Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.2.12.21

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.65997	0.646
27DAP/17DAP	1.07165	0.89
39DAP/27DAP	0.8164	0.507
41DAP/39DAP	1.20955	0.591
42DAP/41DAP	1.12263	0.871
43DAP/42DAP	0.93086	0.788
47DAP/43DAP	1.27918	0.442
52DAP/47DAP	1.01297	0.938
57DAP/52DAP	0.80288	0.8

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94267	0.254
17DAP/reference	1.01362	0.907
27DAP/reference	1.01295	0.934
39DAP/reference	0.97534	0.651
41DAP/reference	1.0375	0.587
42DAP/reference	0.92269	0.134
43DAP/reference	1.10718	0.133
47DAP/reference	1.04775	0.379
52DAP/reference	0.98741	0.618
57DAP/reference	0.92029	0.138

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.84719	0.238
27DAP/17DAP	0.86688	0.684
39DAP/27DAP	1.03535	0.824
41DAP/39DAP	1.02839	1
42DAP/41DAP	0.85472	0.353
43DAP/42DAP	0.84309	0.172
47DAP/43DAP	1.11895	0.69
52DAP/47DAP	0.96128	0.9
57DAP/52DAP	0.86762	0.352
57DAP/7DAP	1.66991

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97012	0.495
17DAP/reference	0.97474	0.389
27DAP/reference	0.93121	0.03
39DAP/reference	0.95006	0.17
41DAP/reference	0.94307	0.111
42DAP/reference	0.97827	0.393
43DAP/reference	0.87979	0.061
47DAP/reference	1.00838	1
52DAP/reference	0.9219	0.077
57DAP/reference	0.97137	0.27

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03287	0.979
17DAP/reference	0.88624	0.099
27DAP/reference	0.94684	0.381
39DAP/reference	0.95732	0.322
41DAP/reference	1.08362	0.846
42DAP/reference	0.86187	0.108
43DAP/reference	0.97598	0.581
47DAP/reference	0.98731	0.512
52DAP/reference	0.91012	0.131
57DAP/reference	0.98587	0.649

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02199	0.846
17DAP/reference	0.93712	0.335
27DAP/reference	0.89464	0.069
39DAP/reference	0.97404	0.464
41DAP/reference	0.95404	0.371
42DAP/reference	0.97902	0.671
43DAP/reference	0.87562	0.092
47DAP/reference	0.95981	0.335
52DAP/reference	0.99788	0.908
57DAP/reference	0.94679	0.315

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.01097	1
26DAP/20DAP	1.11881	1
34DAP/26DAP	1.78036	1
51DAP/34DAP	1.58657
52DAP/51DAP	1.01718	1
53DAP/52DAP	1.05923	0.845
55DAP/53DAP	1.25976	0.855
57DAP/55DAP	1.06723	0.826
62DAP/57DAP	1.05967	1
68DAP/62DAP	0.76609	0.314
68DAP/14DAP	0.69723	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.34284	0.032

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.04186	0.666
Mature Green Tomato/Ripe Tomato	1.3372	0.478
Immature Eggplant/Mature Eggplant	1.17175	0.067
Ripe Pepper/Ripe Tomato	1.06124	1
Mature Eggplant/Ripe Tomato	0.48622	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.9642	0.944
1-1-2/M82	0.9817	1
12-2/M82	0.98607	1
12-4/M82	0.89246	0.33
1-3/M82	1.2036	0.26
2-1-1/M82	1.05844	0.229
2-1/M82	0.93892	1
2-6/M82	1.00356	1
3-2/M82	N/A	N/A
4-1-1/M82	0.99833	1
4-1/M82	0.9241
4-3-2/M82	1.12419
4-3/M82	0.98387	1
5-3/M82	1.03029	1
6-2/M82	1.01833	1
6-3/M82	1.05976	1
7-1/M82	N/A	N/A
7-2/M82	1.08046	1
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.44352	0.427
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.10609	1
IL12-4/WTpooled	0.95112	1
IL1-4/WTpooled	1.18656	1
WT/WTpooled	0.93416	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	1.07955	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.08247	0.894
DC3000/delta hrp 6h	1.03452	0.95
DC3000/delta hrp 12h	1.09552	1
DC3000/delta hrp 24h	1.07668	0.582

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.69189
DC3000 delta B/DC3000 delta AB	1.15675	0.335

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.10185	1
Exp 36h	1.21835	0.489
Exp 60h	1.19463	0.221

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99066	1
Var 0h	1.36036	0.936
Var 12h I row2-row1	1.19429	0.379
Var 12h NI row2-row1	1.00852	1
Var 36h I row2-row1	0.98894	1
Var 36h NI row2-row1	0.90922	0.706
Var 60h I row2-row1	0.77218	0.439
Var 60h NI row2-row1	1.05755	1
Time course 0hI-0hNI	1.1794	0.262
Time course 12hI-12hNI	1.10746	0.422
Time course 36hI-36hNI	1.21003	0.218
Time course 60hI-60hNI	2.66844	0.008

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)	0.97766	0.454
transgenic ySAMdc/azygous control (breaker)	1.18069	0.162
transgenic ySAMdc/azygous control (red)	1.01439	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.05039	0.287

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.65074	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.96367	1
Manapal/WT (break)	0.89042	1
Manapal/WT (red)	0.74735	0.181