Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.4.14.17

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.82333	0.195
27DAP/17DAP	1.10821	0.88
39DAP/27DAP	1.14388	0.782
41DAP/39DAP	1.08158	0.964
42DAP/41DAP	1.41999	0.614
43DAP/42DAP	0.86729	0.736
47DAP/43DAP	1.17313	0.746
52DAP/47DAP	1.02954	0.973
57DAP/52DAP	1.20585	0.912

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90982	0.182
17DAP/reference	0.84519	0.085
27DAP/reference	0.89791	0.24
39DAP/reference	0.8117	0.09
41DAP/reference	0.69093	0.012
42DAP/reference	0.83198	0.007
43DAP/reference	0.87595	0.129
47DAP/reference	0.96033	0.258
52DAP/reference	1.07585	0.548
57DAP/reference	1.06936	0.744

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.19564	0.547
27DAP/17DAP	1.03767	1
39DAP/27DAP	1.08056	0.862
41DAP/39DAP	0.95994	0.923
42DAP/41DAP	1.0796	0.916
43DAP/42DAP	1.19523	0.23
47DAP/43DAP	1.15738	0.744
52DAP/47DAP	0.97301	0.898
57DAP/52DAP	1.3987	0.167
57DAP/7DAP	1.75454	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.88978	0.095
17DAP/reference	1.30121	0.016
27DAP/reference	1.28077	0.06
39DAP/reference	1.18379	0.186
41DAP/reference	1.37792	0.075
42DAP/reference	1.21991	0.405
43DAP/reference	1.13674	0.157
47DAP/reference	1.04442	1
52DAP/reference	1.01788	0.74
57DAP/reference	1.08245	0.536

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.83321	0.076
17DAP/reference	0.78616	0.011
27DAP/reference	0.91781	0.155
39DAP/reference	0.90711	0.159
41DAP/reference	0.83955	0.083
42DAP/reference	0.91219	0.121
43DAP/reference	0.80853	0.108
47DAP/reference	0.77404	0.038
52DAP/reference	0.77597	0.007
57DAP/reference	0.63541	0.007

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96888	0.455
17DAP/reference	1.00014	0.763
27DAP/reference	1.26509	0.1
39DAP/reference	1.16276	0.342
41DAP/reference	1.00403	0.826
42DAP/reference	1.11449	0.34
43DAP/reference	0.98715	0.639
47DAP/reference	0.84929	0.054
52DAP/reference	1.28878	0.509
57DAP/reference	0.99436	0.742

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.42488	0.966
26DAP/20DAP	1.10559	0.77
34DAP/26DAP	1.0564	1
51DAP/34DAP	1.37919	0.402
52DAP/51DAP	1.20424	0.446
53DAP/52DAP	1.71562	0.623
55DAP/53DAP	1.02007	0.876
57DAP/55DAP	0.80088	0.222
62DAP/57DAP	0.95432	0.994
68DAP/62DAP	1.23985	0.899
68DAP/14DAP	1.36044	0.131

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.72057	0.229

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.95989	0.113
Mature Green Tomato/Ripe Tomato	0.874	0.317
Immature Eggplant/Mature Eggplant	1.72364	0.056
Ripe Pepper/Ripe Tomato	0.46214	0.293
Mature Eggplant/Ripe Tomato	0.83119	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.92499	0.934
1-1-2/M82	1.08304
12-2/M82	1.05751
12-4/M82	0.8592	0.259
1-3/M82	N/A	N/A
2-1-1/M82	0.97003
2-1/M82	0.91908
2-6/M82	1.10492
3-2/M82	0.93889
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	0.90695	1
6-2/M82	0.94997
6-3/M82	1.02257
7-1/M82	1.04439
7-2/M82	1.32092
9-3-2/M82	1.15649

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.88616
IL2-6/WTpooled	0.82817	0.473
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.44258	1
IL12-4/WTpooled	0.99788	1
IL1-4/WTpooled	0.84595	0.834
WT/WTpooled	1.10334	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	0.90822	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.05962	0.921
DC3000/delta hrp 6h	0.94992	0.95
DC3000/delta hrp 12h	1.03507	1
DC3000/delta hrp 24h	0.83782	0.145

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.73637	0.151
DC3000 delta B/DC3000 delta AB	0.74301	0.075

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.96787	1
Exp 36h	0.75333	0.471
Exp 60h	0.8897	0.454

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

hybridization	ratio	FDR (corrected p value)
self-self	1.07998	1
Var 0h	0.96747	1
Var 12h I row2-row1	0.90973	0.467
Var 12h NI row2-row1	0.9856	0.906
Var 36h I row2-row1	0.99605	1
Var 36h NI row2-row1	0.77784	0.478
Var 60h I row2-row1	0.92883	0.952
Var 60h NI row2-row1	0.97208	1
Time course 0hI-0hNI	1.13705	0.662
Time course 12hI-12hNI	0.86237	0.128
Time course 36hI-36hNI	0.88734	0.096
Time course 60hI-60hNI	0.51963	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)	1.15521	0.289
transgenic ySAMdc/azygous control (breaker)	0.83311	0.49
transgenic ySAMdc/azygous control (red)	1.00291	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.08992	0.135

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.9259	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.73084	0.172
Manapal/WT (break)	0.94925	1
Manapal/WT (red)	0.66846	0.181