Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.1.7.13

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.12868	0.77
27DAP/17DAP	0.97152	0.966
39DAP/27DAP	1.83338	0.108
41DAP/39DAP	0.57376	0.054
42DAP/41DAP	1.26379	0.898
43DAP/42DAP	1.05017	1
47DAP/43DAP	0.66154	0.175
52DAP/47DAP	1.12185	0.945
57DAP/52DAP	1.33217	0.948

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.08632	0.403
17DAP/reference	0.98211	0.701
27DAP/reference	1.06661	0.415
39DAP/reference	0.99023	0.816
41DAP/reference	0.94765	0.341
42DAP/reference	1.01988	0.931
43DAP/reference	0.90914	0.155
47DAP/reference	1.26036	0.001
52DAP/reference	1.22492	0.096
57DAP/reference	1.23029	0.03

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.19294	0.192
27DAP/17DAP	1.08982	0.905
39DAP/27DAP	0.78734	0.095
41DAP/39DAP	1.33387	0.69
42DAP/41DAP	1.01068	0.887
43DAP/42DAP	0.84657	0.28
47DAP/43DAP	1.00526	0.997
52DAP/47DAP	0.97041	0.907
57DAP/52DAP	1.08926	0.567
57DAP/7DAP	0.89243	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.5097	0.039
17DAP/reference	1.29144	0.016
27DAP/reference	1.33091	0.02
39DAP/reference	1.28178	0.015
41DAP/reference	1.45539	0.011
42DAP/reference	1.30411	0.024
43DAP/reference	1.40236	0.007
47DAP/reference	1.52854	0.014
52DAP/reference	1.65317	0.008
57DAP/reference	1.49586	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.88847	0.17
17DAP/reference	1.22842	0.161
27DAP/reference	1.87944	0.018
39DAP/reference	1.47426	0.044
41DAP/reference	1.41658	0.026
42DAP/reference	1.4345	0.062
43DAP/reference	1.04317	0.814
47DAP/reference	1.19876	0.169
52DAP/reference	1.21128	0.043
57DAP/reference	0.97861	0.61

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.10766	0.142
17DAP/reference	0.94951	0.499
27DAP/reference	1.17767	0.025
39DAP/reference	1.361	0.018
41DAP/reference	1.01743	0.984
42DAP/reference	1.24963	0.239
43DAP/reference	1.42035	0.02
47DAP/reference	1.02427	0.646
52DAP/reference	1.29942	0.225
57DAP/reference	1.95222	0.008

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.86677	1
26DAP/20DAP	1.61023	0.102
34DAP/26DAP	0.84078	0.171
51DAP/34DAP	1.1282	0.706
52DAP/51DAP	0.84859	0.151
53DAP/52DAP	1.06474	0.623
55DAP/53DAP	0.79752	0.12
57DAP/55DAP	1.17159	0.728
62DAP/57DAP	1.2964	0.902
68DAP/62DAP	0.88645	0.543
68DAP/14DAP	2.0965

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.86976	0.304

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.93953	0.591
Mature Green Tomato/Ripe Tomato	1.84969	0.267
Immature Eggplant/Mature Eggplant	1.23887	0.053
Ripe Pepper/Ripe Tomato	2.51746	0.256
Mature Eggplant/Ripe Tomato	1.14568	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.8824	0.841
1-1-2/M82	1.24154	1
12-2/M82	0.64055
12-4/M82	0.99515	0.319
1-3/M82	2.48904	0.255
2-1-1/M82	N/A	N/A
2-1/M82	0.7237	0.74
2-6/M82	0.71363	1
3-2/M82	1.83598
4-1-1/M82	0.90605	1
4-1/M82	0.89659
4-3-2/M82	1.21664	0.508
4-3/M82	1.05329	1
5-3/M82	1.13359	0.496
6-2/M82	1.05873	1
6-3/M82	0.95833	1
7-1/M82	0.96115
7-2/M82	1.55927	1
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.86409	0.247
IL2-6/WTpooled	0.94836	1
IL7-5/WTpooled	1.27016	0.792
IL7-3/WTpooled	0.86212	0.31
IL12-4/WTpooled	1.00677	1
IL1-4/WTpooled	1.03187	1
WT/WTpooled	0.97834	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	1.11324	0.309

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.99312	1
DC3000/delta hrp 6h	0.97606	0.95
DC3000/delta hrp 12h	1.04679	1
DC3000/delta hrp 24h	0.8225	0.107

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.20711	0.05
DC3000 delta B/DC3000 delta AB	1.13754	0.304

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

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

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00063	1
Var 0h	0.74053	0.933
Var 12h I row2-row1	1.01844	1
Var 12h NI row2-row1	1.13014	1
Var 36h I row2-row1	1.10557	0.368
Var 36h NI row2-row1	0.8982	0.743
Var 60h I row2-row1	0.89742	0.832
Var 60h NI row2-row1	0.86086	0.63
Time course 0hI-0hNI	0.89995	0.24
Time course 12hI-12hNI	1.12489	0.036
Time course 36hI-36hNI	1.25153	0.056
Time course 60hI-60hNI	1.22268	0.013

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)	1.17057	0.277
transgenic ySAMdc/azygous control (breaker)	0.59961	0.139
transgenic ySAMdc/azygous control (red)	0.93117	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	2.17571	0.04

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.76437	0.255

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.66862	0.172
Manapal/WT (break)	1.09318	1
Manapal/WT (red)	1.90616	0.222