Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.4.19.1

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.90949	0.568
27DAP/17DAP	0.96731	0.863
39DAP/27DAP	0.95433	0.682
41DAP/39DAP	1.02854	0.685
42DAP/41DAP	1.12247	1
43DAP/42DAP	1.05921	0.937
47DAP/43DAP	1.07503	0.979
52DAP/47DAP	2.98703	0.24
57DAP/52DAP	1.52343	0.977

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.88082	0.103
17DAP/reference	0.93887	0.419
27DAP/reference	0.91846	0.194
39DAP/reference	0.94171	0.424
41DAP/reference	0.78237	0.039
42DAP/reference	0.96064	0.176
43DAP/reference	0.84801	0.088
47DAP/reference	0.88396	0.055
52DAP/reference	0.89742	0.135
57DAP/reference	0.81813	0.101

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.81799	0.105
27DAP/17DAP	1.2441	0.719
39DAP/27DAP	0.85992	0.181
41DAP/39DAP	0.9937	1
42DAP/41DAP	0.79429	0.143
43DAP/42DAP	1.22454	0.382
47DAP/43DAP	1.04064	0.973
52DAP/47DAP	1.1916	0.66
57DAP/52DAP	1.07159	0.852
57DAP/7DAP	1.60969	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.0015	1
17DAP/reference	0.94849	0.389
27DAP/reference	0.88852	0.171
39DAP/reference	0.97488	0.474
41DAP/reference	0.90072	0.203
42DAP/reference	0.94388	0.304
43DAP/reference	0.86999	0.086
47DAP/reference	0.91892	0.383
52DAP/reference	0.87506	0.097
57DAP/reference	1.00808	0.804

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.86146	0.134
17DAP/reference	0.83046	0.013
27DAP/reference	0.74651	0.044
39DAP/reference	0.70436	0.031
41DAP/reference	0.81785	0.071
42DAP/reference	0.89629	0.121
43DAP/reference	0.88773	0.17
47DAP/reference	0.84874	0.021
52DAP/reference	0.90482	0.086
57DAP/reference	0.79141	0.037

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9468	0.311
17DAP/reference	0.89328	0.125
27DAP/reference	0.97401	0.49
39DAP/reference	0.95138	0.36
41DAP/reference	0.94307	0.459
42DAP/reference	0.93771	0.552
43DAP/reference	0.88372	0.092
47DAP/reference	0.90012	0.168
52DAP/reference	0.92665	0.493
57DAP/reference	0.79765	0.016

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.90338	1
26DAP/20DAP	2.21941	0.101
34DAP/26DAP	0.84468	0.412
51DAP/34DAP	1.14624	0.924
52DAP/51DAP	1.18024	0.404
53DAP/52DAP	1.11161	0.712
55DAP/53DAP	1.16848	0.696
57DAP/55DAP	1.16203	1
62DAP/57DAP	1.26037	0.678
68DAP/62DAP	1.5682	0.079
68DAP/14DAP	1.09223	0.915

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.6681	0.087

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.07321	0.058
Mature Green Tomato/Ripe Tomato	7.65315	0.015
Immature Eggplant/Mature Eggplant	1.08643	0.659
Ripe Pepper/Ripe Tomato	0.67718	1
Mature Eggplant/Ripe Tomato	2.3392	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.61702
1-1-2/M82	1.16501
12-2/M82	N/A	N/A
12-4/M82	0.8662
1-3/M82	N/A	N/A
2-1-1/M82	0.94827
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
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	N/A	N/A
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	0.49699
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.75523	0.243
IL2-6/WTpooled	1.03054	1
IL7-5/WTpooled	1.83065	0.792
IL7-3/WTpooled	1.17885	0.362
IL12-4/WTpooled	1.15575	0.546
IL1-4/WTpooled	0.93541	1
WT/WTpooled	1.05725	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	0.9247	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.11969	0.921
DC3000/delta hrp 6h	1.3156	1
DC3000/delta hrp 12h	0.98481	1
DC3000/delta hrp 24h	1.36766	0.604

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	0.32152

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.85197	1
Exp 36h	1.07907	1
Exp 60h	0.76711	0.343

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99786	1
Var 0h	1.04697	1
Var 12h I row2-row1	1.00296	1
Var 12h NI row2-row1	0.95822	0.906
Var 36h I row2-row1	0.72719	0.313
Var 36h NI row2-row1	0.77274	0.29
Var 60h I row2-row1	1.04895	1
Var 60h NI row2-row1	1.08343	0.904
Time course 0hI-0hNI	0.91022	0.292
Time course 12hI-12hNI	0.97322	0.82
Time course 36hI-36hNI	0.66614	0.078
Time course 60hI-60hNI	0.35503	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)	0.97511	0.789
transgenic ySAMdc/azygous control (breaker)	1.05484	1
transgenic ySAMdc/azygous control (red)	0.9226	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.92136	0.126

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.86122	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)	0.76901	0.36