Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-3.3.17.16

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.00164	0.876
27DAP/17DAP	1.198	0.808
39DAP/27DAP	1.17344	0.658
41DAP/39DAP	1.25082	0.432
42DAP/41DAP	1.03113	1
43DAP/42DAP	0.87923	0.827
47DAP/43DAP	0.76964	0.334
52DAP/47DAP	1.94588	0.23
57DAP/52DAP	0.86842	0.852

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97112	0.589
17DAP/reference	0.79351	0.147
27DAP/reference	1.12185	0.599
39DAP/reference	0.91677	0.541
41DAP/reference	0.89001	0.201
42DAP/reference	0.85039	0.009
43DAP/reference	0.98439	0.785
47DAP/reference	0.95085	0.322
52DAP/reference	1.14275	0.524
57DAP/reference	1.31553	0.136

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.40772	0.132
27DAP/17DAP	0.95704	0.821
39DAP/27DAP	0.80886	0.058
41DAP/39DAP	1.24084	0.623
42DAP/41DAP	0.80824	0.099
43DAP/42DAP	1.14415	0.324
47DAP/43DAP	1.06075	0.805
52DAP/47DAP	1.13535	0.63
57DAP/52DAP	1.00826	0.913
57DAP/7DAP	1.64743	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.778	0.05
17DAP/reference	0.73174	0.012
27DAP/reference	0.81774	0.016
39DAP/reference	0.72799	0.011
41DAP/reference	0.96828	0.449
42DAP/reference	0.70922	0.011
43DAP/reference	0.7106	0.023
47DAP/reference	0.9927	0.671
52DAP/reference	0.64158	0.015
57DAP/reference	0.70809	0.013

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.59749	0.008
17DAP/reference	0.82691	0.143
27DAP/reference	0.76651	0.229
39DAP/reference	1.05598	0.725
41DAP/reference	1.05466	0.683
42DAP/reference	1.05951	1
43DAP/reference	1.01132	0.692
47DAP/reference	0.83764	0.007
52DAP/reference	1.21297	0.747
57DAP/reference	1.00206	0.834

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.86511	0.038
17DAP/reference	0.93035	0.328
27DAP/reference	0.80074	0.076
39DAP/reference	0.7972	0.026
41DAP/reference	0.90715	0.293
42DAP/reference	0.9175	0.361
43DAP/reference	0.84246	0.15
47DAP/reference	0.95237	0.525
52DAP/reference	0.80264	0.242
57DAP/reference	1.04736	0.79

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.24607	0.966
26DAP/20DAP	0.87338	0.317
34DAP/26DAP	1.23496	1
51DAP/34DAP	0.91229	0.618
52DAP/51DAP	1.17589	0.481
53DAP/52DAP	0.95016	0.783
55DAP/53DAP	1.20384	0.319
57DAP/55DAP	1.24151	0.969
62DAP/57DAP	1.38257	0.445
68DAP/62DAP	1.30196	0.872
68DAP/14DAP	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.85605	0.341

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.99624	N/A
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	19.7534	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.13232	0.877
1-1-2/M82	0.67814	N/A
12-2/M82	N/A	N/A
12-4/M82	1.13682	N/A
1-3/M82	0.86479	0.378
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	1.04481	1
3-2/M82	N/A	N/A
4-1-1/M82	0.50524	N/A
4-1/M82	1.50911	N/A
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	0.9179	0.49
6-2/M82	0.55148	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	0.89128	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	0.9662	1
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	1.46233	0.532
IL1-4/WTpooled	0.86437	N/A
WT/WTpooled	1.17684	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	1.07504	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.07871	0.846
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	1.02337	1
DC3000/delta hrp 24h	0.93354	0.513

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.04194	1
DC3000 delta B/DC3000 delta AB	0.91068	0.456

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	1.02252	1
Var 0h	0.30218	1
Var 12h I row2-row1	1.27512	0.443
Var 12h NI row2-row1	0.85073	0.627
Var 36h I row2-row1	0.844	0.805
Var 36h NI row2-row1	1.35825	1
Var 60h I row2-row1	1.08513	0.562
Var 60h NI row2-row1	1.18053	0.904
Time course 0hI-0hNI	1.05378	0.833
Time course 12hI-12hNI	0.81541	0.033
Time course 36hI-36hNI	0.70855	0.032
Time course 60hI-60hNI	0.96878	0.646

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)	N/A	N/A
transgenic ySAMdc/azygous control (red)	N/A	N/A

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.74399	0.239

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)	0.92988	1
Manapal/WT (red)	1.28486	0.164