Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.4.20.21

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.7496	0.77
27DAP/17DAP	0.96262	0.928
39DAP/27DAP	1.09757	0.798
41DAP/39DAP	1.54535	0.459
42DAP/41DAP	0.77213	1
43DAP/42DAP	0.87235	0.77
47DAP/43DAP	1.04115	0.744
52DAP/47DAP	2.30685	0.068
57DAP/52DAP	0.84171	0.824

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99274	0.616
17DAP/reference	1.27753	0.04
27DAP/reference	1.00902	0.966
39DAP/reference	1.02964	0.639
41DAP/reference	1.2599	0.079
42DAP/reference	0.9348	0.072
43DAP/reference	0.98849	0.785
47DAP/reference	0.99355	0.602
52DAP/reference	0.89534	0.172
57DAP/reference	0.84685	0.031

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	2.31306	0.076
27DAP/17DAP	1.0919	0.912
39DAP/27DAP	0.88903	0.482
41DAP/39DAP	1.15556	0.735
42DAP/41DAP	0.70683	0.031
43DAP/42DAP	1.0388	1
47DAP/43DAP	1.28805	0.735
52DAP/47DAP	1.08653	0.933
57DAP/52DAP	0.98267	0.695
57DAP/7DAP	2.06979

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99431	0.682
17DAP/reference	0.96165	0.389
27DAP/reference	0.88044	0.159
39DAP/reference	0.91808	0.354
41DAP/reference	0.88464	0.194
42DAP/reference	0.8256	0.169
43DAP/reference	1.00714	0.637
47DAP/reference	0.90546	0.383
52DAP/reference	0.72486	0.033
57DAP/reference	1.18343	0.198

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97963	0.706
17DAP/reference	1.10153	0.806
27DAP/reference	0.93565	0.393
39DAP/reference	0.83778	0.022
41DAP/reference	0.85936	0.096
42DAP/reference	0.85073	0.061
43DAP/reference	1.1773	0.122
47DAP/reference	0.93253	0.133
52DAP/reference	0.98396	0.5
57DAP/reference	0.99978	0.789

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.11789	0.659
17DAP/reference	0.99167	0.739
27DAP/reference	0.86312	0.056
39DAP/reference	0.98365	0.643
41DAP/reference	0.82871	0.148
42DAP/reference	1.01365	0.816
43DAP/reference	0.91797	0.319
47DAP/reference	1.01175	1
52DAP/reference	1.04186	0.838
57DAP/reference	1.19276	0.694

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.16013	0.966
26DAP/20DAP	1.05477	1
34DAP/26DAP	0.92215	0.879
51DAP/34DAP	0.97336	0.856
52DAP/51DAP	1.13312	0.848
53DAP/52DAP	1.30653	0.537
55DAP/53DAP	0.88557	0.293
57DAP/55DAP	1.34872	0.144
62DAP/57DAP	1.14608	0.935
68DAP/62DAP	0.99147	0.914
68DAP/14DAP	0.72387	0.09

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.04696	0.774

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.34933	0.017
Immature Eggplant/Mature Eggplant	0.73242
Ripe Pepper/Ripe Tomato	0.5375
Mature Eggplant/Ripe Tomato	N/A	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.43324
12-2/M82	N/A	N/A
12-4/M82	0.95291	1
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	0.92717
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	1.14004
5-3/M82	0.91237
6-2/M82	0.96115
6-3/M82	1.5988
7-1/M82	0.98056
7-2/M82	0.87929
9-3-2/M82	0.9395	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	N/A	N/A
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	0.84099

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.11353	0.875
DC3000/delta hrp 6h	1.02045
DC3000/delta hrp 12h	0.88189	1
DC3000/delta hrp 24h	0.83337	0.088

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	0.97564	1
Exp 36h	N/A	N/A
Exp 60h	0.82858	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	N/A	N/A
Var 12h I row2-row1	1.85722
Var 12h NI row2-row1	0.75677
Var 36h I row2-row1	N/A	N/A
Var 36h NI row2-row1	5.16548	1
Var 60h I row2-row1	1.39951	0.562
Var 60h NI row2-row1	0.59149	0.977
Time course 0hI-0hNI	1.65944	0.867
Time course 12hI-12hNI	0.81853	0.759
Time course 36hI-36hNI	0.64218	0.117
Time course 60hI-60hNI	0.95844	0.187

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)	0.80409	0.338
transgenic ySAMdc/azygous control (breaker)	0.86125	0.49
transgenic ySAMdc/azygous control (red)	1.04133	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.97521	0.334

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.19601	0.222

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.19351	0.307
Manapal/WT (break)	0.73003	0.333
Manapal/WT (red)	0.5774	0.229