Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-2.4.12.16

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.08698	0.838
27DAP/17DAP	1.22683	0.881
39DAP/27DAP	1.03153	1
41DAP/39DAP	1.10757	0.642
42DAP/41DAP	1.0729	0.937
43DAP/42DAP	0.95482	0.877
47DAP/43DAP	0.95033	0.821
52DAP/47DAP	1.11948	0.794
57DAP/52DAP	1.14839	0.688

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.13626	0.46
17DAP/reference	1.15952	0.017
27DAP/reference	1.06022	0.211
39DAP/reference	1.07422	0.104
41DAP/reference	1.08783	0.067
42DAP/reference	0.83704	0.007
43DAP/reference	0.995	0.861
47DAP/reference	0.82874	0.012
52DAP/reference	0.75663	0.017
57DAP/reference	0.7831	0.03

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.95261	0.428
27DAP/17DAP	1.02644	0.915
39DAP/27DAP	1.02433	0.677
41DAP/39DAP	1.02958	0.781
42DAP/41DAP	0.99691	0.907
43DAP/42DAP	1.01566	0.585
47DAP/43DAP	0.99107	0.954
52DAP/47DAP	1.00044	1
57DAP/52DAP	0.97779	0.591
57DAP/7DAP	1.05912	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.88942	0.402
17DAP/reference	1.06925	0.525
27DAP/reference	0.98697	0.53
39DAP/reference	1.01245	1
41DAP/reference	0.84591	0.067
42DAP/reference	0.80849	0.034
43DAP/reference	0.82162	0.016
47DAP/reference	0.81611	0.128
52DAP/reference	0.79547	0.018
57DAP/reference	0.89507	0.066

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.18988	0.193
17DAP/reference	1.08974	0.285
27DAP/reference	0.91701	0.249
39DAP/reference	1.0533	1
41DAP/reference	0.84087	0.042
42DAP/reference	0.83656	0.01
43DAP/reference	1.262	0.112
47DAP/reference	0.951	0.137
52DAP/reference	1.05047	0.667
57DAP/reference	1.22942	0.063

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.13361	0.055
17DAP/reference	0.98738	0.739
27DAP/reference	0.99179	0.691
39DAP/reference	0.96528	0.246
41DAP/reference	0.92921	0.331
42DAP/reference	0.79302	0.041
43DAP/reference	0.7581	0.052
47DAP/reference	0.89467	0.231
52DAP/reference	0.86008	0.087
57DAP/reference	0.53858	0.016

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.91439	0.841
26DAP/20DAP	0.96211	1
34DAP/26DAP	0.97282	0.92
51DAP/34DAP	0.9117	0.333
52DAP/51DAP	0.9319	1
53DAP/52DAP	0.94746	0.712
55DAP/53DAP	0.91815	0.735
57DAP/55DAP	1.16358	0.348
62DAP/57DAP	1.08082	0.8
68DAP/62DAP	0.77659	0.464
68DAP/14DAP	0.51527	0.09

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.97599	0.443

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	15.4004	0.089
Mature Green Tomato/Ripe Tomato	1.16736	0.523
Immature Eggplant/Mature Eggplant	2.52676	N/A
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	3.91102	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.93748	0.944
1-1-2/M82	0.73187	0.804
12-2/M82	1.13702	1
12-4/M82	1.14575	0.611
1-3/M82	0.71612	0.378
2-1-1/M82	1.11262	1
2-1/M82	1.34614	N/A
2-6/M82	1.19061	0.594
3-2/M82	0.94748	1
4-1-1/M82	1.13828	1
4-1/M82	0.95368	1
4-3-2/M82	0.91219	1
4-3/M82	0.67699	0.611
5-3/M82	0.92568	1
6-2/M82	0.99328	1
6-3/M82	0.96971	1
7-1/M82	1.05523	N/A
7-2/M82	1.18479	N/A
9-3-2/M82	0.78059	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.96751	0.243
IL2-6/WTpooled	1.20625	0.584
IL7-5/WTpooled	0.68511	1
IL7-3/WTpooled	1.06309	1
IL12-4/WTpooled	1.00993	1
IL1-4/WTpooled	1.06063	1
WT/WTpooled	1.03593	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	1.07937	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.98361	1
DC3000/delta hrp 6h	1.01809	1
DC3000/delta hrp 12h	0.88383	1
DC3000/delta hrp 24h	0.99381	0.897

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.06735	0.313
DC3000 delta B/DC3000 delta AB	1.26512	0.126

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.09634	1
Exp 36h	1.09779	1
Exp 60h	0.90591	0.754

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98078	1
Var 0h	1.11167	0.936
Var 12h I row2-row1	0.94379	0.856
Var 12h NI row2-row1	1.04072	1
Var 36h I row2-row1	1.10098	1
Var 36h NI row2-row1	0.67813	0.549
Var 60h I row2-row1	0.87501	0.582
Var 60h NI row2-row1	0.94041	0.818
Time course 0hI-0hNI	1.04476	0.63
Time course 12hI-12hNI	1.07952	0.654
Time course 36hI-36hNI	1.495	0.005
Time course 60hI-60hNI	3.65718	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)	1.27677	0.305
transgenic ySAMdc/azygous control (breaker)	1.13625	1
transgenic ySAMdc/azygous control (red)	1.2032	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.1641	0.035

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.74121	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.04354	1
Manapal/WT (break)	1.38358	0.381
Manapal/WT (red)	1.53058	1