Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.1.20.5

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.09748	0.947
27DAP/17DAP	1.11519	0.872
39DAP/27DAP	0.7251	0.241
41DAP/39DAP	1.42376	0.765
42DAP/41DAP	1.21006	0.937
43DAP/42DAP	0.82471	0.712
47DAP/43DAP	1.21238	0.965
52DAP/47DAP	1.25503	0.649
57DAP/52DAP	0.96113	0.957

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.37103	0.126
17DAP/reference	1.33786	0.066
27DAP/reference	1.15533	0.52
39DAP/reference	1.3963	0.051
41DAP/reference	1.65871	0.015
42DAP/reference	1.24509	0.005
43DAP/reference	1.22822	0.217
47DAP/reference	1.04551	0.91
52DAP/reference	1.08651	0.524
57DAP/reference	0.78546	0.034

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.93541	0.47
27DAP/17DAP	1.04873	0.887
39DAP/27DAP	1.1261	0.267
41DAP/39DAP	1.08648	1
42DAP/41DAP	1.01366	0.934
43DAP/42DAP	1.0614	0.413
47DAP/43DAP	1.01309	0.973
52DAP/47DAP	1.01781	0.965
57DAP/52DAP	0.93916	0.501
57DAP/7DAP	1.17628	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.82715	0.129
17DAP/reference	0.75311	0.011
27DAP/reference	0.74675	0.01
39DAP/reference	0.74465	0.011
41DAP/reference	0.76187	0.035
42DAP/reference	0.67476	0.01
43DAP/reference	0.68891	0.011
47DAP/reference	0.7597	0.066
52DAP/reference	0.62519	0.012
57DAP/reference	0.66711	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.46398	0.083
17DAP/reference	1.52279	0.007
27DAP/reference	1.1542	0.396
39DAP/reference	1.129	0.463
41DAP/reference	1.20865	0.014
42DAP/reference	1.44511	0.081
43DAP/reference	1.64409	0.014
47DAP/reference	1.21105	0.032
52DAP/reference	1.40596	0.008
57DAP/reference	1.8701	0.017

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.8467	0.169
17DAP/reference	1.01969	0.839
27DAP/reference	0.82253	0.076
39DAP/reference	0.78747	0.054
41DAP/reference	0.86038	0.148
42DAP/reference	0.71421	0.015
43DAP/reference	0.77315	0.081
47DAP/reference	1.21623	0.048
52DAP/reference	0.71516	0.122
57DAP/reference	0.64997	0.039

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.96619	1
26DAP/20DAP	0.87467	0.512
34DAP/26DAP	1.13485	1
51DAP/34DAP	0.85116	0.123
52DAP/51DAP	1.13503	0.446
53DAP/52DAP	1.01804	0.935
55DAP/53DAP	1.01651	0.982
57DAP/55DAP	1.14231	0.745
62DAP/57DAP	0.97719	0.994
68DAP/62DAP	0.70886	0.166
68DAP/14DAP	0.7012	0.121

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.77848	0.083

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.02391	0.835
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	N/A	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.93405	0.944
1-1-2/M82	1.0111	1
12-2/M82	1.28218	1
12-4/M82	1.04818	1
1-3/M82	0.85577	0.441
2-1-1/M82	1.09175	1
2-1/M82	1.40115
2-6/M82	1.10477	1
3-2/M82	0.86964
4-1-1/M82	1.22137	1
4-1/M82	1.28808
4-3-2/M82	0.84417	0.698
4-3/M82	0.77369	0.611
5-3/M82	0.94607	1
6-2/M82	0.91711	1
6-3/M82	1.07039	1
7-1/M82	0.95594	1
7-2/M82	0.95249	1
9-3-2/M82	0.69544

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.54751	0.365
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	0.72464	1
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	0.78137
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	0.90652	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.00405	1
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	1.08033	1
DC3000/delta hrp 24h	1.00864	0.821

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.90766	0.955
DC3000 delta B/DC3000 delta AB	0.96886	0.787

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.40144	1
Exp 36h	N/A	N/A
Exp 60h	1.09586	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.92021	1
Var 0h	N/A	N/A
Var 12h I row2-row1	1.26935	0.263
Var 12h NI row2-row1	0.97374	0.906
Var 36h I row2-row1	0.8377	0.438
Var 36h NI row2-row1	1.07592	1
Var 60h I row2-row1	1.21729	1
Var 60h NI row2-row1	1.19785	0.904
Time course 0hI-0hNI	1.28167	0.662
Time course 12hI-12hNI	0.98844	1
Time course 36hI-36hNI	1.04735	0.651
Time course 60hI-60hNI	1.38541	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)	N/A	N/A
transgenic ySAMdc/azygous control (breaker)	0.85477	0.49
transgenic ySAMdc/azygous control (red)	1.06539	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.93802	0.242

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.48878	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)	0.90479	0.728