Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.3.3.21

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.91721	0.558
27DAP/17DAP	0.80913	0.5
39DAP/27DAP	1.58085	0.26
41DAP/39DAP	0.53984	0.041
42DAP/41DAP	1.24966	0.931
43DAP/42DAP	0.91862	0.827
47DAP/43DAP	0.84368	0.492
52DAP/47DAP	0.87549	0.643
57DAP/52DAP	1.13456	0.927

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.30507	0.078
17DAP/reference	1.29565	0.086
27DAP/reference	1.25421	0.093
39DAP/reference	1.31238	0.091
41DAP/reference	1.22827	0.171
42DAP/reference	1.27387	0.01
43DAP/reference	1.26325	0.011
47DAP/reference	1.17837	0.101
52DAP/reference	1.01204	0.791
57DAP/reference	1.18943	0.019

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.50045	0.042
27DAP/17DAP	1.02026	1
39DAP/27DAP	0.82631	0.227
41DAP/39DAP	1.18326	0.883
42DAP/41DAP	0.98407	0.774
43DAP/42DAP	0.68935	0.024
47DAP/43DAP	1.06146	0.844
52DAP/47DAP	0.98609	0.913
57DAP/52DAP	1.28244	0.159
57DAP/7DAP	1.11193	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.87298	0.024
17DAP/reference	1.49848	0.008
27DAP/reference	1.79966	0.018
39DAP/reference	1.4367	0.026
41DAP/reference	1.45649	0.011
42DAP/reference	1.49564	0.059
43DAP/reference	1.35598	0.02
47DAP/reference	1.47211	0.026
52DAP/reference	1.29402	0.01
57DAP/reference	1.49761	0.005

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.19133	0.456
17DAP/reference	1.36048	0.045
27DAP/reference	1.81723	0.018
39DAP/reference	1.54402	0.016
41DAP/reference	1.46031	0.005
42DAP/reference	1.54078	0.008
43DAP/reference	1.15895	0.59
47DAP/reference	1.71234	0.008
52DAP/reference	1.28016	0.008
57DAP/reference	1.05172	0.916

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.51102	0.017
17DAP/reference	1.15304	0.522
27DAP/reference	1.55775	0.02
39DAP/reference	1.51091	0.007
41DAP/reference	1.21505	0.286
42DAP/reference	1.47063	0.04
43DAP/reference	1.40063	0.076
47DAP/reference	1.34885	0.048
52DAP/reference	1.23748	0.17
57DAP/reference	2.55859	0.008

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.0376	1
26DAP/20DAP	1.59611	0.111
34DAP/26DAP	0.83606	0.575
51DAP/34DAP	0.91794	0.546
52DAP/51DAP	0.77917	1
53DAP/52DAP	0.95644	0.824
55DAP/53DAP	0.73201	0.028
57DAP/55DAP	1.60947	0.144
62DAP/57DAP	1.138	0.723
68DAP/62DAP	1.32789	0.845
68DAP/14DAP	1.40692	0.048

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	2.3392	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.06551	0.417
Mature Green Tomato/Ripe Tomato	1.77824	0.095
Immature Eggplant/Mature Eggplant	1.19045	0.074
Ripe Pepper/Ripe Tomato	0.91341	1
Mature Eggplant/Ripe Tomato	0.88588	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.94762	0.944
1-1-2/M82	1.17674	0.972
12-2/M82	1.05888	1
12-4/M82	1.11357	1
1-3/M82	1.45644	0.248
2-1-1/M82	1.23907	0.366
2-1/M82	1.2005	1
2-6/M82	0.87482	1
3-2/M82	1.32336	0.463
4-1-1/M82	0.79341	1
4-1/M82	1.19595	1
4-3-2/M82	1.07431	1
4-3/M82	1.17406	1
5-3/M82	1.11385	1
6-2/M82	0.99542	1
6-3/M82	1.18525
7-1/M82	1.00804	1
7-2/M82	1.10213	1
9-3-2/M82	1.44366	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.7713	0.321
IL2-6/WTpooled	0.88497	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.79576	0.418
IL12-4/WTpooled	0.86681	1
IL1-4/WTpooled	1.00479	1
WT/WTpooled	0.98288	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	0.88396	0.497

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.11043	0.921
DC3000/delta hrp 6h	1.0678	1
DC3000/delta hrp 12h	1.31078	1
DC3000/delta hrp 24h	1.07553	0.502

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.66361	0.028
DC3000 delta B/DC3000 delta AB	0.63285	0.021

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.93753	1
Exp 36h	1.0309	1
Exp 60h	0.97769	0.994

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01249	1
Var 0h	0.98005	1
Var 12h I row2-row1	0.91584	0.627
Var 12h NI row2-row1	1.03004	1
Var 36h I row2-row1	1.02961	1
Var 36h NI row2-row1	1.27795	1
Var 60h I row2-row1	0.99743	1
Var 60h NI row2-row1	1.10664	1
Time course 0hI-0hNI	0.92804	0.465
Time course 12hI-12hNI	1.02463	0.867
Time course 36hI-36hNI	0.95327	0.25
Time course 60hI-60hNI	0.22452	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)	0.99542	0.931
transgenic ySAMdc/azygous control (breaker)	1.14246	0.172
transgenic ySAMdc/azygous control (red)	1.10522	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.12734	0.204

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.91574	0.241

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.13795	0.105
Manapal/WT (break)	1.05163	1
Manapal/WT (red)	1.30592	0.222