Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.1.3.21

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.45096	0.443
27DAP/17DAP	1.4626	0.592
39DAP/27DAP	1.07618	0.995
41DAP/39DAP	0.80438	0.328
42DAP/41DAP	1.19689	0.978
43DAP/42DAP	1.2173	0.861
47DAP/43DAP	2.66927	0.668
52DAP/47DAP	0.91107	0.757
57DAP/52DAP	1.3041	0.771

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84075	0.025
17DAP/reference	0.80407	0.008
27DAP/reference	0.95718	0.471
39DAP/reference	0.91121	0.174
41DAP/reference	0.73165	0.026
42DAP/reference	0.85153	0.003
43DAP/reference	0.99977	0.882
47DAP/reference	1.07559	0.989
52DAP/reference	1.34906	0.045
57DAP/reference	1.49179	0.008

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.63968	0.047
27DAP/17DAP	0.8205	0.134
39DAP/27DAP	0.93015	0.488
41DAP/39DAP	1.178	0.656
42DAP/41DAP	0.9047	0.52
43DAP/42DAP	0.8005	0.025
47DAP/43DAP	1.02023	0.939
52DAP/47DAP	0.99308	0.947
57DAP/52DAP	1.13446	0.611
57DAP/7DAP	0.47644

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.41095	0.033
17DAP/reference	1.464	0.023
27DAP/reference	1.31256	0.06
39DAP/reference	1.89024	0.008
41DAP/reference	1.78871	0.013
42DAP/reference	1.78156	0.013
43DAP/reference	1.80162	0.012
47DAP/reference	1.41876	0.043
52DAP/reference	1.61588	0.008
57DAP/reference	1.73907	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.80118	0.009
17DAP/reference	0.81385	0.086
27DAP/reference	1.00177	1
39DAP/reference	0.99058	0.682
41DAP/reference	1.20435	0.269
42DAP/reference	0.91515	0.237
43DAP/reference	0.79425	0.082
47DAP/reference	0.90299	0.056
52DAP/reference	0.90191	0.009
57DAP/reference	0.77722	0.046

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.23844	0.153
17DAP/reference	1.01646	0.839
27DAP/reference	1.43097	0.038
39DAP/reference	1.62313	0.017
41DAP/reference	1.61772	0.01
42DAP/reference	1.46052	0.011
43DAP/reference	1.57616	0.02
47DAP/reference	0.94371	0.383
52DAP/reference	1.61025	0.058
57DAP/reference	1.95978	0.007

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.92764	1
26DAP/20DAP	1.14513	0.629
34DAP/26DAP	0.82116	0.619
51DAP/34DAP	1.23866	0.73
52DAP/51DAP	1.21351	0.733
53DAP/52DAP	1.16261	0.83
55DAP/53DAP	1.07992	0.927
57DAP/55DAP	0.82036	0.508
62DAP/57DAP	0.79607	0.681
68DAP/62DAP	1.59032	0.202
68DAP/14DAP	2.05819	0.024

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.42531	0.369

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.9457	0.591
Mature Green Tomato/Ripe Tomato	1.27085	0.119
Immature Eggplant/Mature Eggplant	1.13311	0.528
Ripe Pepper/Ripe Tomato	9.58333	0.258
Mature Eggplant/Ripe Tomato	0.75973

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	0.61191	0.33
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	N/A	N/A
5-3/M82	1.28371
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	1.01471
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	1.11772	0.365
IL2-6/WTpooled	0.68703
IL7-5/WTpooled	0.81607	1
IL7-3/WTpooled	1.01344
IL12-4/WTpooled	1.01583	1
IL1-4/WTpooled	1.21618	0.421
WT/WTpooled	0.91733	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	1.12318	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.63732
DC3000/delta hrp 6h	1.38593	0.95
DC3000/delta hrp 12h	0.91467	1
DC3000/delta hrp 24h	0.8208	0.198

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.19993
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	1.31324	1
Exp 36h	N/A	N/A
Exp 60h	1.1521	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.94185	1
Var 0h	0.86053	1
Var 12h I row2-row1	0.89857	0.39
Var 12h NI row2-row1	1.19605	1
Var 36h I row2-row1	1.19043	0.489
Var 36h NI row2-row1	1.12681	1
Var 60h I row2-row1	1.19595	0.483
Var 60h NI row2-row1	0.82997	0.298
Time course 0hI-0hNI	0.95811	0.721
Time course 12hI-12hNI	0.97614	0.831
Time course 36hI-36hNI	1.10087	0.651
Time course 60hI-60hNI	1.06935	0.495

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)	1.18774	0.339
transgenic ySAMdc/azygous control (breaker)	0.97744	1
transgenic ySAMdc/azygous control (red)	1.25867	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.27704	0.038

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.72585	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.05713	1
Manapal/WT (break)	1.74125	0.381
Manapal/WT (red)	1.02372	1