Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.2.3.18

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.12254	0.851
27DAP/17DAP	1.20962	0.784
39DAP/27DAP	0.97892	0.733
41DAP/39DAP	0.92586	0.697
42DAP/41DAP	0.93135	1
43DAP/42DAP	1.07418	1
47DAP/43DAP	1.23619	0.412
52DAP/47DAP	0.984	0.89
57DAP/52DAP	1.14073	0.935

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.85004	0.106
17DAP/reference	0.9133	0.24
27DAP/reference	1.04364	0.599
39DAP/reference	0.89108	0.121
41DAP/reference	0.75615	0.009
42DAP/reference	0.90168	0.067
43DAP/reference	0.96754	0.611
47DAP/reference	1.17465	0.199
52DAP/reference	1.36357	0.026
57DAP/reference	1.41388	0.008

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.16059	0.438
27DAP/17DAP	1.03371	0.923
39DAP/27DAP	0.94691	0.737
41DAP/39DAP	1.03782	1
42DAP/41DAP	1.04933	0.861
43DAP/42DAP	0.86033	0.082
47DAP/43DAP	1.01572	0.957
52DAP/47DAP	1.068	0.742
57DAP/52DAP	1.11518	0.462
57DAP/7DAP	1.25795	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.94994	0.025
17DAP/reference	1.54408	0.032
27DAP/reference	1.22015	0.246
39DAP/reference	2.0872	0.005
41DAP/reference	1.63215	0.011
42DAP/reference	1.70328	0.007
43DAP/reference	1.60481	0.007
47DAP/reference	1.31298	0.073
52DAP/reference	1.57687	0.013
57DAP/reference	1.50059	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84432	0.19
17DAP/reference	0.76996	0.011
27DAP/reference	0.94454	0.366
39DAP/reference	1.15013	0.316
41DAP/reference	1.14011	0.241
42DAP/reference	0.99436	0.655
43DAP/reference	0.77946	0.049
47DAP/reference	0.9363	0.077
52DAP/reference	0.90935	0.093
57DAP/reference	0.74393	0.032

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.29903	0.244
17DAP/reference	1.04047	0.87
27DAP/reference	1.30235	0.049
39DAP/reference	1.30136	0.059
41DAP/reference	1.24085	0.065
42DAP/reference	1.30669	0.099
43DAP/reference	1.3666	0.044
47DAP/reference	0.88235	0.191
52DAP/reference	1.48283	0.11
57DAP/reference	2.05673	0.008

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.89025	0.915
26DAP/20DAP	0.91675	1
34DAP/26DAP	0.92667	0.816
51DAP/34DAP	0.92531	0.631
52DAP/51DAP	0.85907	0.151
53DAP/52DAP	1.23117	0.162
55DAP/53DAP	0.90828	0.53
57DAP/55DAP	1.29677	0.06
62DAP/57DAP	1.37947	0.767
68DAP/62DAP	1.98444	0.03
68DAP/14DAP	2.40744	0.022

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.0781	0.7

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.94795	0.635
Mature Green Tomato/Ripe Tomato	1.11914	0.632
Immature Eggplant/Mature Eggplant	1.11734	0.198
Ripe Pepper/Ripe Tomato	0.90447	1
Mature Eggplant/Ripe Tomato	1.02361	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.82958	0.673
1-1-2/M82	0.98894	1
12-2/M82	0.88221
12-4/M82	0.71916	0.282
1-3/M82	1.33673	0.248
2-1-1/M82	0.92401	0.92
2-1/M82	1.07644	1
2-6/M82	0.92347	1
3-2/M82	1.11806
4-1-1/M82	0.77914
4-1/M82	0.67524
4-3-2/M82	1.0566	1
4-3/M82	1.06504	1
5-3/M82	1.36406	0.455
6-2/M82	0.76133
6-3/M82	0.89555	1
7-1/M82	0.85671
7-2/M82	1.03966	1
9-3-2/M82	1.06671	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.15487	0.365
IL2-6/WTpooled	0.97043	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.95605	1
IL12-4/WTpooled	1.03642	0.525
IL1-4/WTpooled	0.9843	1
WT/WTpooled	0.998	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	1.01347	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.15962	0.846
DC3000/delta hrp 6h	1.20952	1
DC3000/delta hrp 12h	0.92661	1
DC3000/delta hrp 24h	1.09358	0.453

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.03811	0.648
DC3000 delta B/DC3000 delta AB	1.16239	0.302

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.10605	1
Exp 36h	0.95524	0.879
Exp 60h	0.97819	0.994

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

hybridization	ratio	FDR (corrected p value)
self-self	N/A	N/A
Var 0h	0.81279	1
Var 12h I row2-row1	1.07562	0.692
Var 12h NI row2-row1	0.89812	0.906
Var 36h I row2-row1	1.07525	0.908
Var 36h NI row2-row1	1.01563	1
Var 60h I row2-row1	0.9104	0.285
Var 60h NI row2-row1	1.00186	1
Time course 0hI-0hNI	1.0367	0.719
Time course 12hI-12hNI	0.95351	0.847
Time course 36hI-36hNI	1.29386	0.005
Time course 60hI-60hNI	1.81002	0.009

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)	0.77853	0.314
transgenic ySAMdc/azygous control (breaker)	1.02814	1
transgenic ySAMdc/azygous control (red)	1.0044	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.96055	0.5

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.91832	0.308

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.81436	1
Manapal/WT (break)	0.87732	0.333
Manapal/WT (red)	1.02992	1