Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.1.6.9

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.8619	0.445
27DAP/17DAP	1.28198	0.758
39DAP/27DAP	1.12461	0.725
41DAP/39DAP	0.76525	0.281
42DAP/41DAP	0.86785	1
43DAP/42DAP	1.15217	0.88
47DAP/43DAP	0.90085	0.603
52DAP/47DAP	1.19838	0.844
57DAP/52DAP	1.45883	0.962

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91343	0.067
17DAP/reference	1.13193	0.08
27DAP/reference	0.98515	0.711
39DAP/reference	1.00538	0.975
41DAP/reference	1.01809	1
42DAP/reference	0.92412	0.111
43DAP/reference	1.10657	0.471
47DAP/reference	1.04078	0.885
52DAP/reference	0.96932	0.489
57DAP/reference	0.92982	0.131

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.20044	0.356
27DAP/17DAP	0.95392	0.724
39DAP/27DAP	1.04087	0.718
41DAP/39DAP	0.98483	1
42DAP/41DAP	0.92137	0.484
43DAP/42DAP	1.17784	0.478
47DAP/43DAP	0.82316	0.098
52DAP/47DAP	0.88009	0.233
57DAP/52DAP	0.95274	0.673
57DAP/7DAP	0.82117	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.16587	0.613
17DAP/reference	0.9618	0.447
27DAP/reference	0.68595	0.016
39DAP/reference	1.19697	0.511
41DAP/reference	1.29557	0.28
42DAP/reference	1.13522	0.686
43DAP/reference	0.91559	0.22
47DAP/reference	0.93377	0.504
52DAP/reference	1.43321	0.081
57DAP/reference	0.91193	0.149

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84361	0.115
17DAP/reference	1.09654	0.756
27DAP/reference	0.92699	0.352
39DAP/reference	1.08504	0.764
41DAP/reference	1.17798	0.153
42DAP/reference	0.71014	0.189
43DAP/reference	0.99792	0.774
47DAP/reference	0.92612	0.194
52DAP/reference	1.20729	0.079
57DAP/reference	1.04618	0.64

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.71081	0.329
17DAP/reference	1.11585	0.572
27DAP/reference	0.73272	0.126
39DAP/reference	0.99769	0.889
41DAP/reference	0.90283	0.371
42DAP/reference	1.87445	0.22
43DAP/reference	1.01361	0.858
47DAP/reference	0.91885	0.269
52DAP/reference	1.29461	0.412
57DAP/reference	0.8974	0.097

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.82866	0.89
26DAP/20DAP	1.04295	1
34DAP/26DAP	1.70902	0.819
51DAP/34DAP	0.8426	0.508
52DAP/51DAP	1.03108	0.925
53DAP/52DAP	0.75589	0.136
55DAP/53DAP	1.18635	0.547
57DAP/55DAP	0.98801	0.935
62DAP/57DAP	N/A	N/A
68DAP/62DAP	1.26134	0.422
68DAP/14DAP	2.02609

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.07542	0.415

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	11.7747	0.015
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	3.97424
Mature Eggplant/Ripe Tomato	1.68909

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.85541	0.613
1-1-2/M82	0.79569	0.958
12-2/M82	N/A	N/A
12-4/M82	0.89679	0.619
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	1.02063	1
3-2/M82	N/A	N/A
4-1-1/M82	1.04928	0.977
4-1/M82	N/A	N/A
4-3-2/M82	1.06926
4-3/M82	1.08277	1
5-3/M82	0.8621	0.364
6-2/M82	1.018
6-3/M82	1.07884	1
7-1/M82	N/A	N/A
7-2/M82	0.77714
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.09767	1
IL2-6/WTpooled	0.95118	1
IL7-5/WTpooled	1.20132	0.792
IL7-3/WTpooled	1.14067	1
IL12-4/WTpooled	0.80348	0.543
IL1-4/WTpooled	1.02296	1
WT/WTpooled	0.88913	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	0.91812	0.341

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.88653	0.941
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	0.99028	1
DC3000/delta hrp 24h	1.08732	0.582

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	N/A
DC3000 delta B/DC3000 delta AB	0.80849	0.245

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	1.05498	1
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	0.98533	1
Var 0h	N/A	N/A
Var 12h I row2-row1	0.99871	1
Var 12h NI row2-row1	0.95151	0.82
Var 36h I row2-row1	1.11334	0.742
Var 36h NI row2-row1	1.2755	0.482
Var 60h I row2-row1	0.83586	0.285
Var 60h NI row2-row1	1.17592	0.904
Time course 0hI-0hNI	1.03528	0.63
Time course 12hI-12hNI	0.92677	0.312
Time course 36hI-36hNI	0.76763	0.023
Time course 60hI-60hNI	0.42558	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)	1.20827	0.612
transgenic ySAMdc/azygous control (breaker)	1.62442	0.172
transgenic ySAMdc/azygous control (red)	1.06428	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.97524	0.486

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.90554	0.431

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.31311	0.09
Manapal/WT (break)	1.29718	0.381
Manapal/WT (red)	0.83529	0.181