Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.1.3.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.09672	0.812
27DAP/17DAP	0.98543	1
39DAP/27DAP	0.99587	0.82
41DAP/39DAP	1.43146	0.306
42DAP/41DAP	0.98223	1
43DAP/42DAP	1.00904	1
47DAP/43DAP	0.89416	0.645
52DAP/47DAP	1.39791	0.403
57DAP/52DAP	0.92512	0.759

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01966	1
17DAP/reference	0.98308	0.664
27DAP/reference	0.97084	0.201
39DAP/reference	0.9549	0.35
41DAP/reference	0.96198	0.434
42DAP/reference	0.97045	0.037
43DAP/reference	0.99011	0.805
47DAP/reference	0.97852	0.345
52DAP/reference	1.05442	0.354
57DAP/reference	0.93758	0.21

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.07023	0.569
27DAP/17DAP	0.94137	0.684
39DAP/27DAP	1.02458	0.698
41DAP/39DAP	1.02322	0.801
42DAP/41DAP	0.96666	0.746
43DAP/42DAP	0.96553	0.751
47DAP/43DAP	0.99117	0.961
52DAP/47DAP	0.98569	0.925
57DAP/52DAP	0.95055	0.511
57DAP/7DAP	1.05606	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.21743	0.181
17DAP/reference	1.07	0.269
27DAP/reference	1.30052	0.018
39DAP/reference	2.05157	0.005
41DAP/reference	1.23709	0.045
42DAP/reference	1.87128	0.007
43DAP/reference	2.18843	0.007
47DAP/reference	1.52275	0.337
52DAP/reference	2.13211	0.009
57DAP/reference	1.63237	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99029	0.831
17DAP/reference	1.06395	0.357
27DAP/reference	0.99648	0.735
39DAP/reference	0.95072	0.081
41DAP/reference	0.94231	0.124
42DAP/reference	0.99562	0.655
43DAP/reference	0.98124	0.633
47DAP/reference	0.96959	0.133
52DAP/reference	0.97904	0.351
57DAP/reference	0.91931	0.085

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.09475	0.433
17DAP/reference	1.03497	0.854
27DAP/reference	1.62257	0.024
39DAP/reference	1.62533	0.019
41DAP/reference	1.4056	0.02
42DAP/reference	1.26153	0.209
43DAP/reference	1.29855	0.077
47DAP/reference	0.89139	0.139
52DAP/reference	1.18465	0.363
57DAP/reference	0.95757	0.461

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.99183	1
26DAP/20DAP	0.92716
34DAP/26DAP	0.95993	0.783
51DAP/34DAP	1.13612	0.387
52DAP/51DAP	0.97488	1
53DAP/52DAP	0.95808	0.824
55DAP/53DAP	1.01262	0.925
57DAP/55DAP	0.85251	0.486
62DAP/57DAP	0.98399	1
68DAP/62DAP	1.02048	0.956
68DAP/14DAP	0.81163	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.14135	0.151

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.12072	0.287
Mature Green Tomato/Ripe Tomato	0.84393	0.2
Immature Eggplant/Mature Eggplant	0.79132	0.407
Ripe Pepper/Ripe Tomato	2.25467
Mature Eggplant/Ripe Tomato	1.66827	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.03979	1
1-1-2/M82	1.02335	1
12-2/M82	1.01874	1
12-4/M82	0.9739	1
1-3/M82	0.95528	0.378
2-1-1/M82	1.07705	0.689
2-1/M82	0.96666	1
2-6/M82	0.95664	0.501
3-2/M82	1.16089
4-1-1/M82	1.0487	1
4-1/M82	0.87985	1
4-3-2/M82	0.99241	1
4-3/M82	0.96122	1
5-3/M82	0.99725	1
6-2/M82	0.99084	1
6-3/M82	0.99631	1
7-1/M82	1.09657	0.578
7-2/M82	1.00249	1
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.21821	0.493
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	0.937	1
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	0.92286
IL1-4/WTpooled	0.97353	1
WT/WTpooled	N/A	N/A

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	0.96504	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.98656	1
DC3000/delta hrp 6h	1.21219	1
DC3000/delta hrp 12h	0.99982	1
DC3000/delta hrp 24h	1.01892	0.821

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.0583	0.333
DC3000 delta B/DC3000 delta AB	0.98092	0.849

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.27296	1
Exp 36h	1.05105	1
Exp 60h	0.84904	0.664

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

hybridization	ratio	FDR (corrected p value)
self-self	N/A	N/A
Var 0h	1.08867	1
Var 12h I row2-row1	1.3943	0.176
Var 12h NI row2-row1	1.10636	0.649
Var 36h I row2-row1	1.30521	0.742
Var 36h NI row2-row1	0.90096	0.791
Var 60h I row2-row1	1.07132
Var 60h NI row2-row1	1.06876	0.904
Time course 0hI-0hNI	0.97747	0.962
Time course 12hI-12hNI	1.04172	0.77
Time course 36hI-36hNI	0.97919	0.621
Time course 60hI-60hNI	0.7286	0.005

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)	1.27653	0.612
transgenic ySAMdc/azygous control (breaker)	1.50789	0.248
transgenic ySAMdc/azygous control (red)	1.22599	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.97743	0.393

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.95085	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	N/A	N/A
Manapal/WT (break)	N/A	N/A
Manapal/WT (red)	1.09168	1