Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.1.1.21

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.16067	0.534
27DAP/17DAP	0.90512	0.784
39DAP/27DAP	1.33855	0.384
41DAP/39DAP	0.77303	0.238
42DAP/41DAP	1.24686	0.876
43DAP/42DAP	1.20725	0.778
47DAP/43DAP	0.80293	0.35
52DAP/47DAP	0.87037	0.618
57DAP/52DAP	1.34357	0.892

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.10995	0.384
17DAP/reference	0.93457	0.474
27DAP/reference	1.01195	1
39DAP/reference	1.22385	0.203
41DAP/reference	1.03026	1
42DAP/reference	1.22694	0.001
43DAP/reference	1.25733	0.023
47DAP/reference	1.45666	0.001
52DAP/reference	1.23458	0.05
57DAP/reference	1.23458	0.009

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.00788	1
27DAP/17DAP	0.90546	0.537
39DAP/27DAP	0.96045	0.682
41DAP/39DAP	1.13363	0.774
42DAP/41DAP	0.98853	0.823
43DAP/42DAP	1.13894	0.297
47DAP/43DAP	1.00475	1
52DAP/47DAP	0.9672	0.848
57DAP/52DAP	0.84416	0.311
57DAP/7DAP	0.82622	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.4288	0.061
17DAP/reference	1.13849	0.297
27DAP/reference	1.04935	0.453
39DAP/reference	1.10705	0.077
41DAP/reference	1.34624	0.012
42DAP/reference	1.29385	0.007
43DAP/reference	1.17302	0.023
47DAP/reference	1.48588	0.026
52DAP/reference	1.22183	0.171
57DAP/reference	1.21539	0.033

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93037	0.441
17DAP/reference	1.05324	0.459
27DAP/reference	1.05939	0.948
39DAP/reference	1.07109	0.67
41DAP/reference	1.21821	0.076
42DAP/reference	0.96595	0.433
43DAP/reference	1.06337	0.655
47DAP/reference	1.28084	0.026
52DAP/reference	0.84845	0.06
57DAP/reference	0.77353	0.005

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.36819	0.095
17DAP/reference	1.1159	0.522
27DAP/reference	0.9675	0.319
39DAP/reference	1.11548	0.307
41DAP/reference	1.11154	0.455
42DAP/reference	1.46822	0.008
43DAP/reference	1.61789	0.011
47DAP/reference	1.43185	0.032
52DAP/reference	1.50677	0.054
57DAP/reference	1.76238	0.048

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.98248	1
26DAP/20DAP	1.03297	1
34DAP/26DAP	1.48324	1
51DAP/34DAP	1.64859
52DAP/51DAP	0.68591	1
53DAP/52DAP	1.0832	0.961
55DAP/53DAP	0.81351	0.163
57DAP/55DAP	1.14116	0.986
62DAP/57DAP	1.00882	1
68DAP/62DAP	0.89371	0.668
68DAP/14DAP	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	2.55807	0.017

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.33236	0.058
Mature Green Tomato/Ripe Tomato	1.34049	0.209
Immature Eggplant/Mature Eggplant	0.98183	0.72
Ripe Pepper/Ripe Tomato	0.70136	0.293
Mature Eggplant/Ripe Tomato	0.86824	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.99094	1
1-1-2/M82	1.15955	0.977
12-2/M82	0.8577	0.74
12-4/M82	1.04589	1
1-3/M82	1.67538	0.248
2-1-1/M82	1.14931	0.689
2-1/M82	0.90546	0.74
2-6/M82	1.04144	1
3-2/M82	1.07061
4-1-1/M82	1.15884	0.876
4-1/M82	1.43925	1
4-3-2/M82	1.46257	0.241
4-3/M82	0.99148	1
5-3/M82	1.00992	1
6-2/M82	1.24596	0.253
6-3/M82	0.92473	1
7-1/M82	0.982	1
7-2/M82	1.31962	0.385
9-3-2/M82	1.35163	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.00232	1
IL2-6/WTpooled	0.62455
IL7-5/WTpooled	1.00823
IL7-3/WTpooled	0.97546
IL12-4/WTpooled	0.84649
IL1-4/WTpooled	0.91247	0.834
WT/WTpooled	1.04868	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	0.97829	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.0877	0.921
DC3000/delta hrp 6h	0.90649	0.95
DC3000/delta hrp 12h	1.01138	1
DC3000/delta hrp 24h	0.88048	0.216

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.15596	0.229
DC3000 delta B/DC3000 delta AB	0.86783	0.236

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.17902	1
Exp 36h	1.06284	1
Exp 60h	1.24311	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00338	1
Var 0h	0.33546	1
Var 12h I row2-row1	0.73363	0.565
Var 12h NI row2-row1	1.21149	0.34
Var 36h I row2-row1	1.18292	0.601
Var 36h NI row2-row1	1.10375	1
Var 60h I row2-row1	0.89216	0.832
Var 60h NI row2-row1	0.92254	0.977
Time course 0hI-0hNI	1.07683	0.603
Time course 12hI-12hNI	0.90914	0.144
Time course 36hI-36hNI	0.9864	0.632
Time course 60hI-60hNI	1.48126	0.008

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)	0.93893	0.567
transgenic ySAMdc/azygous control (breaker)	0.98732	1
transgenic ySAMdc/azygous control (red)	1.11972	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.86991	0.122

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.94307	0.35

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.97294	1
Manapal/WT (break)	0.84958	0.299
Manapal/WT (red)	0.8583	0.187