Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.4.13.6

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.49875	0.24
27DAP/17DAP	0.9012	0.779
39DAP/27DAP	1.11481	0.702
41DAP/39DAP	0.70022	0.114
42DAP/41DAP	1.04129	0.994
43DAP/42DAP	1.01423	0.932
47DAP/43DAP	1.1385	0.659
52DAP/47DAP	1.37117	0.428
57DAP/52DAP	1.10421	0.935

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87366	0.121
17DAP/reference	0.97044	0.567
27DAP/reference	1.07224	0.58
39DAP/reference	1.01859	0.857
41DAP/reference	0.96279	0.542
42DAP/reference	0.84884	0.003
43DAP/reference	0.95938	0.538
47DAP/reference	1.40251	0.057
52DAP/reference	1.2527	0.114
57DAP/reference	1.23544	0.034

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.13773	0.135
27DAP/17DAP	0.96056	0.418
39DAP/27DAP	1.01869	0.707
41DAP/39DAP	0.8532	0.512
42DAP/41DAP	1.03265	0.961
43DAP/42DAP	0.98516	0.751
47DAP/43DAP	0.97521	0.861
52DAP/47DAP	1.00019	0.987
57DAP/52DAP	1.0016	1
57DAP/7DAP	1.05626	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90331	0.077
17DAP/reference	0.94976	0.192
27DAP/reference	0.96161	0.231
39DAP/reference	1.22253	0.006
41DAP/reference	0.92196	0.079
42DAP/reference	1.16934	0.018
43DAP/reference	1.05458	0.289
47DAP/reference	1.01463	1
52DAP/reference	0.98902	0.571
57DAP/reference	0.97802	0.367

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.88993	0.064
17DAP/reference	0.9483	0.182
27DAP/reference	0.87118	0.093
39DAP/reference	0.95308	0.322
41DAP/reference	0.82965	0.096
42DAP/reference	0.93708	0.039
43DAP/reference	0.86999	0.008
47DAP/reference	0.98475	0.512
52DAP/reference	0.87278	0.017
57DAP/reference	0.85166	0.013

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87016	0.028
17DAP/reference	0.9137	0.093
27DAP/reference	0.93396	0.076
39DAP/reference	1.07559	0.365
41DAP/reference	1.11975	0.031
42DAP/reference	1.02345	0.907
43DAP/reference	0.91806	0.081
47DAP/reference	0.94595	0.259
52DAP/reference	1.01773	0.979
57DAP/reference	1.51955	0.034

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.97921	1
26DAP/20DAP	1.05348	0.855
34DAP/26DAP	0.96105	0.834
51DAP/34DAP	0.93931	0.482
52DAP/51DAP	0.96548	0.151
53DAP/52DAP	0.98717	0.902
55DAP/53DAP	1.03521	0.771
57DAP/55DAP	1.04508	0.975
62DAP/57DAP	0.98549	0.994
68DAP/62DAP	1.00763	0.885
68DAP/14DAP	1.03564	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.51401	0.021

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.86934	0.356
Mature Green Tomato/Ripe Tomato	0.89771	0.347
Immature Eggplant/Mature Eggplant	2.2116	0.05
Ripe Pepper/Ripe Tomato	0.97805	1
Mature Eggplant/Ripe Tomato	0.56426	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.99432	1
1-1-2/M82	0.9874	1
12-2/M82	0.93801	0.955
12-4/M82	1.03624	1
1-3/M82	1.12887	1
2-1-1/M82	0.91318	0.565
2-1/M82	1.02441	1
2-6/M82	0.94758	1
3-2/M82	0.9984	1
4-1-1/M82	0.98957	1
4-1/M82	1.14236	0.853
4-3-2/M82	1.02786	1
4-3/M82	0.94444	0.72
5-3/M82	0.9774	1
6-2/M82	0.94111	1
6-3/M82	1.05603	1
7-1/M82	1.03523	0.598
7-2/M82	0.96661	1
9-3-2/M82	1.09385	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.95506	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.99028	1
IL12-4/WTpooled	0.98235	1
IL1-4/WTpooled	0.72094	0.699
WT/WTpooled	1.09518	0.911

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	0.97402	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.0485	0.692
DC3000/delta hrp 6h	0.71273	0.914
DC3000/delta hrp 12h	1.02627	1
DC3000/delta hrp 24h	1.04925	0.673

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.03091	0.384
DC3000 delta B/DC3000 delta AB	1.1833	0.196

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.48704	1
Exp 36h	1.06265	1
Exp 60h	1.06201	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.9738	1
Var 0h	1.06757	0.782
Var 12h I row2-row1	1.11279	0.242
Var 12h NI row2-row1	1.01909	1
Var 36h I row2-row1	0.76559	0.805
Var 36h NI row2-row1	1.00153	1
Var 60h I row2-row1	1.1266	1
Var 60h NI row2-row1	1.17124	0.904
Time course 0hI-0hNI	1.1037	0.719
Time course 12hI-12hNI	1.04088	0.756
Time course 36hI-36hNI	0.98738	0.611
Time course 60hI-60hNI	1.39624	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)	0.98571	0.862
transgenic ySAMdc/azygous control (breaker)	0.58117	0.132
transgenic ySAMdc/azygous control (red)	0.98756	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.2098	0.044

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.64	0.255

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.95428	1
Manapal/WT (break)	1.06989	0.381
Manapal/WT (red)	0.49811	0.181