Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.3.4.16

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.89384	0.456
27DAP/17DAP	1.17553	0.842
39DAP/27DAP	0.68555	0.241
41DAP/39DAP	1.27407	0.225
42DAP/41DAP	1.17757	0.913
43DAP/42DAP	1.1744	0.875
47DAP/43DAP	1.15423	0.793
52DAP/47DAP	0.74483	0.39
57DAP/52DAP	1.03523	0.983

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96419	0.455
17DAP/reference	1.07735	0.039
27DAP/reference	1.01033	0.847
39DAP/reference	1.01284	0.771
41DAP/reference	1.07233	0.203
42DAP/reference	0.85982	0.009
43DAP/reference	0.99681	0.882
47DAP/reference	1.00609	0.764
52DAP/reference	0.88893	0.147
57DAP/reference	0.89353	0.156

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.87115	0.454
27DAP/17DAP	1.03696	0.924
39DAP/27DAP	1.11886	0.575
41DAP/39DAP	1.37675	0.02
42DAP/41DAP	0.89989	0.443
43DAP/42DAP	1.26443	0.023
47DAP/43DAP	1.1192	0.641
52DAP/47DAP	0.97739	0.919
57DAP/52DAP	1.32603	0.164
57DAP/7DAP	1.08175	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90643
17DAP/reference	N/A	N/A
27DAP/reference	2.93139	0.007
39DAP/reference	3.38881	0.005
41DAP/reference	3.05832	0.027
42DAP/reference	4.02359
43DAP/reference	4.9048	0.006
47DAP/reference	1.88959	0.514
52DAP/reference	3.50723	0.01
57DAP/reference	3.9678	0.003

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.40613	0.47
17DAP/reference	1.53315	0.33
27DAP/reference	0.88188	0.16
39DAP/reference	0.89161	0.281
41DAP/reference	1.00429	0.735
42DAP/reference	0.96619	0.433
43DAP/reference	0.80812	0.186
47DAP/reference	0.98005	0.319
52DAP/reference	1.03272	0.343
57DAP/reference	1.1084	0.034

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.64261	0.153
17DAP/reference	2.00245	0.563
27DAP/reference	4.00788	0.105
39DAP/reference	0.94415	0.014
41DAP/reference	2.52149	0.1
42DAP/reference	1.54543	0.701
43DAP/reference	1.56591	0.58
47DAP/reference	0.96815	0.396
52DAP/reference	2.61226	0.153
57DAP/reference	0.77596	0.04

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.02964	0.966
26DAP/20DAP	0.98346	1
34DAP/26DAP	0.90528	0.857
51DAP/34DAP	1.07121	0.988
52DAP/51DAP	1.0621	0.431
53DAP/52DAP	0.7183	0.489
55DAP/53DAP	1.08703	0.813
57DAP/55DAP	1.04618	0.975
62DAP/57DAP	0.94846	0.681
68DAP/62DAP	1.03121	1
68DAP/14DAP	0.64394	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.91234	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	0.68599	0.182
Immature Eggplant/Mature Eggplant	2.33701	0.05
Ripe Pepper/Ripe Tomato	0.84201
Mature Eggplant/Ripe Tomato	0.70288	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.92772	0.944
1-1-2/M82	0.95996	1
12-2/M82	N/A	N/A
12-4/M82	0.99445	1
1-3/M82	0.80319	0.378
2-1-1/M82	1.19133
2-1/M82	N/A	N/A
2-6/M82	1.13907	0.594
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	1.07067	1
6-2/M82	1.43483	1
6-3/M82	1.36674
7-1/M82	0.91155
7-2/M82	0.96584
9-3-2/M82	0.40259

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.88053	0.243
IL2-6/WTpooled	1.41132	1
IL7-5/WTpooled	0.97545	1
IL7-3/WTpooled	4.15477	0.362
IL12-4/WTpooled	1.43478	0.557
IL1-4/WTpooled	1.32125	1
WT/WTpooled	1.10397	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	0.94915	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.04362	0.921
DC3000/delta hrp 6h	1.03648	1
DC3000/delta hrp 12h	0.99646	1
DC3000/delta hrp 24h	1.08052	0.422

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	0.99592	1
Exp 36h	0.87605	0.699
Exp 60h	0.79178	0.386

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	1.21661	0.782
Var 12h I row2-row1	N/A	N/A
Var 12h NI row2-row1	N/A	N/A
Var 36h I row2-row1	N/A	N/A
Var 36h NI row2-row1	N/A	N/A
Var 60h I row2-row1	N/A	N/A
Var 60h NI row2-row1	N/A	N/A
Time course 0hI-0hNI	N/A	N/A
Time course 12hI-12hNI	N/A	N/A
Time course 36hI-36hNI	N/A	N/A
Time course 60hI-60hNI	N/A	N/A

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)	1.25002	0.431
transgenic ySAMdc/azygous control (breaker)	1.12404	1
transgenic ySAMdc/azygous control (red)	1.13029	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.98925	0.588

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.11447	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	2.2323	0.083
Manapal/WT (break)	1.12186	0.381
Manapal/WT (red)	0.95405	0.728