Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.3.5.7

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.93951	0.683
27DAP/17DAP	0.93428	0.863
39DAP/27DAP	1.08546	0.857
41DAP/39DAP	1.14257	0.715
42DAP/41DAP	0.94144	1
43DAP/42DAP	0.76229	0.589
47DAP/43DAP	0.94064	0.724
52DAP/47DAP	1.25528	0.566
57DAP/52DAP	1.09114	0.98

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98597	0.578
17DAP/reference	1.04082	0.907
27DAP/reference	0.96019	0.497
39DAP/reference	1.12254	0.393
41DAP/reference	1.20826	0.241
42DAP/reference	0.88994	0.072
43DAP/reference	0.9563	0.611
47DAP/reference	0.88312	0.06
52DAP/reference	1.00015	0.546
57DAP/reference	0.96843	0.435

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.15269	0.605
27DAP/17DAP	1.14845
39DAP/27DAP	1.34313	0.465
41DAP/39DAP	1.24611	0.682
42DAP/41DAP	1.18384	0.809
43DAP/42DAP	1.21152	0.83
47DAP/43DAP	0.92532	0.687
52DAP/47DAP	1.5055	0.46
57DAP/52DAP	1.20647	0.657
57DAP/7DAP	1.16739

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01534	1
17DAP/reference	1.03527	1
27DAP/reference	1.16237	0.16
39DAP/reference	1.23103	0.12
41DAP/reference	1.03012	0.811
42DAP/reference	1.35855	0.007
43DAP/reference	1.3641	0.039
47DAP/reference	0.95062	0.671
52DAP/reference	1.04953	1
57DAP/reference	1.06245	0.831

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.06897	0.65
17DAP/reference	1.16391	0.25
27DAP/reference	1.51073	0.097
39DAP/reference	1.3005	0.377
41DAP/reference	1.1218	0.72
42DAP/reference	0.97734	0.482
43DAP/reference	1.28781	0.15
47DAP/reference	1.06475	0.775
52DAP/reference	1.72973
57DAP/reference	1.20765	0.119

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01148	0.75
17DAP/reference	1.17537	0.365
27DAP/reference	0.9113	0.27
39DAP/reference	1.04008	1
41DAP/reference	1.05799	0.692
42DAP/reference	1.11015	0.671
43DAP/reference	1.16983	0.531
47DAP/reference	0.99874	0.754
52DAP/reference	1.47417	0.09
57DAP/reference	1.28495	0.072

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.02433	1
26DAP/20DAP	N/A	N/A
34DAP/26DAP	1.07863	1
51DAP/34DAP	1.04815	0.949
52DAP/51DAP	0.77346
53DAP/52DAP	1.01102	1
55DAP/53DAP	1.71389
57DAP/55DAP	1.2476	0.61
62DAP/57DAP	1.13974
68DAP/62DAP	1.06332	0.792
68DAP/14DAP	0.74215	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.54541	0.264

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	2.24645
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	N/A	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.96557
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	N/A	N/A
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	0.77972	1
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	0.91523
6-2/M82	0.77532
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
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	1.05634	1
IL2-6/WTpooled	1.23226	0.531
IL7-5/WTpooled	0.66937	1
IL7-3/WTpooled	1.0936	1
IL12-4/WTpooled	1.04595	0.785
IL1-4/WTpooled	1.30362	1
WT/WTpooled	0.94202	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	1.57389	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.99358	1
DC3000/delta hrp 6h	0.90033	0.95
DC3000/delta hrp 12h	1.29624	1
DC3000/delta hrp 24h	1.00476	1

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	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.97401	1
Exp 36h	N/A	N/A
Exp 60h	1.00231	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98211	1
Var 0h	0.96775	0.291
Var 12h I row2-row1	N/A	N/A
Var 12h NI row2-row1	0.85095
Var 36h I row2-row1	1.39133	0.489
Var 36h NI row2-row1	0.97216	0.852
Var 60h I row2-row1	1.08716	0.543
Var 60h NI row2-row1	0.99143	1
Time course 0hI-0hNI	1.04558	0.852
Time course 12hI-12hNI	1.1769	0.867
Time course 36hI-36hNI	1.45746	0.009
Time course 60hI-60hNI	2.0895	0.011

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)	0.95117	0.409
transgenic ySAMdc/azygous control (breaker)	0.98098	1
transgenic ySAMdc/azygous control (red)	0.98628	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.87075	0.038

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.92097	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.83062	1
Manapal/WT (break)	0.75779	1
Manapal/WT (red)	1.14011	1