Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.2.10.18

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.83747	0.297
27DAP/17DAP	0.98428	1
39DAP/27DAP	1.23131	0.47
41DAP/39DAP	0.74377	0.205
42DAP/41DAP	0.99076	1
43DAP/42DAP	0.92286	0.743
47DAP/43DAP	0.93995	0.768
52DAP/47DAP	1.11079	0.906
57DAP/52DAP	0.87344	0.679

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98618	0.601
17DAP/reference	0.84533	0.079
27DAP/reference	0.90569	0.265
39DAP/reference	0.98666	0.762
41DAP/reference	0.88453	0.267
42DAP/reference	0.93279	0.12
43DAP/reference	1.03643	0.705
47DAP/reference	1.00561	0.674
52DAP/reference	0.95323	0.36
57DAP/reference	1.10783	0.249

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.1416	0.094
27DAP/17DAP	1.00554	0.943
39DAP/27DAP	0.9792	0.87
41DAP/39DAP	0.98631	0.986
42DAP/41DAP	0.92247	0.589
43DAP/42DAP	1.03317	0.513
47DAP/43DAP	1.18262	0.383
52DAP/47DAP	1.18532	0.593
57DAP/52DAP	1.77666	0.049
57DAP/7DAP	1.33469	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93275	0.326
17DAP/reference	1.07277	1
27DAP/reference	1.07516	0.301
39DAP/reference	0.97551	0.552
41DAP/reference	1.09589	0.215
42DAP/reference	1.11612	0.405
43DAP/reference	1.01465	1
47DAP/reference	0.99612	1
52DAP/reference	0.93173	0.363
57DAP/reference	1.05955	0.07

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.30095	0.38
17DAP/reference	0.87131	0.201
27DAP/reference	0.96291	0.467
39DAP/reference	1.06035	0.502
41DAP/reference	0.92676	0.299
42DAP/reference	1.03858	1
43DAP/reference	1.059	0.526
47DAP/reference	1.05273	0.274
52DAP/reference	1.13551	0.789
57DAP/reference	0.9585	0.519

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03329	0.918
17DAP/reference	1.08519	0.522
27DAP/reference	1.15557	0.198
39DAP/reference	1.03534	0.912
41DAP/reference	1.04005	0.984
42DAP/reference	0.94258	0.445
43DAP/reference	1.00034	0.827
47DAP/reference	1.07654	1
52DAP/reference	0.97355	0.718
57DAP/reference	0.95821	0.468

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.89639	0.807
26DAP/20DAP	1.04136	1
34DAP/26DAP	0.96887
51DAP/34DAP	1.52372	0.387
52DAP/51DAP	0.70288	1
53DAP/52DAP	1.6094	0.104
55DAP/53DAP	0.7083	0.163
57DAP/55DAP	1.05214	1
62DAP/57DAP	1.25651	0.902
68DAP/62DAP	1.11287	0.885
68DAP/14DAP	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.20013	0.391

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.45327	0.094
Mature Green Tomato/Ripe Tomato	0.92011	0.522
Immature Eggplant/Mature Eggplant	1.45973	0.055
Ripe Pepper/Ripe Tomato	1.11983	1
Mature Eggplant/Ripe Tomato	1.35216	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.04709	1
1-1-2/M82	1.1022	1
12-2/M82	N/A	N/A
12-4/M82	1.26799	1
1-3/M82	0.53962
2-1-1/M82	0.84808	0.465
2-1/M82	N/A	N/A
2-6/M82	0.66785
3-2/M82	0.86256
4-1-1/M82	0.61755
4-1/M82	N/A	N/A
4-3-2/M82	0.93269
4-3/M82	N/A	N/A
5-3/M82	1.02138	1
6-2/M82	0.85939
6-3/M82	1.05268	1
7-1/M82	N/A	N/A
7-2/M82	0.86497	0.881
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.94491	1
IL2-6/WTpooled	0.96469	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.95536	1
IL12-4/WTpooled	1.13303	0.785
IL1-4/WTpooled	1.04669	1
WT/WTpooled	1.08309	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	0.82429	0.163

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.16198	0.875
DC3000/delta hrp 6h	0.75043	0.82
DC3000/delta hrp 12h	0.95921	1
DC3000/delta hrp 24h	1.02912	0.76

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.01238
DC3000 delta B/DC3000 delta AB	0.89961

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.08178	1
Exp 36h	0.92444	0.693
Exp 60h	0.90337	0.754

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

hybridization	ratio	FDR (corrected p value)
self-self	0.9641	1
Var 0h	0.77751	0.457
Var 12h I row2-row1	1.20006	0.379
Var 12h NI row2-row1	1.06828	1
Var 36h I row2-row1	1.0391	1
Var 36h NI row2-row1	0.89028	0.276
Var 60h I row2-row1	0.92346	0.374
Var 60h NI row2-row1	1.12677	0.904
Time course 0hI-0hNI	1.03728	0.574
Time course 12hI-12hNI	1.02457	0.824
Time course 36hI-36hNI	0.91795	0.153
Time course 60hI-60hNI	0.61325	0.006

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)	1.23521	0.272
transgenic ySAMdc/azygous control (breaker)	1.18847	0.178
transgenic ySAMdc/azygous control (red)	1.21698	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.99228	0.694

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.29029	0.229

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.95414	1
Manapal/WT (break)	0.83517	1
Manapal/WT (red)	0.93087	0.607