Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-2.1.3.1

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.58883	0.656
27DAP/17DAP	1.20982	0.801
39DAP/27DAP	2.84804	0.047
41DAP/39DAP	0.88319	0.533
42DAP/41DAP	0.80304	1
43DAP/42DAP	1.31182	1
47DAP/43DAP	0.75683	0.314
52DAP/47DAP	3.37654	0.05
57DAP/52DAP	1.40854	0.98

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.88115	0.293
17DAP/reference	0.53281	0.057
27DAP/reference	0.53503	0.019
39DAP/reference	0.35738	0.013
41DAP/reference	0.25415	0.01
42DAP/reference	1.4753	0.352
43DAP/reference	N/A	N/A
47DAP/reference	1.29269	0.419
52DAP/reference	0.63573	0.046
57DAP/reference	0.70485	N/A

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.64024	0.08
27DAP/17DAP	0.9447	0.724
39DAP/27DAP	1.51562	0.292
41DAP/39DAP	1.31023	1
42DAP/41DAP	1.54199	0.006
43DAP/42DAP	1.30862	0.042
47DAP/43DAP	1.05121	0.779
52DAP/47DAP	0.47746	0.034
57DAP/52DAP	1.16591	0.253
57DAP/7DAP	0.98854	0.186

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.7378	0.025
17DAP/reference	1.00756	1
27DAP/reference	1.4773	0.012
39DAP/reference	0.90332	0.264
41DAP/reference	1.5701	0.017
42DAP/reference	3.1236	0.007
43DAP/reference	4.08021	0.006
47DAP/reference	2.86955	0.018
52DAP/reference	2.30321	0.007
57DAP/reference	0.90978	0.25

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.10364	0.642
17DAP/reference	0.76246	0.12
27DAP/reference	1.56032	0.025
39DAP/reference	1.06566	1
41DAP/reference	1.01378	0.666
42DAP/reference	1.42129	0.02
43DAP/reference	0.54627	0.011
47DAP/reference	0.57037	0.009
52DAP/reference	0.41122	0.004
57DAP/reference	0.39349	0.004

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.13231	0.827
17DAP/reference	0.683	0.099
27DAP/reference	1.03545	0.883
39DAP/reference	1.59692	0.046
41DAP/reference	1.37587	0.01
42DAP/reference	2.74765	0.006
43DAP/reference	3.53585	0.006
47DAP/reference	0.65848	0.015
52DAP/reference	1.47315	0.108
57DAP/reference	1.57866	0.304

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.93436	1
26DAP/20DAP	1.06256	1
34DAP/26DAP	1.34866	1
51DAP/34DAP	1.7441	0.035
52DAP/51DAP	0.68368	0.151
53DAP/52DAP	2.32672	0.034
55DAP/53DAP	0.46151	0.016
57DAP/55DAP	1.26318	0.826
62DAP/57DAP	0.44727	0.002
68DAP/62DAP	2.39993	0.017
68DAP/14DAP	2.20051	0.021

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	5.80882	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.68235	0.182
Mature Green Tomato/Ripe Tomato	0.53368	0.02
Immature Eggplant/Mature Eggplant	1.93149	0.05
Ripe Pepper/Ripe Tomato	0.52962	0.293
Mature Eggplant/Ripe Tomato	0.35494	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.57188	0.877
1-1-2/M82	1.4142	1
12-2/M82	0.89446	0.955
12-4/M82	1.49272	1
1-3/M82	5.52327	0.277
2-1-1/M82	1.11828	1
2-1/M82	0.6672	0.519
2-6/M82	1.81108	0.351
3-2/M82	1.35562	0.967
4-1-1/M82	1.26319	1
4-1/M82	0.57234	N/A
4-3-2/M82	1.95198	0.284
4-3/M82	1.30128	1
5-3/M82	1.42641	1
6-2/M82	2.71537	0.253
6-3/M82	1.03401	1
7-1/M82	1.27096	1
7-2/M82	3.28973	0.385
9-3-2/M82	2.5896	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.98911	1
IL2-6/WTpooled	1.20971	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.94766	N/A
IL12-4/WTpooled	0.86536	1
IL1-4/WTpooled	1.20104	1
WT/WTpooled	1.02596	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	1.51833	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.87887	0.807
DC3000/delta hrp 6h	0.87686	0.95
DC3000/delta hrp 12h	1.50347	1
DC3000/delta hrp 24h	1.10485	1

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.03946	1
DC3000 delta B/DC3000 delta AB	1.25107	0.308

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.17709	1
Exp 36h	1.24648	0.489
Exp 60h	1.0166	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.89122	1
Var 0h	0.94576	1
Var 12h I row2-row1	0.94343	0.77
Var 12h NI row2-row1	0.9894	1
Var 36h I row2-row1	1.05016	1
Var 36h NI row2-row1	1.34801	0.482
Var 60h I row2-row1	1.08895	1
Var 60h NI row2-row1	1.24449	0.539
Time course 0hI-0hNI	0.9342	0.482
Time course 12hI-12hNI	1.05511	0.724
Time course 36hI-36hNI	0.86281	0.052
Time course 60hI-60hNI	0.12655	0.005

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)	1.17103	0.654
transgenic ySAMdc/azygous control (breaker)	0.80926	0.173
transgenic ySAMdc/azygous control (red)	0.95427	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.7504	0.045

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.09715	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.0924	0.307
Manapal/WT (break)	1.05756	0.381
Manapal/WT (red)	1.07256	0.413