Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.3.13.16

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.05133	0.863
27DAP/17DAP	1.02086	0.92
39DAP/27DAP	0.99204	0.82
41DAP/39DAP	0.8915	0.568
42DAP/41DAP	1.01283	1
43DAP/42DAP	1.05932	0.993
47DAP/43DAP	1.10879	0.527
52DAP/47DAP	0.86038	0.612
57DAP/52DAP	0.99783	0.988

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97541	0.362
17DAP/reference	1.00193	0.874
27DAP/reference	1.03013	0.405
39DAP/reference	0.97736	0.513
41DAP/reference	1.03616	0.667
42DAP/reference	0.97735	0.188
43DAP/reference	0.97714	0.675
47DAP/reference	1.01034	0.817
52DAP/reference	0.97248	0.449
57DAP/reference	1.03954	0.643

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.00468	1
27DAP/17DAP	1.02537	0.942
39DAP/27DAP	1.02022	0.718
41DAP/39DAP	0.9837	1
42DAP/41DAP	0.98331	0.776
43DAP/42DAP	0.98622	0.684
47DAP/43DAP	0.99685	0.997
52DAP/47DAP	1.03432	0.851
57DAP/52DAP	1.02788	0.864
57DAP/7DAP	0.98471	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.88822	0.046
17DAP/reference	3.30961	0.006
27DAP/reference	2.52011	0.006
39DAP/reference	3.05041	0.005
41DAP/reference	3.27779	0.011
42DAP/reference	3.47654	0.006
43DAP/reference	4.44485	0.007
47DAP/reference	2.83331	0.121
52DAP/reference	3.1906	0.007
57DAP/reference	2.73212	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00311	1
17DAP/reference	1.0083	0.873
27DAP/reference	0.93764	0.16
39DAP/reference	0.97657	0.359
41DAP/reference	0.91165	0.121
42DAP/reference	0.99214	0.655
43DAP/reference	0.84713	0.269
47DAP/reference	1.05735	0.079
52DAP/reference	0.99831	0.713
57DAP/reference	1.01234	0.786

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.16579	0.19
17DAP/reference	1.5395	0.45
27DAP/reference	3.41032	0.025
39DAP/reference	3.2475	0.011
41DAP/reference	2.35609	0.024
42DAP/reference	2.58508	0.016
43DAP/reference	2.32759	0.042
47DAP/reference	1.00431	0.754
52DAP/reference	2.9571	0.086
57DAP/reference	1.86246	0.47

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.01253	0.966
26DAP/20DAP	1.02384	0.953
34DAP/26DAP	1.07256	1
51DAP/34DAP	0.99814	0.96
52DAP/51DAP	1.00348	0.954
53DAP/52DAP	1.04618	0.697
55DAP/53DAP	1.00226	0.964
57DAP/55DAP	1.10361	0.997
62DAP/57DAP	0.94088	0.681
68DAP/62DAP	1.0093	1
68DAP/14DAP	1.2287	0.419

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.97692	0.422

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.92739	0.577
Mature Green Tomato/Ripe Tomato	0.95545	0.487
Immature Eggplant/Mature Eggplant	1.5832	0.105
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	2.8549

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.9755	0.944
1-1-2/M82	0.98908	1
12-2/M82	0.89096	0.955
12-4/M82	0.96988	0.619
1-3/M82	1.00268	1
2-1-1/M82	0.84229	0.565
2-1/M82	1.1377	1
2-6/M82	0.96728	1
3-2/M82	0.90204	0.752
4-1-1/M82	0.98457	1
4-1/M82	0.89639	0.737
4-3-2/M82	0.89208	1
4-3/M82	0.99648	1
5-3/M82	0.99315	1
6-2/M82	1.06285	1
6-3/M82	0.99364	1
7-1/M82	1.07725	0.598
7-2/M82	0.96886	1
9-3-2/M82	0.8479	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.95473	1
IL2-6/WTpooled	1.15726	0.584
IL7-5/WTpooled	1.06141	1
IL7-3/WTpooled	0.74988	0.298
IL12-4/WTpooled	0.92893	0.71
IL1-4/WTpooled	1.06137	1
WT/WTpooled	0.9496	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	0.62363

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.01594	0.921
DC3000/delta hrp 6h	1.22405	1
DC3000/delta hrp 12h	0.97719	1
DC3000/delta hrp 24h	1.07768	0.322

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.23318	0.042
DC3000 delta B/DC3000 delta AB	1.24649	0.129

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	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	0.95851	1
Var 0h	0.89074	0.457
Var 12h I row2-row1	1.18039	0.198
Var 12h NI row2-row1	0.9436	0.906
Var 36h I row2-row1	1.30403	1
Var 36h NI row2-row1	1.05454	1
Var 60h I row2-row1	1.13193	0.562
Var 60h NI row2-row1	1.03391	1
Time course 0hI-0hNI	1.06768	0.852
Time course 12hI-12hNI	1.02095	0.854
Time course 36hI-36hNI	0.93256	0.28
Time course 60hI-60hNI	1.11484	0.017

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)	0.87009	0.454
transgenic ySAMdc/azygous control (breaker)	1.66392	0.248
transgenic ySAMdc/azygous control (red)	1.43049	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.97176	0.092

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.20571	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.3509	0.105
Manapal/WT (break)	0.82579	1
Manapal/WT (red)	0.8821	0.36