Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.3.7.5

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.13602	0.656
27DAP/17DAP	0.97394	1
39DAP/27DAP	1.00121	0.782
41DAP/39DAP	0.87689	0.496
42DAP/41DAP	1.18113	0.903
43DAP/42DAP	1.09027	0.956
47DAP/43DAP	1.12198	0.633
52DAP/47DAP	0.75785	0.385
57DAP/52DAP	1.16678	0.87

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.55042	0.027
17DAP/reference	0.50395	0.011
27DAP/reference	0.47326	0.013
39DAP/reference	0.50545	0.048
41DAP/reference	0.37132	0.01
42DAP/reference	0.44631	0.001
43DAP/reference	0.4996	0.016
47DAP/reference	0.44386	0.001
52DAP/reference	0.42281	0.015
57DAP/reference	0.5686	0.008

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.95447	0.629
27DAP/17DAP	0.95091	0.878
39DAP/27DAP	0.86357	0.218
41DAP/39DAP	1.0293	0.861
42DAP/41DAP	0.92021	0.579
43DAP/42DAP	1.00049	1
47DAP/43DAP	1.10368	0.581
52DAP/47DAP	0.90732	0.498
57DAP/52DAP	1.01147	1
57DAP/7DAP	0.86142	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.62341	0.058
17DAP/reference	0.6051	0.011
27DAP/reference	0.76718	0.033
39DAP/reference	0.55369	0.011
41DAP/reference	0.51269	0.012
42DAP/reference	0.56871	0.01
43DAP/reference	0.48642	0.009
47DAP/reference	0.37231	0.034
52DAP/reference	0.45414	0.011
57DAP/reference	0.41603	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.34022	0.005
17DAP/reference	0.40251	0.005
27DAP/reference	0.52953	0.024
39DAP/reference	0.34664	0.008
41DAP/reference	0.40896	0.005
42DAP/reference	0.40736	0.012
43DAP/reference	0.34478	0.002
47DAP/reference	0.43075	0.008
52DAP/reference	0.27769	0.003
57DAP/reference	0.22687	0.002

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90367	0.197
17DAP/reference	0.92416	0.426
27DAP/reference	0.80357	0.174
39DAP/reference	0.58263	0.01
41DAP/reference	0.7659	0.064
42DAP/reference	0.98514	0.671
43DAP/reference	0.86064	0.256
47DAP/reference	0.29294	0.004
52DAP/reference	0.63391	0.145
57DAP/reference	0.91769	0.31

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.55943	0.966
26DAP/20DAP	0.99808	1
34DAP/26DAP	1.34709	0.19
51DAP/34DAP	1.09771	0.706
52DAP/51DAP	1.12735	0.096
53DAP/52DAP	1.00612	1
55DAP/53DAP	0.65846	0.016
57DAP/55DAP	1.03585	0.997
62DAP/57DAP	1.57472	0.723
68DAP/62DAP	0.93124	0.769
68DAP/14DAP	0.78878	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.91077	0.253

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.58448	0.058
Mature Green Tomato/Ripe Tomato	0.76909	0.055
Immature Eggplant/Mature Eggplant	0.41566	0.062
Ripe Pepper/Ripe Tomato	5.35684	1
Mature Eggplant/Ripe Tomato	9.62703	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	1.00148	1
12-2/M82	0.67704
12-4/M82	0.82089	1
1-3/M82	3.49404	0.26
2-1-1/M82	N/A	N/A
2-1/M82	0.62856
2-6/M82	1.17148	1
3-2/M82	0.86612
4-1-1/M82	0.9313	1
4-1/M82	1.40184
4-3-2/M82	1.02568	1
4-3/M82	0.485	0.388
5-3/M82	1.34099	0.572
6-2/M82	2.96033	0.195
6-3/M82	1.38304	1
7-1/M82	1.76203
7-2/M82	1.56855
9-3-2/M82	1.39795	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.84969
IL2-6/WTpooled	0.99846	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.87566	0.418
IL12-4/WTpooled	0.91862	0.581
IL1-4/WTpooled	0.80038	0.415
WT/WTpooled	0.99858	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	1.05668	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.94149	1
DC3000/delta hrp 6h	1.02465	1
DC3000/delta hrp 12h	0.95805	1
DC3000/delta hrp 24h	0.9737	0.831

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.79049	0.045
DC3000 delta B/DC3000 delta AB	0.91681	0.359

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	N/A	N/A
Exp 60h	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01993	1
Var 0h	0.48821	1
Var 12h I row2-row1	1.06778	1
Var 12h NI row2-row1	1.10757	0.649
Var 36h I row2-row1	1.00823	1
Var 36h NI row2-row1	0.68375	0.522
Var 60h I row2-row1	1.35396	1
Var 60h NI row2-row1	0.87215	0.866
Time course 0hI-0hNI	1.02033	1
Time course 12hI-12hNI	1.04376	0.836
Time course 36hI-36hNI	1.56056	0.005
Time course 60hI-60hNI	1.45101	0.115

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)	1.10028	0.748
transgenic ySAMdc/azygous control (breaker)	3.19204	0.248
transgenic ySAMdc/azygous control (red)	0.76774	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.72222	0.172

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.44344	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	9.06708	0.083
Manapal/WT (break)	5.08682	0.123
Manapal/WT (red)	0.45863	0.181