Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.2.3.17

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.11641	0.977
27DAP/17DAP	1.03687	0.926
39DAP/27DAP	0.81271	0.378
41DAP/39DAP	1.23166	0.352
42DAP/41DAP	1.11587	1
43DAP/42DAP	0.84881	0.705
47DAP/43DAP	1.00862	1
52DAP/47DAP	1.11197	0.949
57DAP/52DAP	0.91433	0.912

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00375	1
17DAP/reference	0.943	0.24
27DAP/reference	0.93435	0.406
39DAP/reference	0.80926	0.267
41DAP/reference	0.85467	0.201
42DAP/reference	0.92838	0.028
43DAP/reference	0.72982
47DAP/reference	0.93268	0.098
52DAP/reference	0.90862	0.23
57DAP/reference	N/A	N/A

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.00632	1
27DAP/17DAP	1.00241	1
39DAP/27DAP	1.03633	0.663
41DAP/39DAP	1.01572	1
42DAP/41DAP	0.98014	0.777
43DAP/42DAP	0.98794	0.902
47DAP/43DAP	1.01152	0.957
52DAP/47DAP	1.05084	0.816
57DAP/52DAP	0.99805	0.902
57DAP/7DAP	1.21675	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.88584	0.129
17DAP/reference	0.89991	0.019
27DAP/reference	0.86659	0.017
39DAP/reference	0.95171	0.17
41DAP/reference	0.90029	0.034
42DAP/reference	0.92948	0.106
43DAP/reference	0.86372	0.016
47DAP/reference	0.86495	0.044
52DAP/reference	0.85666	0.072
57DAP/reference	0.91377	0.156

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03686	0.65
17DAP/reference	1.00882	0.839
27DAP/reference	1.18384	0.116
39DAP/reference	0.99906	0.661
41DAP/reference	1.00293	0.683
42DAP/reference	0.871	0.081
43DAP/reference	1.02806	0.785
47DAP/reference	0.8893	0.028
52DAP/reference	0.98887	0.537
57DAP/reference	0.89529	0.073

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.8403	0.049
17DAP/reference	0.98113	0.624
27DAP/reference	0.90797	0.038
39DAP/reference	0.93658	0.076
41DAP/reference	0.9345	0.167
42DAP/reference	0.86795	0.087
43DAP/reference	0.96185	0.334
47DAP/reference	0.95077	0.215
52DAP/reference	0.83935	0.155
57DAP/reference	1.16358	0.245

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.93988	1
26DAP/20DAP	1.00175	1
34DAP/26DAP	1.02821	0.819
51DAP/34DAP	0.96199	0.722
52DAP/51DAP	1.02417	0.77
53DAP/52DAP	1.01003	1
55DAP/53DAP	0.99871	0.917
57DAP/55DAP	1.20317	0.492
62DAP/57DAP	0.93798	0.994
68DAP/62DAP	0.96011	0.863
68DAP/14DAP	1.07386	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.14301	0.264

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.63358	0.058
Mature Green Tomato/Ripe Tomato	1.18778	0.399
Immature Eggplant/Mature Eggplant	0.55361	0.062
Ripe Pepper/Ripe Tomato	1.94098	1
Mature Eggplant/Ripe Tomato	2.8403	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.96375	0.944
1-1-2/M82	1.07818	1
12-2/M82	1.1072
12-4/M82	0.97548	1
1-3/M82	0.9763	1
2-1-1/M82	0.96787
2-1/M82	N/A	N/A
2-6/M82	0.96773	1
3-2/M82	1.07017
4-1-1/M82	0.98013	1
4-1/M82	0.85628	0.737
4-3-2/M82	1.08453	1
4-3/M82	1.17882
5-3/M82	1.03947	1
6-2/M82	1.14521	1
6-3/M82	0.97959	1
7-1/M82	1.08509	0.992
7-2/M82	0.96127	1
9-3-2/M82	1.00859

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.02789	1
IL2-6/WTpooled	0.94787	1
IL7-5/WTpooled	0.95277	1
IL7-3/WTpooled	1.13449	0.362
IL12-4/WTpooled	1.03171	0.785
IL1-4/WTpooled	0.9365	0.834
WT/WTpooled	0.98634	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	0.8334	0.497

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.99147	1
DC3000/delta hrp 6h	1.08242	1
DC3000/delta hrp 12h	0.95167	1
DC3000/delta hrp 24h	1.04207	0.604

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.98629	1
DC3000 delta B/DC3000 delta AB	1.0318	0.579

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.07571	1
Exp 36h	0.75019	0.471
Exp 60h	0.74262	0.343

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

hybridization	ratio	FDR (corrected p value)
self-self	N/A	N/A
Var 0h	0.19139	1
Var 12h I row2-row1	1.11984	0.196
Var 12h NI row2-row1	1.25274	1
Var 36h I row2-row1	1.07921	1
Var 36h NI row2-row1	0.94847	0.791
Var 60h I row2-row1	1.4249
Var 60h NI row2-row1	0.99464	0.977
Time course 0hI-0hNI	1.01138	1
Time course 12hI-12hNI	0.84663	0.624
Time course 36hI-36hNI	0.78496	0.134
Time course 60hI-60hNI	0.80755	0.161

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)	0.93904	0.267
transgenic ySAMdc/azygous control (breaker)	1.33999	1
transgenic ySAMdc/azygous control (red)	1.53676	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.01448	0.587

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.64909	0.237

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	2.88771	0.088
Manapal/WT (break)	2.88501	0.123
Manapal/WT (red)	2.6308	0.126