Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.1.20.17

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.85678	0.445
27DAP/17DAP	1.06347	0.885
39DAP/27DAP	0.85192	0.512
41DAP/39DAP	0.73018	0.189
42DAP/41DAP	1.06817	1
43DAP/42DAP	1.20308	0.929
47DAP/43DAP	1.38043	0.542
52DAP/47DAP	1.05135	0.953
57DAP/52DAP	0.97317	0.963

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.79749	0.172
17DAP/reference	1.13346	0.108
27DAP/reference	0.95511	0.457
39DAP/reference	1.11432	0.125
41DAP/reference	0.97735	0.667
42DAP/reference	0.98831	0.413
43DAP/reference	0.98964	0.805
47DAP/reference	1.00094	0.764
52DAP/reference	1.00328	0.791
57DAP/reference	0.99074	0.61

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.9024	0.26
27DAP/17DAP	1.12583	0.579
39DAP/27DAP	1.61235	0.062
41DAP/39DAP	0.90638	0.68
42DAP/41DAP	1.26375	0.006
43DAP/42DAP	0.98908	0.902
47DAP/43DAP	1.24244	0.025
52DAP/47DAP	0.95912	0.753
57DAP/52DAP	1.07025	0.674
57DAP/7DAP	1.64708	0.249

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92569	0.183
17DAP/reference	1.06159	0.574
27DAP/reference	1.01936	0.8
39DAP/reference	1.08855	0.57
41DAP/reference	1.22	0.223
42DAP/reference	1.29611	0.01
43DAP/reference	1.07412	0.325
47DAP/reference	1.12821	0.337
52DAP/reference	0.9854	0.571
57DAP/reference	0.99726	0.719

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00948	1
17DAP/reference	1.05857	0.508
27DAP/reference	0.94066	0.352
39DAP/reference	1.03563	0.764
41DAP/reference	0.90514	0.051
42DAP/reference	0.9259	0.135
43DAP/reference	0.99496	0.706
47DAP/reference	0.9916	0.643
52DAP/reference	1.07039	0.092
57DAP/reference	1.0375	0.786

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.986	0.607
17DAP/reference	1.02916	0.912
27DAP/reference	1.0466	0.596
39DAP/reference	0.99239	0.693
41DAP/reference	1.06075	0.439
42DAP/reference	1.09284	0.416
43DAP/reference	1.0048	0.827
47DAP/reference	1.01373	0.877
52DAP/reference	1.004	1
57DAP/reference	1.05107	0.614

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.9323	1
26DAP/20DAP	1.55112	0.534
34DAP/26DAP	0.793	0.561
51DAP/34DAP	0.75766	0.268
52DAP/51DAP	1.25638	0.218
53DAP/52DAP	1.0529	0.96
55DAP/53DAP	0.83937	0.43
57DAP/55DAP	1.23741	0.666
62DAP/57DAP	1.2458	0.767
68DAP/62DAP	1.25455	0.5
68DAP/14DAP	1.27257	0.762

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	6.28269	0.015

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.18631	0.075
Mature Green Tomato/Ripe Tomato	1.35422	0.03
Immature Eggplant/Mature Eggplant	1.3857	0.05
Ripe Pepper/Ripe Tomato	0.90718	1
Mature Eggplant/Ripe Tomato	0.56931	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.89935	0.934
1-1-2/M82	1.09524	1
12-2/M82	1.35085	1
12-4/M82	0.8932	0.358
1-3/M82	1.46534	0.277
2-1-1/M82	0.90584	0.465
2-1/M82	0.92583	1
2-6/M82	0.88456	1
3-2/M82	1.44386
4-1-1/M82	0.98558	1
4-1/M82	N/A	N/A
4-3-2/M82	0.89261
4-3/M82	0.96782	1
5-3/M82	1.09133	1
6-2/M82	1.09045	1
6-3/M82	0.98398	1
7-1/M82	0.94518	1
7-2/M82	0.8057	0.57
9-3-2/M82	1.14768

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	0.96409
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	0.95587	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.92798	1
DC3000/delta hrp 6h	1.07023	0.95
DC3000/delta hrp 12h	0.90346	1
DC3000/delta hrp 24h	1.08976	0.567

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.71726
DC3000 delta B/DC3000 delta AB	0.72526	0.021

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.09558	1
Exp 36h	0.87918	0.749
Exp 60h	0.9126	0.754

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99623	1
Var 0h	N/A	N/A
Var 12h I row2-row1	1.08939	0.692
Var 12h NI row2-row1	0.98272	0.906
Var 36h I row2-row1	1.03589	1
Var 36h NI row2-row1	1.22002	0.482
Var 60h I row2-row1	1.06214	1
Var 60h NI row2-row1	1.14726	0.904
Time course 0hI-0hNI	1.02454	0.867
Time course 12hI-12hNI	1.05522	0.544
Time course 36hI-36hNI	0.87826	0.027
Time course 60hI-60hNI	0.84459	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)	0.99876	1
transgenic ySAMdc/azygous control (breaker)	1.00098	1
transgenic ySAMdc/azygous control (red)	1.23501	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.00435	0.723

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.02547	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.83637	1
Manapal/WT (break)	0.74117	1
Manapal/WT (red)	0.96161	0.728