Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.3.20.9

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.81433	0.232
27DAP/17DAP	1.05821	0.92
39DAP/27DAP	0.97404	0.733
41DAP/39DAP	1.35856	0.423
42DAP/41DAP	1.12669	0.844
43DAP/42DAP	1.09647	1
47DAP/43DAP	1.08313	0.909
52DAP/47DAP	0.88405	0.643
57DAP/52DAP	0.96957	0.957

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.8949	0.412
17DAP/reference	1.211	0.546
27DAP/reference	0.98522	0.797
39DAP/reference	1.00308	1
41DAP/reference	1.01245	0.587
42DAP/reference	0.85933	0.048
43DAP/reference	1.14189	0.705
47DAP/reference	0.92184	0.345
52DAP/reference	0.87137	0.283
57DAP/reference	1.97277

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.82696	0.228
27DAP/17DAP	0.91176	0.782
39DAP/27DAP	1.23022	0.27
41DAP/39DAP	1.15947	0.59
42DAP/41DAP	1.00483	0.884
43DAP/42DAP	0.95164	0.641
47DAP/43DAP	1.9321	0.094
52DAP/47DAP	1.00619	0.962
57DAP/52DAP	1.1157	0.529
57DAP/7DAP	2.31309	0.23

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.89029	0.122
17DAP/reference	0.74556	0.011
27DAP/reference	0.75314	0.01
39DAP/reference	0.71558	0.011
41DAP/reference	0.92856	0.311
42DAP/reference	0.7749	0.034
43DAP/reference	0.80962	0.013
47DAP/reference	0.96963	0.671
52DAP/reference	0.94843	0.332
57DAP/reference	0.93028	0.08

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91911	0.329
17DAP/reference	0.81415	0.042
27DAP/reference	0.97531	0.642
39DAP/reference	0.86503	0.168
41DAP/reference	0.80958	0.141
42DAP/reference	0.84825	0.05
43DAP/reference	1.13629	0.429
47DAP/reference	0.93635	0.359
52DAP/reference	0.85479	0.021
57DAP/reference	0.96889	0.519

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.82149	0.052
17DAP/reference	0.92515	0.381
27DAP/reference	0.83202	0.048
39DAP/reference	0.71475	0.012
41DAP/reference	0.89598	0.132
42DAP/reference	0.82911	0.049
43DAP/reference	0.89053	0.131
47DAP/reference	0.91276	0.048
52DAP/reference	0.79392	0.081
57DAP/reference	0.85743	0.234

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.2355	0.966
26DAP/20DAP	1.39172	0.204
34DAP/26DAP	0.75761	0.561
51DAP/34DAP	0.83678	0.631
52DAP/51DAP	1.78862	0.42
53DAP/52DAP	1.2863	0.319
55DAP/53DAP	1.10785	0.798
57DAP/55DAP	0.8623	0.548
62DAP/57DAP	1.32535	0.158
68DAP/62DAP	1.83289	0.464
68DAP/14DAP	1.62609	0.08

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.75686	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	3.17812	0.058
Mature Green Tomato/Ripe Tomato	0.81422	0.347
Immature Eggplant/Mature Eggplant	2.511	0.05
Ripe Pepper/Ripe Tomato	0.69103	0.224
Mature Eggplant/Ripe Tomato	2.39188	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.7703	0.708
1-1-2/M82	0.90266	1
12-2/M82	1.39632	0.389
12-4/M82	0.86657	0.619
1-3/M82	0.91845	1
2-1-1/M82	0.83139	0.92
2-1/M82	1.26283
2-6/M82	0.71013	1
3-2/M82	1.17301	0.443
4-1-1/M82	0.90906	1
4-1/M82	1.34117
4-3-2/M82	0.76243	0.698
4-3/M82	0.88942
5-3/M82	1.032	1
6-2/M82	0.35282
6-3/M82	1.17127	1
7-1/M82	1.05051
7-2/M82	0.78798	0.54
9-3-2/M82	0.6106	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.45708	0.277
IL2-6/WTpooled	0.57805	0.383
IL7-5/WTpooled	1.16502	0.792
IL7-3/WTpooled	1.52461	1
IL12-4/WTpooled	0.92075	0.71
IL1-4/WTpooled	1.26583	1
WT/WTpooled	0.99512	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	0.82344	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.11924	0.894
DC3000/delta hrp 6h	1.10747	1
DC3000/delta hrp 12h	1.16659	1
DC3000/delta hrp 24h	1.14788	0.051

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.55521
DC3000 delta B/DC3000 delta AB	0.37966	0.23

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.04522	1
Exp 36h	0.85239	0.699
Exp 60h	0.79558	0.664

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

hybridization	ratio	FDR (corrected p value)
self-self	0.95869	1
Var 0h	N/A	N/A
Var 12h I row2-row1	1.12513	0.379
Var 12h NI row2-row1	0.96705	0.906
Var 36h I row2-row1	0.94593	1
Var 36h NI row2-row1	1.22804	1
Var 60h I row2-row1	1.16139	0.483
Var 60h NI row2-row1	1.453	0.904
Time course 0hI-0hNI	1.04419	0.63
Time course 12hI-12hNI	0.80667	0.048
Time course 36hI-36hNI	0.54818	0.023
Time course 60hI-60hNI	0.45251	0.007

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)	0.84356	0.338
transgenic ySAMdc/azygous control (breaker)	1.79016	0.166
transgenic ySAMdc/azygous control (red)	1.02088	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.99801	0.911

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.00252	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.95855	1
Manapal/WT (break)	1.22922	0.183
Manapal/WT (red)	0.97236	0.728