Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-4.2.4.13

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.78677	0.182
27DAP/17DAP	1.16553	0.902
39DAP/27DAP	1.12711	1
41DAP/39DAP	1.05499	1
42DAP/41DAP	1.15557	0.844
43DAP/42DAP	0.78524	0.664
47DAP/43DAP	0.68923	0.199
52DAP/47DAP	1.15899	0.828
57DAP/52DAP	1.01108	0.971

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.13111	0.29
17DAP/reference	1.04059	0.442
27DAP/reference	1.05877	0.672
39DAP/reference	1.16018	0.256
41DAP/reference	1.10369	0.02
42DAP/reference	1.63275	0.012
43DAP/reference	1.39101	0.007
47DAP/reference	1.01763	0.963
52DAP/reference	1.06482	0.951
57DAP/reference	0.86614	0.042

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.00727	0.899
27DAP/17DAP	1.05969	0.905
39DAP/27DAP	1.18413	0.369
41DAP/39DAP	1.21632	0.623
42DAP/41DAP	0.90514	0.434
43DAP/42DAP	0.72874	0.049
47DAP/43DAP	1.04803	0.884
52DAP/47DAP	0.98411	0.93
57DAP/52DAP	0.96265	0.732
57DAP/7DAP	N/A	N/A

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.0175	1
17DAP/reference	0.89679	0.144
27DAP/reference	0.86216	0.076
39DAP/reference	0.80452	0.073
41DAP/reference	0.87282	0.079
42DAP/reference	0.82024	0.034
43DAP/reference	0.62604	0.015
47DAP/reference	0.84635	0.293
52DAP/reference	0.84995	0.03
57DAP/reference	0.94701	0.367

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.33461	0.149
17DAP/reference	0.97095	0.561
27DAP/reference	1.0209	0.765
39DAP/reference	1.13367	0.316
41DAP/reference	1.22836	0.053
42DAP/reference	1.09003	0.288
43DAP/reference	1.36763	0.014
47DAP/reference	1.07587	0.467
52DAP/reference	1.29423	0.368
57DAP/reference	1.03319	0.908

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.203	0.029
17DAP/reference	1.22168	0.197
27DAP/reference	1.20007	0.271
39DAP/reference	0.98099	0.591
41DAP/reference	0.88935	0.167
42DAP/reference	0.80723	0.049
43DAP/reference	1.00017	0.858
47DAP/reference	1.02881	1
52DAP/reference	0.71577	0.077
57DAP/reference	1.00136	0.73

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.0942	0.966
26DAP/20DAP	1.51802	0.17
34DAP/26DAP	0.83335	0.322
51DAP/34DAP	1.0907	0.898
52DAP/51DAP	1.00716	1
53DAP/52DAP	0.9149	0.79
55DAP/53DAP	1.14003	0.869
57DAP/55DAP	1.15904	0.626
62DAP/57DAP	1.55589	0.723
68DAP/62DAP	1.04375	0.939
68DAP/14DAP	1.05403	0.936

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.46367	0.036

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.85887	0.666
Mature Green Tomato/Ripe Tomato	4.72927	0.02
Immature Eggplant/Mature Eggplant	0.27003	0.067
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	24.4717	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.00837	1
1-1-2/M82	0.80097	N/A
12-2/M82	0.93687	N/A
12-4/M82	N/A	N/A
1-3/M82	0.80518	0.501
2-1-1/M82	1.52121	N/A
2-1/M82	N/A	N/A
2-6/M82	1.06252	0.695
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	1.36177	1
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	0.94698	1
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	1.22162	N/A
7-2/M82	0.95498	0.881
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.42502	N/A
IL12-4/WTpooled	0.99333	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	0.90832	0.497

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.02019	0.921
DC3000/delta hrp 6h	1.35803	1
DC3000/delta hrp 12h	1.0151	1
DC3000/delta hrp 24h	1.09935	0.422

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	N/A
DC3000 delta B/DC3000 delta AB	2.31181	N/A

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.80081	1
Exp 36h	1.39651	1
Exp 60h	1.11808	1

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	0.9318	1
Var 12h I row2-row1	N/A	N/A
Var 12h NI row2-row1	N/A	N/A
Var 36h I row2-row1	N/A	N/A
Var 36h NI row2-row1	N/A	N/A
Var 60h I row2-row1	N/A	N/A
Var 60h NI row2-row1	N/A	N/A
Time course 0hI-0hNI	N/A	N/A
Time course 12hI-12hNI	N/A	N/A
Time course 36hI-36hNI	N/A	N/A
Time course 60hI-60hNI	N/A	N/A

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)	0.84581	0.267
transgenic ySAMdc/azygous control (breaker)	1.60416	0.166
transgenic ySAMdc/azygous control (red)	1.09267	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.97625	0.323

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.40233	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	N/A	N/A
Manapal/WT (break)	N/A	N/A
Manapal/WT (red)	0.8942	0.607