Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.3.8.8

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.93257	0.578
27DAP/17DAP	1.36366	0.742
39DAP/27DAP	0.77138	0.153
41DAP/39DAP	1.27232	0.451
42DAP/41DAP	1.54763	0.244
43DAP/42DAP	1.32392	0.787
47DAP/43DAP	0.90362	0.667
52DAP/47DAP	1.17149	0.702
57DAP/52DAP	1.07269	1

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.82139	0.149
17DAP/reference	0.93718	0.321
27DAP/reference	1.07687	0.405
39DAP/reference	1.06363	0.386
41DAP/reference	0.83184	0.085
42DAP/reference	1.1204	0.166
43DAP/reference	1.17438	0.36
47DAP/reference	0.98202	0.503
52DAP/reference	1.34025	0.065
57DAP/reference	1.31472	0.01

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.03265	0.947
27DAP/17DAP	0.94633	0.878
39DAP/27DAP	0.94464	0.579
41DAP/39DAP	1.02562	1
42DAP/41DAP	1.30089	0.378
43DAP/42DAP	1.82253	0.016
47DAP/43DAP	1.12191	0.172
52DAP/47DAP	1.19399	0.444
57DAP/52DAP	0.85857	0.405
57DAP/7DAP	1.33131	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96586	0.495
17DAP/reference	0.95931	0.389
27DAP/reference	1.00023	0.8
39DAP/reference	1.1833	0.186
41DAP/reference	1.17208	0.416
42DAP/reference	1.30558	0.174
43DAP/reference	1.42058	0.05
47DAP/reference	1.40964	0.279
52DAP/reference	0.94908	0.332
57DAP/reference	0.81571	0.039

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84471	0.09
17DAP/reference	0.78209	0.007
27DAP/reference	0.86286	0.111
39DAP/reference	1.0461	0.783
41DAP/reference	1.15189	0.439
42DAP/reference	0.96415	0.433
43DAP/reference	0.95595	0.486
47DAP/reference	1.05585	0.675
52DAP/reference	0.9715	0.537
57DAP/reference	0.76307	0.054

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.79943	0.061
17DAP/reference	0.84116	0.205
27DAP/reference	0.84529	0.048
39DAP/reference	1.06261	0.962
41DAP/reference	0.90448	0.237
42DAP/reference	1.21005	0.078
43DAP/reference	1.25484	0.16
47DAP/reference	1.17117	0.11
52DAP/reference	0.9424	0.518
57DAP/reference	1.1776	0.153

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.00518	1
26DAP/20DAP	0.8847	1
34DAP/26DAP	0.97785	0.998
51DAP/34DAP	0.66189	0.054
52DAP/51DAP	1.90515	0.04
53DAP/52DAP	0.74774	0.049
55DAP/53DAP	1.42429	0.041
57DAP/55DAP	0.82068	0.259
62DAP/57DAP	1.00518	1
68DAP/62DAP	1.64768	0.448
68DAP/14DAP	1.27526	0.594

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.75934	0.065

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.62954	0.096
Immature Eggplant/Mature Eggplant	2.86622
Ripe Pepper/Ripe Tomato	0.03563	1
Mature Eggplant/Ripe Tomato	0.04437	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.78876	0.634
1-1-2/M82	0.87829	0.958
12-2/M82	0.99166
12-4/M82	0.94788	0.619
1-3/M82	0.44838
2-1-1/M82	0.68824	0.683
2-1/M82	1.07271	1
2-6/M82	0.7484	0.501
3-2/M82	1.48652
4-1-1/M82	0.58057	0.962
4-1/M82	0.84396
4-3-2/M82	0.53002
4-3/M82	0.16427	0.396
5-3/M82	0.84816	1
6-2/M82	1.93831	0.214
6-3/M82	1.11444	1
7-1/M82	1.10382	1
7-2/M82	0.38849
9-3-2/M82	0.86292	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.49926
IL2-6/WTpooled	0.82457
IL7-5/WTpooled	0.68886
IL7-3/WTpooled	1.30926	1
IL12-4/WTpooled	0.66561	0.543
IL1-4/WTpooled	1.01511
WT/WTpooled	0.87423	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	1.02326	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.04372	0.921
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	0.97268	1
DC3000/delta hrp 24h	1.11058	0.483

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.0668	0.598
DC3000 delta B/DC3000 delta AB	1.04617	0.636

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.94297	1
Exp 36h	0.79851	0.165
Exp 60h	0.84889	0.754

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99863	1
Var 0h	1.07522	0.421
Var 12h I row2-row1	0.93535	0.77
Var 12h NI row2-row1	0.75808	0.627
Var 36h I row2-row1	1.12427	1
Var 36h NI row2-row1	1.12888	0.482
Var 60h I row2-row1	1.04557	1
Var 60h NI row2-row1	0.9875	1
Time course 0hI-0hNI	1.02925	0.764
Time course 12hI-12hNI	1.00001	1
Time course 36hI-36hNI	0.87573	0.179
Time course 60hI-60hNI	0.68441	0.015

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)	6.72533	0.455
transgenic ySAMdc/azygous control (breaker)	1.51253	1
transgenic ySAMdc/azygous control (red)	1.90714	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.95138	0.117

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.92119	0.431

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)	N/A	N/A