Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.4.7.9

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.16745	0.755
27DAP/17DAP	1.2795	0.744
39DAP/27DAP	1.0233	0.876
41DAP/39DAP	0.98763	0.815
42DAP/41DAP	1.01542	1
43DAP/42DAP	1.04817	1
47DAP/43DAP	1.20014	0.415
52DAP/47DAP	0.86568	0.626
57DAP/52DAP	0.87932	0.803

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92668	0.293
17DAP/reference	1.04059	0.565
27DAP/reference	1.00591	1
39DAP/reference	1.02157	0.889
41DAP/reference	0.92831	0.542
42DAP/reference	0.9817	0.348
43DAP/reference	1.13518	0.074
47DAP/reference	1.07558	0.048
52DAP/reference	0.96669	0.371
57DAP/reference	1.04046	0.829

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.09045	0.356
27DAP/17DAP	0.9015	0.418
39DAP/27DAP	0.95464	0.45
41DAP/39DAP	1.04107	0.895
42DAP/41DAP	1.17726	0.032
43DAP/42DAP	0.87966	0.052
47DAP/43DAP	0.90154	0.225
52DAP/47DAP	1.57714	0.106
57DAP/52DAP	1.56903	0.073
57DAP/7DAP	1.34144	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.86395	0.146
17DAP/reference	1.1146	0.361
27DAP/reference	1.03778	0.664
39DAP/reference	0.95719	0.307
41DAP/reference	1.30936	0.017
42DAP/reference	1.09799	0.405
43DAP/reference	1.03095	0.83
47DAP/reference	1.00067	1
52DAP/reference	1.15735	0.247
57DAP/reference	1.11149	0.288

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87114	0.152
17DAP/reference	0.89788	0.058
27DAP/reference	0.8899	0.173
39DAP/reference	0.9685	0.359
41DAP/reference	0.99776	0.666
42DAP/reference	0.96489	0.261
43DAP/reference	0.83826	0.095
47DAP/reference	0.9772	0.338
52DAP/reference	0.94531	0.203
57DAP/reference	0.8789	0.099

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96475	0.422
17DAP/reference	0.94367	0.462
27DAP/reference	0.98924	0.657
39DAP/reference	0.98918	0.693
41DAP/reference	1.17602	0.058
42DAP/reference	0.99398	0.816
43DAP/reference	1.13187	0.465
47DAP/reference	0.8951	0.048
52DAP/reference	1.0004	0.854
57DAP/reference	1.0287	1

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.91536	0.981
26DAP/20DAP	1.03409	1
34DAP/26DAP	1.45324	0.819
51DAP/34DAP	1.08921	1
52DAP/51DAP	2.46216	0.034
53DAP/52DAP	0.69739	0.049
55DAP/53DAP	1.47162	0.04
57DAP/55DAP	0.65573	0.091
62DAP/57DAP	1.07281	0.902
68DAP/62DAP	1.26575	0.813
68DAP/14DAP	1.07951	0.802

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.4209	0.019

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.64758	0.197
Mature Green Tomato/Ripe Tomato	0.91483	0.715
Immature Eggplant/Mature Eggplant	1.39245	0.074
Ripe Pepper/Ripe Tomato	1.66371	1
Mature Eggplant/Ripe Tomato	1.46583

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	N/A	N/A
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	1.27015
4-3/M82	N/A	N/A
5-3/M82	N/A	N/A
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	0.88251

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.28049	0.277
IL2-6/WTpooled	0.8311	0.473
IL7-5/WTpooled	1.06176	0.792
IL7-3/WTpooled	1.08617	1
IL12-4/WTpooled	0.99578	1
IL1-4/WTpooled	0.95562	0.699
WT/WTpooled	0.98216	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	0.85507	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.26948
DC3000/delta hrp 6h	0.99777	0.95
DC3000/delta hrp 12h	1.07634	1
DC3000/delta hrp 24h	1.07305	0.633

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.50677	0.094
DC3000 delta B/DC3000 delta AB	1.46231	0.123

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	1.01677	1
Var 0h	0.80874	0.98
Var 12h I row2-row1	0.79963	0.467
Var 12h NI row2-row1	0.97693	0.906
Var 36h I row2-row1	0.94543	1
Var 36h NI row2-row1	1.29125	0.229
Var 60h I row2-row1	0.78071	0.285
Var 60h NI row2-row1	0.99028	1
Time course 0hI-0hNI	0.90761	0.446
Time course 12hI-12hNI	1.03218	0.876
Time course 36hI-36hNI	1.00209	0.742
Time course 60hI-60hNI	1.57239	0.015

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)	1.06705	0.3
transgenic ySAMdc/azygous control (breaker)	1.06956	0.172
transgenic ySAMdc/azygous control (red)	1.09272	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.11528	0.148

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.37262	0.239

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.61472	0.084
Manapal/WT (break)	1.54009	0.123
Manapal/WT (red)	1.42025	0.142