Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.1.15.15

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.88634	0.486
27DAP/17DAP	1.36546	0.618
39DAP/27DAP	1.0163	0.876
41DAP/39DAP	1.09804	0.788
42DAP/41DAP	0.74729	0.774
43DAP/42DAP	1.01309	0.925
47DAP/43DAP	2.77106	0.285
52DAP/47DAP	2.11995	0.147
57DAP/52DAP	0.73474	0.726

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91617	0.402
17DAP/reference	0.99686	0.957
27DAP/reference	1.00034	1
39DAP/reference	1.00284	1
41DAP/reference	0.97946	0.542
42DAP/reference	0.9434	0.12
43DAP/reference	1.03003	0.269
47DAP/reference	0.9519	0.116
52DAP/reference	0.882	0.189
57DAP/reference	0.97189	0.221

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.1263	0.797
27DAP/17DAP	1.00352	1
39DAP/27DAP	1.09732	0.742
41DAP/39DAP	0.8371	0.265
42DAP/41DAP	0.97541	0.737
43DAP/42DAP	1.09986	0.627
47DAP/43DAP	1.05771	0.92
52DAP/47DAP	1.93343	0.053
57DAP/52DAP	3.45298	0.035
57DAP/7DAP	2.14312	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.14388	0.325
17DAP/reference	1.26736	0.007
27DAP/reference	1.13727	0.008
39DAP/reference	1.30679	0.006
41DAP/reference	1.18325	0.035
42DAP/reference	1.24955	0.006
43DAP/reference	1.43752	0.008
47DAP/reference	1.10207	0.404
52DAP/reference	1.33004	0.009
57DAP/reference	1.50512	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97321	0.655
17DAP/reference	0.94968	0.287
27DAP/reference	0.95149	0.304
39DAP/reference	0.90217	0.119
41DAP/reference	0.86886	0.098
42DAP/reference	0.86396	0.037
43DAP/reference	0.97635	0.592
47DAP/reference	0.91347	0.01
52DAP/reference	1.0129	0.838
57DAP/reference	1.02975	0.807

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.07194	0.518
17DAP/reference	0.94633	0.477
27DAP/reference	1.17049	0.027
39DAP/reference	1.12338	0.069
41DAP/reference	1.06648	0.249
42DAP/reference	0.97685	0.671
43DAP/reference	1.06164	0.667
47DAP/reference	1.00602	1
52DAP/reference	1.1083	0.428
57DAP/reference	0.99689	0.753

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.99109	1
26DAP/20DAP	0.90685	0.512
34DAP/26DAP	0.97239	0.98
51DAP/34DAP	1.00489	0.967
52DAP/51DAP	1.06627	0.722
53DAP/52DAP	0.88896	0.475
55DAP/53DAP	1.22454	0.368
57DAP/55DAP	0.96702	0.821
62DAP/57DAP	1.15724	0.257
68DAP/62DAP	0.88098	0.195
68DAP/14DAP	1.09797	0.936

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.24153	0.212

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.01408	1
Mature Green Tomato/Ripe Tomato	0.10386	0.017
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.12018	0.224
Mature Eggplant/Ripe Tomato	0.08381	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.25481	0.742
1-1-2/M82	1.10681	1
12-2/M82	2.6249
12-4/M82	0.81352	0.619
1-3/M82	1.12804
2-1-1/M82	0.96859	1
2-1/M82	N/A	N/A
2-6/M82	1.74989	0.594
3-2/M82	0.77908
4-1-1/M82	3.08594
4-1/M82	1.00104
4-3-2/M82	N/A	N/A
4-3/M82	1.2338	1
5-3/M82	0.47776	0.419
6-2/M82	N/A	N/A
6-3/M82	1.02263
7-1/M82	0.94792
7-2/M82	1.26366	0.324
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.95867
IL2-6/WTpooled	0.86899	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.97806	1
IL12-4/WTpooled	1.03827	0.891
IL1-4/WTpooled	0.81203
WT/WTpooled	1.07888	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	0.76319	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.30614	0.396
DC3000/delta hrp 6h	1.11484	1
DC3000/delta hrp 12h	1.25123	1
DC3000/delta hrp 24h	1.23027	0.06

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	0.95856	0.745

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.92278	0.328
Exp 36h	N/A	N/A
Exp 60h	1.21908	0.283

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

hybridization	ratio	FDR (corrected p value)
self-self	0.96821	1
Var 0h	0.79667	0.933
Var 12h I row2-row1	1.29167	0.324
Var 12h NI row2-row1	0.74229	0.466
Var 36h I row2-row1	0.83607	0.805
Var 36h NI row2-row1	1.25863	1
Var 60h I row2-row1	1.65051	0.562
Var 60h NI row2-row1	1.22497	0.904
Time course 0hI-0hNI	1.10977	0.799
Time course 12hI-12hNI	1.02552	0.849
Time course 36hI-36hNI	1.00491	0.975
Time course 60hI-60hNI	1.06481	0.254

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)	1.0043	1
transgenic ySAMdc/azygous control (breaker)	0.84152	0.49
transgenic ySAMdc/azygous control (red)	0.92285	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.01407	0.261

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.38265	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.67931	1
Manapal/WT (break)	0.89708	1
Manapal/WT (red)	0.91995	0.607