Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.1.3.17

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.37581	0.014
27DAP/17DAP	0.66361	0.185
39DAP/27DAP	1.11993	0.899
41DAP/39DAP	1.13173	0.949
42DAP/41DAP	0.81265	1
43DAP/42DAP	0.78454	0.664
47DAP/43DAP	1.05209	0.965
52DAP/47DAP	0.84503	0.666
57DAP/52DAP	0.88312	0.622

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94118	0.362
17DAP/reference	0.70445	0.011
27DAP/reference	0.82707	0.012
39DAP/reference	0.9565	0.704
41DAP/reference	0.66535	0.008
42DAP/reference	0.72168	0.001
43DAP/reference	0.70514
47DAP/reference	0.6986	0.003
52DAP/reference	1.20946	0.096
57DAP/reference	1.32486

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.82319	0.27
27DAP/17DAP	0.83301	0.537
39DAP/27DAP	0.90539	0.529
41DAP/39DAP	1.17857	0.663
42DAP/41DAP	1.08012	0.961
43DAP/42DAP	1.19157	0.413
47DAP/43DAP	1.06459	0.941
52DAP/47DAP	1.35753	0.969
57DAP/52DAP	0.9541	0.697
57DAP/7DAP	0.78472

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.38727	0.057
17DAP/reference	1.6491	0.006
27DAP/reference	1.50819	0.009
39DAP/reference	1.84172	0.005
41DAP/reference	1.64423	0.01
42DAP/reference	1.73195	0.013
43DAP/reference	1.85058	0.009
47DAP/reference	1.25658	0.169
52DAP/reference	1.51212	0.007
57DAP/reference	1.35871	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.22959	0.33
17DAP/reference	0.65932	0.005
27DAP/reference	0.81375	0.029
39DAP/reference	0.99163	0.554
41DAP/reference	1.04443	0.925
42DAP/reference	1.06497	0.583
43DAP/reference	0.82065	0.037
47DAP/reference	1.04918	0.589
52DAP/reference	0.95719	0.22
57DAP/reference	0.6563	0.009

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.87688	0.046
17DAP/reference	1.09748	0.977
27DAP/reference	1.36641	0.088
39DAP/reference	1.29674	0.062
41DAP/reference	1.40025	0.009
42DAP/reference	1.85748	0.008
43DAP/reference	1.60119	0.025
47DAP/reference	0.9135	0.325
52DAP/reference	1.53339	0.324
57DAP/reference	2.38187	0.007

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.99231	1
26DAP/20DAP	1.54793	0.121
34DAP/26DAP	0.95899	0.97
51DAP/34DAP	1.73208
52DAP/51DAP	1.5902	0.377
53DAP/52DAP	1.00245	1
55DAP/53DAP	1.88156	0.681
57DAP/55DAP	0.84635	0.41
62DAP/57DAP	1.57682	0.723
68DAP/62DAP	2.89501	0.013
68DAP/14DAP	4.00178	0.018

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.07538	1

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.14546	0.666
Mature Green Tomato/Ripe Tomato	N/A	N/A
Immature Eggplant/Mature Eggplant	3.21178	0.05
Ripe Pepper/Ripe Tomato	0.88035	1
Mature Eggplant/Ripe Tomato	9.9833	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.12104	0.742
1-1-2/M82	0.96947
12-2/M82	1.29101
12-4/M82	1.1394	1
1-3/M82	0.76561	0.378
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	0.88131	0.501
3-2/M82	0.93505
4-1-1/M82	0.92978	1
4-1/M82	1.08452	1
4-3-2/M82	0.95255
4-3/M82	0.84548
5-3/M82	0.98726	1
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	1.11324
7-2/M82	0.82869	0.578
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.81757	0.243
IL2-6/WTpooled	0.85362	1
IL7-5/WTpooled	0.94967	1
IL7-3/WTpooled	1.09994	1
IL12-4/WTpooled	1.00209	1
IL1-4/WTpooled	1.02789	1
WT/WTpooled	0.98254	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	1.01678	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.07249	0.894
DC3000/delta hrp 6h	1.29804	1
DC3000/delta hrp 12h	0.91984	1
DC3000/delta hrp 24h	3.3532	0.029

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.12908	0.384
DC3000 delta B/DC3000 delta AB	1.08197	0.535

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.03043	1
Exp 36h	1.3438	0.409
Exp 60h	1.10107	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.02788
Var 0h	0.97703	1
Var 12h I row2-row1	0.9496	0.856
Var 12h NI row2-row1	1.06469
Var 36h I row2-row1	1.0424	0.283
Var 36h NI row2-row1	1.00159	1
Var 60h I row2-row1	1.79359
Var 60h NI row2-row1	1.30524	0.904
Time course 0hI-0hNI	1.07686	0.833
Time course 12hI-12hNI	1.08342	0.693
Time course 36hI-36hNI	1.02024	0.975
Time course 60hI-60hNI	1.21577	0.042

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)	0.82992	0.237
transgenic ySAMdc/azygous control (breaker)	0.90803	0.251
transgenic ySAMdc/azygous control (red)	1.02577	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.99261	0.651

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.6488	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.09468	0.14
Manapal/WT (break)	0.97841	1
Manapal/WT (red)	1.14864	0.413