Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.3.6.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.80112	0.173
27DAP/17DAP	0.91882	0.819
39DAP/27DAP	1.08952	0.85
41DAP/39DAP	1.13951	0.367
42DAP/41DAP	1.10683	0.954
43DAP/42DAP	0.93315	0.71
47DAP/43DAP	0.95765	0.779
52DAP/47DAP	1.18402	0.721
57DAP/52DAP	0.96636	0.949

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92197	0.293
17DAP/reference	1.00856	0.764
27DAP/reference	1.04209	0.587
39DAP/reference	1.02275	0.603
41DAP/reference	0.97843	0.667
42DAP/reference	0.93151	0.069
43DAP/reference	0.9771	0.653
47DAP/reference	0.97579	0.392
52DAP/reference	0.84011	0.079
57DAP/reference	0.90429	0.082

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.99936	0.899
27DAP/17DAP	0.98495	0.854
39DAP/27DAP	1.01817	0.718
41DAP/39DAP	1.06892	0.65
42DAP/41DAP	0.9742	0.759
43DAP/42DAP	0.9927	0.96
47DAP/43DAP	1.03384	0.833
52DAP/47DAP	1.01524	0.945
57DAP/52DAP	1.01949	0.957
57DAP/7DAP	0.98948	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.808	0.076
17DAP/reference	0.84274	0.02
27DAP/reference	0.81649	0.01
39DAP/reference	0.84808	0.011
41DAP/reference	0.83661	0.027
42DAP/reference	0.82257	0.01
43DAP/reference	0.83642	0.023
47DAP/reference	0.85203	0.044
52DAP/reference	0.87829	0.02
57DAP/reference	0.97963	0.477

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98465	0.77
17DAP/reference	0.9312	0.17
27DAP/reference	0.99183	0.619
39DAP/reference	0.93251	0.227
41DAP/reference	0.88299	0.112
42DAP/reference	0.9143	0.089
43DAP/reference	0.99858	0.801
47DAP/reference	0.95399	0.126
52DAP/reference	0.92292	0.093
57DAP/reference	1.06847	0.626

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.88228	0.059
17DAP/reference	0.899	0.286
27DAP/reference	0.84838	0.031
39DAP/reference	0.79402	0.011
41DAP/reference	0.88203	0.064
42DAP/reference	0.69391	0.016
43DAP/reference	0.82731	0.032
47DAP/reference	1.01374	1
52DAP/reference	0.73982	0.072
57DAP/reference	0.72756	0.032

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.95513	1
26DAP/20DAP	N/A	N/A
34DAP/26DAP	0.9317
51DAP/34DAP	1.02411	0.936
52DAP/51DAP	N/A	N/A
53DAP/52DAP	1.04783	0.91
55DAP/53DAP	1.03129	0.994
57DAP/55DAP	1.07501	0.841
62DAP/57DAP	1.02876	0.767
68DAP/62DAP	0.94962	0.787
68DAP/14DAP	1.02852	0.936

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.16297	0.285

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.52046	0.417
Mature Green Tomato/Ripe Tomato	0.91903	0.487
Immature Eggplant/Mature Eggplant	1.03097	0.683
Ripe Pepper/Ripe Tomato	0.62137	0.293
Mature Eggplant/Ripe Tomato	0.78608	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.95237	0.944
1-1-2/M82	0.96427	1
12-2/M82	0.96315	0.955
12-4/M82	1.00223	1
1-3/M82	1.03217	1
2-1-1/M82	0.97611
2-1/M82	0.73635
2-6/M82	0.96626	1
3-2/M82	0.93723	0.752
4-1-1/M82	1.07528	0.968
4-1/M82	1.09685	0.444
4-3-2/M82	1.23611	1
4-3/M82	0.95548	0.72
5-3/M82	1.09352	1
6-2/M82	1.06932	1
6-3/M82	0.935	0.916
7-1/M82	1.01803	1
7-2/M82	1.00097	1
9-3-2/M82	0.89772	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.27548
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	1.16066	0.839
IL1-4/WTpooled	1.02903	1
WT/WTpooled	0.95362	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	0.87797	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.98371	1
DC3000/delta hrp 6h	1.27846	1
DC3000/delta hrp 12h	1.12844	1
DC3000/delta hrp 24h	1.16497	0.264

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.1955	0.063
DC3000 delta B/DC3000 delta AB	1.20774	0.159

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.18149	1
Exp 36h	0.99106	1
Exp 60h	1.13086	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98555	1
Var 0h	0.77885	0.933
Var 12h I row2-row1	1.19575	0.224
Var 12h NI row2-row1	1.05076	0.266
Var 36h I row2-row1	1.1284	1
Var 36h NI row2-row1	0.87986	0.421
Var 60h I row2-row1	1.06141	0.562
Var 60h NI row2-row1	1.12687	0.904
Time course 0hI-0hNI	0.92148	0.545
Time course 12hI-12hNI	1.0251	0.81
Time course 36hI-36hNI	0.89211	0.136
Time course 60hI-60hNI	1.25543	0.015

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)	0.93651	0.485
transgenic ySAMdc/azygous control (breaker)	0.58186	0.134
transgenic ySAMdc/azygous control (red)	1.12501	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.02382	0.083

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.98393	0.59

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.19199	0.14
Manapal/WT (break)	1.12632	0.381
Manapal/WT (red)	0.85677	0.315