Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.3.7.10

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.15327	0.977
27DAP/17DAP	0.59489	0.053
39DAP/27DAP	0.81724	0.522
41DAP/39DAP	0.52685	0.041
42DAP/41DAP	0.75519	0.397
43DAP/42DAP	1.25413	0.835
47DAP/43DAP	0.30197	0.041
52DAP/47DAP	0.65131	0.282
57DAP/52DAP	0.89177	0.853

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03973	1
17DAP/reference	0.8173	0.147
27DAP/reference	0.8101	0.092
39DAP/reference	0.73355	0.053
41DAP/reference	0.56642	0.021
42DAP/reference	0.87081	0.045
43DAP/reference	0.6059	0.015
47DAP/reference	0.78093	0.011
52DAP/reference	0.98461	0.564
57DAP/reference	0.96009	0.395

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.51601	0.103
27DAP/17DAP	0.89744	0.782
39DAP/27DAP	0.34343	0.028
41DAP/39DAP	1.06691	0.763
42DAP/41DAP	1.06922	0.947
43DAP/42DAP	0.42059	0.021
47DAP/43DAP	0.72415	0.074
52DAP/47DAP	1.16445	0.933
57DAP/52DAP	1.55625	0.123
57DAP/7DAP	0.26029	0.186

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.16164	1
17DAP/reference	1.13496	0.971
27DAP/reference	0.93517	0.375
39DAP/reference	0.80879	0.017
41DAP/reference	0.74089	0.023
42DAP/reference	0.71227	0.013
43DAP/reference	0.66349	0.011
47DAP/reference	0.6611	0.079
52DAP/reference	0.92805	0.232
57DAP/reference	0.77636	0.009

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.65547	0.015
17DAP/reference	0.63836	0.011
27DAP/reference	1.10233	1
39DAP/reference	1.13134	0.639
41DAP/reference	1.13469	0.766
42DAP/reference	1.00555	0.723
43DAP/reference	0.64267	0.036
47DAP/reference	0.58463	0.009
52DAP/reference	0.83587	0.156
57DAP/reference	0.44861	0.005

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.96077	0.015
17DAP/reference	1.87589	0.111
27DAP/reference	1.50483	0.02
39DAP/reference	1.35133	0.012
41DAP/reference	1.09875	0.296
42DAP/reference	1.11805	0.648
43DAP/reference	1.25764	0.331
47DAP/reference	0.74072	0.028
52DAP/reference	0.63928	0.063
57DAP/reference	2.29843	0.009

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.51699	0.008
26DAP/20DAP	0.80505	0.512
34DAP/26DAP	1.37261	0.819
51DAP/34DAP	1.26838	1
52DAP/51DAP	2.08545	0.033
53DAP/52DAP	0.64232	0.083
55DAP/53DAP	1.47004	0.07
57DAP/55DAP	0.50989	0.017
62DAP/57DAP	2.12057	0.004
68DAP/62DAP	2.25543	0.225
68DAP/14DAP	2.35877	0.055

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.91022	0.493

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	3.43607	0.058
Mature Green Tomato/Ripe Tomato	65.1784	0.015
Immature Eggplant/Mature Eggplant	0.48296	0.064
Ripe Pepper/Ripe Tomato	3.61332
Mature Eggplant/Ripe Tomato	31.0023	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.58123
12-2/M82	0.17147
12-4/M82	0.8756
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	N/A	N/A
3-2/M82	N/A	N/A
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	4.54995	0.426
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	1.89485
7-2/M82	N/A	N/A
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	28.7904
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	N/A	N/A
WT/WTpooled	N/A	N/A

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	0.96059	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.91306	1
DC3000/delta hrp 6h	0.96177	0.95
DC3000/delta hrp 12h	1.21206	1
DC3000/delta hrp 24h	0.92778	0.564

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.5928	0.03
DC3000 delta B/DC3000 delta AB	0.547	0.021

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.90895	1
Exp 36h	0.7639	0.504
Exp 60h	0.90332	0.586

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

hybridization	ratio	FDR (corrected p value)
self-self	0.96378	1
Var 0h	0.55286	0.457
Var 12h I row2-row1	0.83941	0.418
Var 12h NI row2-row1	0.9771	0.906
Var 36h I row2-row1	1.03304	1
Var 36h NI row2-row1	1.0457	1
Var 60h I row2-row1	1.26832	0.562
Var 60h NI row2-row1	0.99907	1
Time course 0hI-0hNI	1.01958	1
Time course 12hI-12hNI	0.99701	1
Time course 36hI-36hNI	1.03389	1
Time course 60hI-60hNI	0.2006	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)	1.18321	0.699
transgenic ySAMdc/azygous control (breaker)	4.42075	0.166
transgenic ySAMdc/azygous control (red)	1.58241	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.55781	0.107

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.58931	0.237

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	5.18624	0.084
Manapal/WT (break)	10.8015	0.126
Manapal/WT (red)	10.5379	0.133