Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-6.3.12.3

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.86807	0.436
27DAP/17DAP	0.91402	0.819
39DAP/27DAP	0.79232	0.435
41DAP/39DAP	1.12666	0.663
42DAP/41DAP	1.17141	0.877
43DAP/42DAP	1.12938	1
47DAP/43DAP	0.98224	0.859
52DAP/47DAP	0.97875	0.828
57DAP/52DAP	1.2916	0.969

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.30806	0.093
17DAP/reference	0.76931	0.031
27DAP/reference	0.9668	0.595
39DAP/reference	1.15703	0.318
41DAP/reference	0.90141	0.341
42DAP/reference	1.50644	0.001
43DAP/reference	1.3795	0.013
47DAP/reference	1.45351	0.001
52DAP/reference	1.37755	0.102
57DAP/reference	1.68352	0.008

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.98378	0.75
27DAP/17DAP	0.9604	0.854
39DAP/27DAP	0.72471	0.068
41DAP/39DAP	1.15261	0.774
42DAP/41DAP	0.92318	0.499
43DAP/42DAP	0.74968	0.029
47DAP/43DAP	0.85212	0.243
52DAP/47DAP	1.17589	0.563
57DAP/52DAP	0.95131	0.721
57DAP/7DAP	1.06319	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92775	0.402
17DAP/reference	1.13488	0.297
27DAP/reference	1.12115	0.551
39DAP/reference	0.88193	0.17
41DAP/reference	1.00111	0.512
42DAP/reference	0.92926	0.275
43DAP/reference	1.13062	0.289
47DAP/reference	1.54949	0.353
52DAP/reference	0.94905	0.398
57DAP/reference	1.30704	0.17

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92189	0.487
17DAP/reference	0.95495	0.461
27DAP/reference	1.38606	0.166
39DAP/reference	1.55031	0.061
41DAP/reference	2.233	0.005
42DAP/reference	1.65303	0.008
43DAP/reference	1.60682	0.053
47DAP/reference	1.75001	0.008
52DAP/reference	1.14701	0.279
57DAP/reference	1.00105	0.68

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93818	0.135
17DAP/reference	1.22789	0.347
27DAP/reference	1.26056	0.038
39DAP/reference	0.95641	0.36
41DAP/reference	1.21517	0.439
42DAP/reference	1.33608	0.391
43DAP/reference	1.21827	0.827
47DAP/reference	1.59352	0.11
52DAP/reference	0.8638	0.342
57DAP/reference	2.55314	0.026

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.71655	0.966
26DAP/20DAP	1.00018	1
34DAP/26DAP	2.22093	1
51DAP/34DAP	0.97118	0.698
52DAP/51DAP	3.95314	0.033
53DAP/52DAP	0.9177	0.677
55DAP/53DAP	1.30445	0.124
57DAP/55DAP	0.37851	0.019
62DAP/57DAP	1.8962	0.013
68DAP/62DAP	4.2482	0.102
68DAP/14DAP	5.43642	0.016

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.87812	0.466

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	8.83373	0.015
Immature Eggplant/Mature Eggplant	1.01604	1
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	15.0069	N/A

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	0.76172	N/A
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	0.59071	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	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.94708	N/A
IL2-6/WTpooled	1.17114	0.788
IL7-5/WTpooled	1.12773	1
IL7-3/WTpooled	1.11848	1
IL12-4/WTpooled	1.04567	1
IL1-4/WTpooled	0.85686	0.444
WT/WTpooled	1.09026	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	1.30001	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.52165	N/A
DC3000/delta hrp 6h	0.8699	0.95
DC3000/delta hrp 12h	1.00806	1
DC3000/delta hrp 24h	2.437	0.118

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.67206	0.023
DC3000 delta B/DC3000 delta AB	0.68848	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.09172	1
Exp 36h	N/A	N/A
Exp 60h	0.48487	0.29

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98506	1
Var 0h	1.12285	0.782
Var 12h I row2-row1	0.63531	0.344
Var 12h NI row2-row1	0.87771	0.438
Var 36h I row2-row1	0.7386	0.805
Var 36h NI row2-row1	1.20699	0.482
Var 60h I row2-row1	1.66326	0.543
Var 60h NI row2-row1	0.94627	1
Time course 0hI-0hNI	1.02211	0.867
Time course 12hI-12hNI	0.97222	0.698
Time course 36hI-36hNI	0.79805	0.023
Time course 60hI-60hNI	0.1047	0.005

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)	1.03493	1
transgenic ySAMdc/azygous control (breaker)	1.17354	1
transgenic ySAMdc/azygous control (red)	1.29671	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.96494	0.104

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.87309	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.84647	0.14
Manapal/WT (break)	1.87365	0.381
Manapal/WT (red)	N/A	N/A