Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.3.9.16

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.30938	0.394
27DAP/17DAP	1.2233	0.793
39DAP/27DAP	0.8582	0.512
41DAP/39DAP	1.17379	0.685
42DAP/41DAP	1.6081	0.614
43DAP/42DAP	0.9571	0.877
47DAP/43DAP	1.01661	0.943
52DAP/47DAP	1.1926	0.791
57DAP/52DAP	0.89297	0.81

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99328	0.707
17DAP/reference	1.03341	0.318
27DAP/reference	0.99856	0.885
39DAP/reference	1.04784	0.514
41DAP/reference	0.99859	1
42DAP/reference	0.92929	0.103
43DAP/reference	1.01267	0.812
47DAP/reference	0.94917	0.046
52DAP/reference	0.89499	0.172
57DAP/reference	0.94555	0.199

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.99304	0.826
27DAP/17DAP	1.01542	0.954
39DAP/27DAP	1.01183	0.799
41DAP/39DAP	0.95732	0.839
42DAP/41DAP	1.0197	0.947
43DAP/42DAP	0.96066	0.351
47DAP/43DAP	0.97093	0.701
52DAP/47DAP	1.03726	0.856
57DAP/52DAP	1.06181	0.58
57DAP/7DAP	1.10183	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97407	0.168
17DAP/reference	1.03036	0.477
27DAP/reference	0.98102	0.283
39DAP/reference	0.99589	0.64
41DAP/reference	0.99358	0.619
42DAP/reference	1.02965	0.405
43DAP/reference	1.01635	0.432
47DAP/reference	0.96919	0.383
52DAP/reference	1.00066	1
57DAP/reference	1.02414	0.331

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01626	0.65
17DAP/reference	1.04318	0.357
27DAP/reference	1.02457	0.961
39DAP/reference	1.03012	0.639
41DAP/reference	0.97308	0.322
42DAP/reference	0.94682	0.169
43DAP/reference	1.01785	0.885
47DAP/reference	0.92266	0.027
52DAP/reference	1.00044	1
57DAP/reference	1.05685	0.161

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00758	1
17DAP/reference	0.95834	0.364
27DAP/reference	0.96731	0.442
39DAP/reference	0.99275	0.643
41DAP/reference	0.96594	0.331
42DAP/reference	0.97326	0.816
43DAP/reference	0.94258	0.305
47DAP/reference	0.96089	0.396
52DAP/reference	0.96035	0.444
57DAP/reference	0.82253	0.056

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.98888	1
26DAP/20DAP	1.09078	0.642
34DAP/26DAP	0.97706	0.893
51DAP/34DAP	0.88081	0.079
52DAP/51DAP	1.02718	0.704
53DAP/52DAP	0.93185	0.772
55DAP/53DAP	1.06836	0.653
57DAP/55DAP	0.96838	0.854
62DAP/57DAP	1.04743	0.868
68DAP/62DAP	1.16829	0.689
68DAP/14DAP	0.91645	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.07442	0.184

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.44262	0.058
Mature Green Tomato/Ripe Tomato	1.63838	0.119
Immature Eggplant/Mature Eggplant	1.18549	0.321
Ripe Pepper/Ripe Tomato	0.66644	0.224
Mature Eggplant/Ripe Tomato	1.63284	0.268

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.03935	1
1-1-2/M82	1.04923	1
12-2/M82	1.00678	1
12-4/M82	1.0232	0.611
1-3/M82	0.99239	1
2-1-1/M82	1.22501	0.764
2-1/M82	N/A	N/A
2-6/M82	0.95036	1
3-2/M82	1.0953
4-1-1/M82	0.99461	1
4-1/M82	1.0515
4-3-2/M82	N/A	N/A
4-3/M82	1.09855	1
5-3/M82	1.03543	1
6-2/M82	0.96074	1
6-3/M82	1.10857	1
7-1/M82	N/A	N/A
7-2/M82	0.87662	0.578
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.29675	0.365
IL2-6/WTpooled	1.03202	1
IL7-5/WTpooled	1.49908	0.792
IL7-3/WTpooled	1.16164	0.362
IL12-4/WTpooled	1.18733	0.737
IL1-4/WTpooled	1.25871	1
WT/WTpooled	1.00636	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	0.95361	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.02919	0.921
DC3000/delta hrp 6h	1.00673	0.95
DC3000/delta hrp 12h	0.97169	1
DC3000/delta hrp 24h	1.0784	0.535

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.04047	0.476
DC3000 delta B/DC3000 delta AB	1.05559	0.477

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.95281	1
Exp 36h	1.0886	0.693
Exp 60h	1.28011	0.283

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01519	1
Var 0h	0.9493	0.933
Var 12h I row2-row1	1.27951	0.228
Var 12h NI row2-row1	1.01338	1
Var 36h I row2-row1	1.17434	1
Var 36h NI row2-row1	0.96043	0.743
Var 60h I row2-row1	1.12644	1
Var 60h NI row2-row1	1.10553	1
Time course 0hI-0hNI	1.09062	0.799
Time course 12hI-12hNI	1.06457	0.611
Time course 36hI-36hNI	1.17776	0.015
Time course 60hI-60hNI	1.21199	0.025

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)	0.95427	0.324
transgenic ySAMdc/azygous control (breaker)	0.77214	0.131
transgenic ySAMdc/azygous control (red)	0.87263	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.03072	0.587

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.83295	0.229

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.79257	0.172
Manapal/WT (break)	0.90952	1
Manapal/WT (red)	1.24793	0.413