Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.3.19.19

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.88217	0.464
27DAP/17DAP	1.23683	0.845
39DAP/27DAP	1.34765	0.558
41DAP/39DAP	0.88612	0.615
42DAP/41DAP	0.76235	0.774
43DAP/42DAP	1.04467	0.937
47DAP/43DAP	1.18904	0.756
52DAP/47DAP	1.52658	0.327
57DAP/52DAP	2.04973	0.955

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90254	0.293
17DAP/reference	1.0162	1
27DAP/reference	1.10894	0.648
39DAP/reference	1.02385	0.747
41DAP/reference	0.86896	0.341
42DAP/reference	0.9782	0.413
43DAP/reference	1.19619	0.325
47DAP/reference	1.21549	0.495
52DAP/reference	0.96881	0.475
57DAP/reference	1.15284	0.249

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.33598	0.069
27DAP/17DAP	1.19378	0.645
39DAP/27DAP	0.87915	0.601
41DAP/39DAP	1.40434	0.336
42DAP/41DAP	0.7141	0.201
43DAP/42DAP	0.93914	0.684
47DAP/43DAP	1.23403	0.788
52DAP/47DAP	1.17077	0.927
57DAP/52DAP	1.5549	0.611
57DAP/7DAP	1.63828	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87522	0.115
17DAP/reference	0.93846	0.072
27DAP/reference	0.95882	0.109
39DAP/reference	0.87249	0.012
41DAP/reference	0.75118	0.024
42DAP/reference	0.65895	0.01
43DAP/reference	0.84273	0.069
47DAP/reference	0.89408	0.383
52DAP/reference	0.75124	0.027
57DAP/reference	0.76106	0.032

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.83901	0.14
17DAP/reference	0.94958	0.548
27DAP/reference	1.1008	0.367
39DAP/reference	0.93855	0.33
41DAP/reference	0.97343	0.459
42DAP/reference	0.98173	0.594
43DAP/reference	1.02896	1
47DAP/reference	0.94573	0.188
52DAP/reference	1.02874	1
57DAP/reference	1.0757	0.649

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90512	0.05
17DAP/reference	0.85237	0.221
27DAP/reference	1.00682	0.843
39DAP/reference	0.87794	0.025
41DAP/reference	0.89821	0.05
42DAP/reference	0.93446	0.22
43DAP/reference	1.08449	0.599
47DAP/reference	1.29221	1
52DAP/reference	1.05588	0.952
57DAP/reference	1.00189	0.79

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.83772	1
26DAP/20DAP	1.1314	0.793
34DAP/26DAP	2.38298	0.819
51DAP/34DAP	1.39931	0.613
52DAP/51DAP	1.26445	0.783
53DAP/52DAP	0.70692
55DAP/53DAP	1.06265	0.964
57DAP/55DAP	0.74853	0.452
62DAP/57DAP	1.05691	1
68DAP/62DAP	0.72966	0.049
68DAP/14DAP	0.57216

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.05366	0.855

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.67405	0.331
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.41404	1
Mature Eggplant/Ripe Tomato	2.09436

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.93755	0.944
1-1-2/M82	0.8297
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	0.96022
5-3/M82	0.96528	1
6-2/M82	N/A	N/A
6-3/M82	1.43511
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	0.92118	1
IL7-5/WTpooled	0.52654
IL7-3/WTpooled	1.11778	1
IL12-4/WTpooled	1.13324	0.538
IL1-4/WTpooled	1.12038	1
WT/WTpooled	1.01038	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	0.87568	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.82111	1
DC3000/delta hrp 6h	1.03571	0.95
DC3000/delta hrp 12h	0.93311	1
DC3000/delta hrp 24h	0.79348	0.04

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	N/A	N/A
Exp 36h	N/A	N/A
Exp 60h	0.88309	0.249

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

hybridization	ratio	FDR (corrected p value)
self-self	1.25435	1
Var 0h	0.39574	1
Var 12h I row2-row1	1.39093	0.443
Var 12h NI row2-row1	1.33412	1
Var 36h I row2-row1	1.24812	1
Var 36h NI row2-row1	0.66064	0.61
Var 60h I row2-row1	0.99958	1
Var 60h NI row2-row1	0.77137	0.977
Time course 0hI-0hNI	1.12688	0.852
Time course 12hI-12hNI	1.18144	0.587
Time course 36hI-36hNI	1.13925	0.401
Time course 60hI-60hNI	0.83521	0.319

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)	1.01964	0.921
transgenic ySAMdc/azygous control (breaker)	0.78204	0.251
transgenic ySAMdc/azygous control (red)	1.08698	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.04881	0.811

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.81189	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.94507	1
Manapal/WT (break)	1.11438	0.381
Manapal/WT (red)	0.90934	0.181