Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.4.14.19

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.97721	0.847
27DAP/17DAP	3.75149	0.293
39DAP/27DAP	0.85345	0.583
41DAP/39DAP	1.23003	0.084
42DAP/41DAP	0.85801	1
43DAP/42DAP	0.85607	0.613
47DAP/43DAP	1.29322	0.595
52DAP/47DAP	1.28663	0.786
57DAP/52DAP	1.08775	0.992

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.78368	0.029
17DAP/reference	0.89753	0.079
27DAP/reference	1.00122	0.847
39DAP/reference	0.89602	0.213
41DAP/reference	0.83377	0.021
42DAP/reference	0.93159	0.139
43DAP/reference	0.93667	0.287
47DAP/reference	0.96575	0.345
52DAP/reference	1.11077	0.335
57DAP/reference	0.92881	0.248

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	3.33253	0.34
27DAP/17DAP	1.3129	0.154
39DAP/27DAP	0.83948	0.412
41DAP/39DAP	1.75566	0.207
42DAP/41DAP	1.42682	0.759
43DAP/42DAP	0.83915	0.415
47DAP/43DAP	1.3744	0.281
52DAP/47DAP	1.01815	0.982
57DAP/52DAP	1.88476	0.083
57DAP/7DAP	1.27855

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.07804	0.664
17DAP/reference	1.35232	0.03
27DAP/reference	1.21989	0.02
39DAP/reference	1.28056	0.007
41DAP/reference	1.26039	0.054
42DAP/reference	1.29818	0.012
43DAP/reference	1.43475	0.009
47DAP/reference	1.06309	0.745
52DAP/reference	1.16601	0.113
57DAP/reference	1.30239	0.008

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.81018	0.034
17DAP/reference	0.74978	0.009
27DAP/reference	0.84172	0.022
39DAP/reference	0.89081	0.074
41DAP/reference	0.90248	0.152
42DAP/reference	0.94507	0.108
43DAP/reference	0.73916	0.019
47DAP/reference	0.86685	0.094
52DAP/reference	0.87831	0.101
57DAP/reference	0.89691	0.278

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.43538	0.016
17DAP/reference	1.34652	0.279
27DAP/reference	1.53335	0.021
39DAP/reference	1.39862	0.018
41DAP/reference	1.1716	0.168
42DAP/reference	1.19577	0.364
43DAP/reference	1.02234	1
47DAP/reference	0.94252	0.259
52DAP/reference	1.27801	0.398
57DAP/reference	1.21971	0.118

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.06992	1
26DAP/20DAP	0.99045	1
34DAP/26DAP	1.28937	1
51DAP/34DAP	1.1055	0.978
52DAP/51DAP	2.57322	0.047
53DAP/52DAP	1.92316	0.723
55DAP/53DAP	1.21897	0.434
57DAP/55DAP	0.87814	0.433
62DAP/57DAP	1.18259	0.833
68DAP/62DAP	1.08354	0.956
68DAP/14DAP	1.28424	0.453

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.87068	0.399

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.94745
Immature Eggplant/Mature Eggplant	0.34857
Ripe Pepper/Ripe Tomato	0.65629	0.293
Mature Eggplant/Ripe Tomato	N/A	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.75115
12-2/M82	1.02599
12-4/M82	0.95841
1-3/M82	N/A	N/A
2-1-1/M82	1.07606
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	0.8503
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	1.03613

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.67225	0.277
IL2-6/WTpooled	1.03625	1
IL7-5/WTpooled	2.2047	0.792
IL7-3/WTpooled	0.79716	0.418
IL12-4/WTpooled	0.91336	0.71
IL1-4/WTpooled	0.7907	0.699
WT/WTpooled	1.04935	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	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.24486	0.921
DC3000/delta hrp 6h	2.21812
DC3000/delta hrp 12h	0.98162	1
DC3000/delta hrp 24h	N/A	N/A

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	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.96331	1
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	N/A	N/A
Var 0h	0.68071	1
Var 12h I row2-row1	0.75152	0.77
Var 12h NI row2-row1	0.65535
Var 36h I row2-row1	1.13556
Var 36h NI row2-row1	1.15315	1
Var 60h I row2-row1	0.8909	0.582
Var 60h NI row2-row1	1.32478
Time course 0hI-0hNI	0.91717	0.824
Time course 12hI-12hNI	0.41207	1
Time course 36hI-36hNI	1.93184	0.28
Time course 60hI-60hNI	4.43872	0.115

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)	1.17904	0.397
transgenic ySAMdc/azygous control (breaker)	0.94235	1
transgenic ySAMdc/azygous control (red)	1.58761	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.92612	0.056

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.74378	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.64144	1
Manapal/WT (break)	0.98416	1
Manapal/WT (red)	0.8508	0.607