0.54758
5-3/M82	1.43529	0.572
6-2/M82	N/A	N/A
6-3/M82	1.04468	1
7-1/M82	1.46306
7-2/M82	1.49165	0.282
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.80463
IL2-6/WTpooled	1.22138	0.415
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.78634	0.298
IL12-4/WTpooled	0.88044	0.71
IL1-4/WTpooled	1.08819	1
WT/WTpooled	0.94061	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	1.18083	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.03986	0.921
DC3000/delta hrp 6h	1.04738	1
DC3000/delta hrp 12h	N/A	N/A
DC3000/delta hrp 24h	1.69336	0.029

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	2.33371	0.042
DC3000 delta B/DC3000 delta AB	5.0387	0.019

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.71397	0.227
Exp 36h	1.92103	0.489
Exp 60h	3.10842	0.227

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00544	1
Var 0h	1.05346	0.936
Var 12h I row2-row1	1.02585	1
Var 12h NI row2-row1	2.24147	0.649
Var 36h I row2-row1	1.24182	1
Var 36h NI row2-row1	0.53273	0.478
Var 60h I row2-row1	0.96819	0.832
Var 60h NI row2-row1	0.59721	0.292
Time course 0hI-0hNI	1.51089	0.486
Time course 12hI-12hNI	1.18505	0.786
Time course 36hI-36hNI	3.79301	0.004
Time course 60hI-60hNI	104.228	0.008

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)	1.45519	0.571
transgenic ySAMdc/azygous control (breaker)	0.94284	1
transgenic ySAMdc/azygous control (red)	0.75942	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.96229	0.078

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.71366	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	4.77741	0.105
Manapal/WT (break)	2.40495	1
Manapal/WT (red)	0.93037	0.728