Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.1.3.13

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.20807	0.656
27DAP/17DAP	1.16253	0.883
39DAP/27DAP	0.46946	0.443
41DAP/39DAP	1.43517	0.806
42DAP/41DAP	0.63574	0.774
43DAP/42DAP	1.19221	0.923
47DAP/43DAP	2.03295	0.633
52DAP/47DAP	1.21431	0.941
57DAP/52DAP	1.06989	0.983

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.70557	0.028
17DAP/reference	0.63876	0.097
27DAP/reference	0.51843	0.013
39DAP/reference	0.61497	0.11
41DAP/reference	0.68307	0.201
42DAP/reference	2.64429	0.119
43DAP/reference	2.45664	0.287
47DAP/reference	2.7811	0.001
52DAP/reference	1.4027	0.092
57DAP/reference	N/A	N/A

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.13432	0.34
27DAP/17DAP	0.92296	0.537
39DAP/27DAP	0.87266	0.154
41DAP/39DAP	1.08001	0.799
42DAP/41DAP	0.99042	0.845
43DAP/42DAP	0.97323	0.774
47DAP/43DAP	1.04598	0.897
52DAP/47DAP	0.86165	0.261
57DAP/52DAP	1.04008	0.874
57DAP/7DAP	0.75611	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.83718	0.088
17DAP/reference	0.95375	0.338
27DAP/reference	0.93715	0.215
39DAP/reference	1.02638	0.74
41DAP/reference	1.01774	1
42DAP/reference	1.09876	0.233
43DAP/reference	0.97296	0.44
47DAP/reference	1.59984	0.049
52DAP/reference	0.96353	0.278
57DAP/reference	0.87969	0.05

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.72964	0.045
17DAP/reference	0.82955	0.058
27DAP/reference	0.84232	0.181
39DAP/reference	0.57206	0.028
41DAP/reference	1.00084	0.615
42DAP/reference	0.90652	0.121
43DAP/reference	0.68076	0.036
47DAP/reference	0.80333	0.081
52DAP/reference	0.45654	0.004
57DAP/reference	0.5861	0.015

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.78489	0.074
17DAP/reference	0.79496	0.177
27DAP/reference	0.96722	0.516
39DAP/reference	0.79894	0.076
41DAP/reference	0.8705	0.148
42DAP/reference	2.37381	0.068
43DAP/reference	3.52162	0.047
47DAP/reference	2.90868	0.006
52DAP/reference	1.90366	0.1
57DAP/reference	1.91395	0.019

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.43957	0.966
26DAP/20DAP	1.26465	0.409
34DAP/26DAP	1.0152	1
51DAP/34DAP	0.89361	0.472
52DAP/51DAP	0.86878	1
53DAP/52DAP	0.82865	0.535
55DAP/53DAP	0.69361	0.062
57DAP/55DAP	1.19228	0.626
62DAP/57DAP	0.88219	0.003
68DAP/62DAP	0.78139	0.787
68DAP/14DAP	0.99919	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.24447	0.122

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.04351	0.666
Mature Green Tomato/Ripe Tomato	1.86187	0.019
Immature Eggplant/Mature Eggplant	0.80034	0.092
Ripe Pepper/Ripe Tomato	0.4303	0.293
Mature Eggplant/Ripe Tomato	0.89981	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.72759	0.673
1-1-2/M82	1.23313	1
12-2/M82	1.13744
12-4/M82	0.90493	0.619
1-3/M82	2.76552	0.248
2-1-1/M82	0.95951	0.92
2-1/M82	0.7443
2-6/M82	0.8839	1
3-2/M82	N/A	N/A
4-1-1/M82	0.75008
4-1/M82	0.55261
4-3-2/M82	0.88118
4-3/M82	1.07052	1
5-3/M82	0.91581	1
6-2/M82	1.15953	1
6-3/M82	1.00282	1
7-1/M82	0.91935	1
7-2/M82	1.18322	1
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.04313	0.493
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	1.54124	0.792
IL7-3/WTpooled	0.89505	1
IL12-4/WTpooled	0.89192	1
IL1-4/WTpooled	1.03321	1
WT/WTpooled	0.88867	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	0.97509	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.98282	1
DC3000/delta hrp 6h	1.06012	1
DC3000/delta hrp 12h	1.44996	1
DC3000/delta hrp 24h	0.60499	0.036

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.82496	0.085
DC3000 delta B/DC3000 delta AB	0.7329	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.19009	1
Exp 36h	1.12156	1
Exp 60h	1.26086	0.283

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99539	1
Var 0h	0.48605	1
Var 12h I row2-row1	0.88395	0.514
Var 12h NI row2-row1	1.10581	1
Var 36h I row2-row1	1.10299	0.489
Var 36h NI row2-row1	1.14378	1
Var 60h I row2-row1	0.90434	0.832
Var 60h NI row2-row1	1.04135	1
Time course 0hI-0hNI	0.91937	0.438
Time course 12hI-12hNI	1.01252	0.892
Time course 36hI-36hNI	1.00926	1
Time course 60hI-60hNI	0.56782	0.005

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)	1.05051	0.748
transgenic ySAMdc/azygous control (breaker)	0.92336	0.49
transgenic ySAMdc/azygous control (red)	0.99688	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.0485	0.148

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.57307	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.32508	0.093
Manapal/WT (break)	1.34614	0.14
Manapal/WT (red)	0.89851	0.503