Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.4.8.2

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.90981	0.551
27DAP/17DAP	1.00934	1
39DAP/27DAP	1.02519	0.84
41DAP/39DAP	1.0457	0.973
42DAP/41DAP	1.71088	0.488
43DAP/42DAP	0.91006	0.846
47DAP/43DAP	1.08937	0.926
52DAP/47DAP	1.25922	0.592
57DAP/52DAP	2.13219	0.826

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98953	0.679
17DAP/reference	1.12479	0.028
27DAP/reference	0.96556	0.514
39DAP/reference	1.12604	0.074
41DAP/reference	1.15448	0.073
42DAP/reference	0.88737	0.014
43DAP/reference	0.95285	0.48
47DAP/reference	0.98956	0.535
52DAP/reference	0.82377	0.036
57DAP/reference	0.81523	0.029

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.09557	0.356
27DAP/17DAP	0.95004	0.919
39DAP/27DAP	1.15288	0.471
41DAP/39DAP	0.90251	0.347
42DAP/41DAP	1.00526	0.887
43DAP/42DAP	0.77749	0.041
47DAP/43DAP	0.97404	0.909
52DAP/47DAP	1.21822	0.478
57DAP/52DAP	1.16272	0.36
57DAP/7DAP	1.95589	0.249

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96842	0.495
17DAP/reference	0.93266	0.167
27DAP/reference	1.12445	0.301
39DAP/reference	0.94291	0.264
41DAP/reference	1.0643	0.791
42DAP/reference	0.90768	0.355
43DAP/reference	0.99717	0.637
47DAP/reference	1.03782	0.745
52DAP/reference	1.12706	0.563
57DAP/reference	1.1246	0.183

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.09319	0.33
17DAP/reference	0.99907	0.747
27DAP/reference	1.06308	0.526
39DAP/reference	1.01665	0.769
41DAP/reference	0.99872	0.666
42DAP/reference	0.95462	0.321
43DAP/reference	1.45638	0.051
47DAP/reference	0.95151	0.227
52DAP/reference	1.07049	1
57DAP/reference	1.24715	0.108

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97306	0.566
17DAP/reference	1.11777	0.522
27DAP/reference	0.94656	0.337
39DAP/reference	1.01832	0.813
41DAP/reference	1.19282	0.093
42DAP/reference	0.89792	0.287
43DAP/reference	0.88853	0.216
47DAP/reference	0.97156	0.494
52DAP/reference	0.97	0.704
57DAP/reference	0.93721	0.359

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.90605	1
26DAP/20DAP	1.33558	0.464
34DAP/26DAP	1.10548	1
51DAP/34DAP	1.54268	0.035
52DAP/51DAP	1.37673	0.133
53DAP/52DAP	1.03313	0.944
55DAP/53DAP	1.01775	1
57DAP/55DAP	1.00894	1
62DAP/57DAP	1.08695	0.868
68DAP/62DAP	1.006	0.914
68DAP/14DAP	0.92335	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.27739	0.285

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.04636	0.666
Mature Green Tomato/Ripe Tomato	1.36523	0.166
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	1.58798	1
Mature Eggplant/Ripe Tomato	0.1338	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.72759	0.503
1-1-2/M82	0.84436
12-2/M82	N/A	N/A
12-4/M82	0.78719	0.358
1-3/M82	0.8181	0.378
2-1-1/M82	1.00195	1
2-1/M82	0.95592
2-6/M82	0.95196	1
3-2/M82	1.08888
4-1-1/M82	0.92868	1
4-1/M82	1.21316
4-3-2/M82	N/A	N/A
4-3/M82	0.97774	1
5-3/M82	1.11476	1
6-2/M82	0.8272	1
6-3/M82	1.10491	1
7-1/M82	1.15642
7-2/M82	1.013	1
9-3-2/M82	1.01217

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.53418	0.247
IL2-6/WTpooled	2.42968	0.395
IL7-5/WTpooled	1.30604	1
IL7-3/WTpooled	0.46413	0.298
IL12-4/WTpooled	0.81971	0.71
IL1-4/WTpooled	0.80919	0.562
WT/WTpooled	0.91413	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	1.05677	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.0502	0.921
DC3000/delta hrp 6h	0.87061	0.95
DC3000/delta hrp 12h	1.06286	1
DC3000/delta hrp 24h	2.13496	0.047

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.50329	0.042
DC3000 delta B/DC3000 delta AB	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.94638	1
Exp 36h	1.41468	1
Exp 60h	1.08623	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.03276	1
Var 0h	1.05418	1
Var 12h I row2-row1	1.1425	0.654
Var 12h NI row2-row1	1.21634	0.34
Var 36h I row2-row1	0.91741	1
Var 36h NI row2-row1	0.86303	0.61
Var 60h I row2-row1	0.81551	0.582
Var 60h NI row2-row1	0.87553	0.977
Time course 0hI-0hNI	0.91805	0.478
Time course 12hI-12hNI	1.09512	0.385
Time course 36hI-36hNI	1.18266	0.128
Time course 60hI-60hNI	1.04551	0.495

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)	1.14832	0.261
transgenic ySAMdc/azygous control (breaker)	1.02177	1
transgenic ySAMdc/azygous control (red)	0.94261	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.94481	0.143

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.99571	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.8488	1
Manapal/WT (break)	0.87093	1
Manapal/WT (red)	1.21702	0.142