Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.2.7.15

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.02621	0.912
27DAP/17DAP	0.69122	0.157
39DAP/27DAP	0.8717	0.549
41DAP/39DAP	0.91582	0.59
42DAP/41DAP	0.94589	1
43DAP/42DAP	1.04613	1
47DAP/43DAP	0.90469	0.701
52DAP/47DAP	1.01091	0.927
57DAP/52DAP	0.96523	0.956

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.10249	0.197
17DAP/reference	0.98226	0.63
27DAP/reference	0.97009	0.484
39DAP/reference	0.98728	0.855
41DAP/reference	1.02709	0.667
42DAP/reference	0.93175	0.088
43DAP/reference	0.99076	0.82
47DAP/reference	0.93934	0.098
52DAP/reference	0.96878	0.461
57DAP/reference	0.98376	0.395

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.326	0.031
27DAP/17DAP	1.71906	0.032
39DAP/27DAP	0.48113	0.052
41DAP/39DAP	0.59358	0.104
42DAP/41DAP	1.2558	0.622
43DAP/42DAP	1.18986	0.23
47DAP/43DAP	1.0264	0.957
52DAP/47DAP	1.2175	0.467
57DAP/52DAP	1.00202	0.892
57DAP/7DAP	0.3055	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97331	0.55
17DAP/reference	1.04028	1
27DAP/reference	1.017	0.614
39DAP/reference	1.1194	0.391
41DAP/reference	1.0044	1
42DAP/reference	1.03815	0.889
43DAP/reference	1.17105	0.344
47DAP/reference	0.91238	0.293
52DAP/reference	1.10634	0.781
57DAP/reference	1.20297	0.851

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.07001	0.926
17DAP/reference	1.13835	0.028
27DAP/reference	1.10374	0.239
39DAP/reference	1.12947	0.401
41DAP/reference	1.0126	0.683
42DAP/reference	0.97291	0.433
43DAP/reference	0.9237	0.414
47DAP/reference	0.90997	0.097
52DAP/reference	1.01791	0.938
57DAP/reference	0.94535	0.298

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.09837	0.146
17DAP/reference	1.13789	0.201
27DAP/reference	1.02257	0.883
39DAP/reference	1.12915	0.146
41DAP/reference	0.96109	0.512
42DAP/reference	0.96972	0.671
43DAP/reference	0.87315	0.216
47DAP/reference	0.83554	0.005
52DAP/reference	0.97572	0.675
57DAP/reference	0.86641	0.092

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.10779	0.586
26DAP/20DAP	1.18237	0.924
34DAP/26DAP	0.97673	0.874
51DAP/34DAP	0.68479	0.06
52DAP/51DAP	0.99807	1
53DAP/52DAP	0.92024	0.776
55DAP/53DAP	0.61966	0.026
57DAP/55DAP	0.85093	0.427
62DAP/57DAP	0.77147	0.681
68DAP/62DAP	1.12449	0.939
68DAP/14DAP	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.16939	0.019

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.2803	0.058
Mature Green Tomato/Ripe Tomato	3.78293	0.026
Immature Eggplant/Mature Eggplant	0.494	0.062
Ripe Pepper/Ripe Tomato	3.33475	0.256
Mature Eggplant/Ripe Tomato	7.25255	0.268

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.98923	1
1-1-2/M82	0.98096	1
12-2/M82	1.09647	0.448
12-4/M82	1.08351	0.694
1-3/M82	N/A	N/A
2-1-1/M82	0.97898
2-1/M82	N/A	N/A
2-6/M82	1.0215	1
3-2/M82	0.93691
4-1-1/M82	0.91135	1
4-1/M82	1.18347
4-3-2/M82	1.00598	1
4-3/M82	0.90577	0.72
5-3/M82	1.05718	1
6-2/M82	0.8784	0.481
6-3/M82	0.96173	1
7-1/M82	1.06888
7-2/M82	1.08887
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.21918
IL2-6/WTpooled	0.73055	0.348
IL7-5/WTpooled	0.92808
IL7-3/WTpooled	1.05577	1
IL12-4/WTpooled	0.83438	0.71
IL1-4/WTpooled	0.91446	0.562
WT/WTpooled	0.95173	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	1.36827	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.94909	0.941
DC3000/delta hrp 6h	0.98851	0.95
DC3000/delta hrp 12h	0.74731	1
DC3000/delta hrp 24h	0.81123	0.323

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.47516	0.024
DC3000 delta B/DC3000 delta AB	0.45853	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.93312	1
Exp 36h	0.85228	0.623
Exp 60h	0.82111	0.586

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

hybridization	ratio	FDR (corrected p value)
self-self	1.05481	1
Var 0h	1.11611	1
Var 12h I row2-row1	0.89209	0.627
Var 12h NI row2-row1	0.92909	0.713
Var 36h I row2-row1	1.09818	0.601
Var 36h NI row2-row1	1.24016	1
Var 60h I row2-row1	1.02636	1
Var 60h NI row2-row1	1.03003	1
Time course 0hI-0hNI	1.02627	0.852
Time course 12hI-12hNI	0.92651	0.484
Time course 36hI-36hNI	0.80719	0.023
Time course 60hI-60hNI	0.13406	0.005

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)	1.14175	0.482
transgenic ySAMdc/azygous control (breaker)	2.84102	0.172
transgenic ySAMdc/azygous control (red)	1.18408	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.92159	0.099

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.46803	0.237

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	2.24176	0.09
Manapal/WT (break)	8.4607	0.123
Manapal/WT (red)	4.08841	0.126