Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.1.14.4

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.61531	0.067
27DAP/17DAP	0.90085	0.783
39DAP/27DAP	2.29226	0.05
41DAP/39DAP	1.30985	0.545
42DAP/41DAP	0.53433	0.397
43DAP/42DAP	0.86409	0.717
47DAP/43DAP	0.53075	0.05
52DAP/47DAP	2.46056	0.112
57DAP/52DAP	0.69106	0.622

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	3.12348	0.008
17DAP/reference	1.20089	0.161
27DAP/reference	0.99048	0.725
39DAP/reference	0.99919	0.941
41DAP/reference	0.92006	0.267
42DAP/reference	1.66363	0.001
43DAP/reference	0.91158	0.163
47DAP/reference	0.87926	0.027
52DAP/reference	0.9306	0.283
57DAP/reference	0.81661	0.044

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.4255	0.036
27DAP/17DAP	1.09512	0.754
39DAP/27DAP	1.22671	0.471
41DAP/39DAP	1.28104	0.023
42DAP/41DAP	1.00519	0.776
43DAP/42DAP	2.4917	0.018
47DAP/43DAP	1.24392	0.245
52DAP/47DAP	0.56938	0.093
57DAP/52DAP	2.72052	0.031
57DAP/7DAP	1.3215	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	3.26845	0.024
17DAP/reference	1.169	0.134
27DAP/reference	1.40075	0.012
39DAP/reference	1.42527	0.007
41DAP/reference	2.09612	0.008
42DAP/reference	2.14186	0.007
43DAP/reference	3.44286	0.006
47DAP/reference	2.49062	0.015
52DAP/reference	2.11257	0.007
57DAP/reference	1.08794	0.108

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.65565	0.099
17DAP/reference	1.53884	0.034
27DAP/reference	1.56074	0.024
39DAP/reference	1.84769	0.011
41DAP/reference	2.06941	0.005
42DAP/reference	1.7931	0.012
43DAP/reference	1.03356	0.787
47DAP/reference	1.13389	0.148
52DAP/reference	0.89663	0.203
57DAP/reference	0.9251	0.408

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.97267	0.015
17DAP/reference	1.07257	0.887
27DAP/reference	0.88391	0.257
39DAP/reference	1.28986	0.01
41DAP/reference	0.83945	0.026
42DAP/reference	1.28977	0.47
43DAP/reference	1.3647	0.229
47DAP/reference	0.88821	0.072
52DAP/reference	0.91083	0.444
57DAP/reference	0.85097	0.109

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.07516	1
26DAP/20DAP	0.83523	0.512
34DAP/26DAP	0.93067	0.834
51DAP/34DAP	0.87091	0.436
52DAP/51DAP	1.13466	0.616
53DAP/52DAP	1.34962	0.048
55DAP/53DAP	1.03688	0.82
57DAP/55DAP	0.92952	0.658
62DAP/57DAP	0.6418	0.05
68DAP/62DAP	1.02504	0.939
68DAP/14DAP	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	2.0382	0.016

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.29177	0.017
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.11662	0.293
Mature Eggplant/Ripe Tomato	0.17434	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.69974
1-1-2/M82	0.62173
12-2/M82	N/A	N/A
12-4/M82	0.89477	0.282
1-3/M82	8.40844
2-1-1/M82	0.99414	1
2-1/M82	N/A	N/A
2-6/M82	0.97025
3-2/M82	2.31035
4-1-1/M82	N/A	N/A
4-1/M82	0.74907
4-3-2/M82	1.0441	1
4-3/M82	0.73275	0.611
5-3/M82	1.24991	1
6-2/M82	6.54701	0.253
6-3/M82	0.96453	1
7-1/M82	1.40451
7-2/M82	2.97898	0.324
9-3-2/M82	0.97083	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.90823
IL2-6/WTpooled	0.95162	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.53471
IL12-4/WTpooled	1.40909	0.673
IL1-4/WTpooled	0.89319	0.834
WT/WTpooled	0.98906	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	1.01585	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.61234	0.368
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	N/A	N/A
DC3000/delta hrp 24h	0.95841	0.67

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.73905	0.024
DC3000 delta B/DC3000 delta AB	0.79671	0.087

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.93082	1
Exp 36h	N/A	N/A
Exp 60h	0.9345	0.257

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

hybridization	ratio	FDR (corrected p value)
self-self	1.07684	1
Var 0h	0.69522	0.421
Var 12h I row2-row1	0.90163	0.467
Var 12h NI row2-row1	1.12731	1
Var 36h I row2-row1	0.97668	1
Var 36h NI row2-row1	0.92706	0.743
Var 60h I row2-row1	1.2857	0.562
Var 60h NI row2-row1	1.11148	0.904
Time course 0hI-0hNI	0.96272	0.812
Time course 12hI-12hNI	0.98472	0.931
Time course 36hI-36hNI	0.8192	0.066
Time course 60hI-60hNI	0.62429	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)	2.53757	0.264
transgenic ySAMdc/azygous control (breaker)	N/A	N/A
transgenic ySAMdc/azygous control (red)	0.64611	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.91729	0.16

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.82932	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	N/A	N/A
Manapal/WT (break)	N/A	N/A
Manapal/WT (red)	N/A	N/A