Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.2.10.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.88982	0.496
27DAP/17DAP	0.68724	0.102
39DAP/27DAP	0.9007	0.583
41DAP/39DAP	0.68405	0.113
42DAP/41DAP	0.92543	1
43DAP/42DAP	1.01494	0.94
47DAP/43DAP	1.06323	0.442
52DAP/47DAP	0.9693	0.81
57DAP/52DAP	0.86414	0.622

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.18818	0.11
17DAP/reference	0.81299	0.033
27DAP/reference	0.92121	0.385
39DAP/reference	0.78386	0.028
41DAP/reference	0.72978	0.011
42DAP/reference	1.01428	1
43DAP/reference	0.8246	0.047
47DAP/reference	0.96314	0.322
52DAP/reference	1.14099	0.272
57DAP/reference	1.04107	0.662

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.99367	0.801
27DAP/17DAP	1.02909	0.957
39DAP/27DAP	0.80992	0.274
41DAP/39DAP	1.25803	0.801
42DAP/41DAP	0.96906	0.721
43DAP/42DAP	0.92758	0.576
47DAP/43DAP	0.93557	0.617
52DAP/47DAP	0.96395	0.876
57DAP/52DAP	0.90701	0.628
57DAP/7DAP	0.77226	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.6147	0.027
17DAP/reference	1.4988	0.006
27DAP/reference	1.13627	0.107
39DAP/reference	1.08544	0.101
41DAP/reference	1.06884	0.43
42DAP/reference	1.07862	0.405
43DAP/reference	1.20872	0.099
47DAP/reference	1.00531	1
52DAP/reference	1.033	0.941
57DAP/reference	0.92433	0.162

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01616	0.951
17DAP/reference	0.915	0.239
27DAP/reference	1.16858	0.359
39DAP/reference	1.04898	1
41DAP/reference	1.07418	1
42DAP/reference	1.08264	0.583
43DAP/reference	0.71852	0.031
47DAP/reference	0.87605	0.12
52DAP/reference	0.76613	0.008
57DAP/reference	0.63687	0.021

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.18461	0.019
17DAP/reference	1.0405	0.932
27DAP/reference	1.07958	0.227
39DAP/reference	1.38189	0.069
41DAP/reference	1.0691	0.383
42DAP/reference	1.24014	0.239
43DAP/reference	1.37679	0.038
47DAP/reference	1.06453	0.731
52DAP/reference	0.966	0.637
57DAP/reference	1.59382	0.029

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.02778
26DAP/20DAP	1.16005	0.421
34DAP/26DAP	0.97848	0.944
51DAP/34DAP	1.10775	0.654
52DAP/51DAP	1.00826	1
53DAP/52DAP	1.07174	0.783
55DAP/53DAP	1.02644	0.948
57DAP/55DAP	0.93389	0.694
62DAP/57DAP	0.96897	0.994
68DAP/62DAP	1.29657	0.353
68DAP/14DAP	1.68779	0.03

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.289	0.057

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.30196	0.666
Mature Green Tomato/Ripe Tomato	1.94674	0.149
Immature Eggplant/Mature Eggplant	1.75781	0.055
Ripe Pepper/Ripe Tomato	3.27275	1
Mature Eggplant/Ripe Tomato	13.0563	1

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	N/A	N/A
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	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.76568	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	1.12435	0.673
IL1-4/WTpooled	1.1166	1
WT/WTpooled	1.01199	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	0.90659	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.85355	0.941
DC3000/delta hrp 6h	1.09355	1
DC3000/delta hrp 12h	1.07458	1
DC3000/delta hrp 24h	0.84897	0.119

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.73542	0.024
DC3000 delta B/DC3000 delta AB	0.71713	0.027

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.807	1
Exp 36h	0.92386	0.82
Exp 60h	0.71399	0.386

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00356	1
Var 0h	0.54444	1
Var 12h I row2-row1	0.7326	0.338
Var 12h NI row2-row1	0.96629	0.82
Var 36h I row2-row1	0.91138	1
Var 36h NI row2-row1	0.9996	1
Var 60h I row2-row1	0.92898	0.439
Var 60h NI row2-row1	1.00425	1
Time course 0hI-0hNI	0.96621	0.845
Time course 12hI-12hNI	1.00429	1
Time course 36hI-36hNI	1.02707	0.799
Time course 60hI-60hNI	0.52306	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)	1.05725	0.612
transgenic ySAMdc/azygous control (breaker)	0.99518	1
transgenic ySAMdc/azygous control (red)	0.94623	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.96749	0.112

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.26389	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	2.18839	0.093
Manapal/WT (break)	1.5986	0.13
Manapal/WT (red)	2.41397	0.133