Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.1.1.6

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.9586	0.713
27DAP/17DAP	0.85463	0.585
39DAP/27DAP	1.13161	1
41DAP/39DAP	1.00676	0.958
42DAP/41DAP	1.10602	0.926
43DAP/42DAP	0.92592	0.846
47DAP/43DAP	1.7903	0.316
52DAP/47DAP	1.31589	0.597
57DAP/52DAP	1.17515	0.826

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91192	0.616
17DAP/reference	0.55884	0.011
27DAP/reference	0.84824	0.339
39DAP/reference	0.70115	0.012
41DAP/reference	1.00883	0.814
42DAP/reference	0.91631	0.25
43DAP/reference	0.68568	0.019
47DAP/reference	0.61342	0.011
52DAP/reference	0.89872	0.275
57DAP/reference	0.8414	0.235

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.32051	0.298
27DAP/17DAP	1.09472	0.98
39DAP/27DAP	1.13143	0.56
41DAP/39DAP	1.152	0.837
42DAP/41DAP	1.20964	0.763
43DAP/42DAP	1.06817	0.664
47DAP/43DAP	1.03886	0.873
52DAP/47DAP	1.05256	0.835
57DAP/52DAP	0.91702	0.646
57DAP/7DAP	1.45455	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87053	0.326
17DAP/reference	0.95517	0.056
27DAP/reference	0.98928	0.462
39DAP/reference	0.94876	0.039
41DAP/reference	0.79125	0.079
42DAP/reference	0.8239	0.01
43DAP/reference	0.87284	0.02
47DAP/reference	0.7958	0.168
52DAP/reference	0.89307	0.053
57DAP/reference	0.90947	0.015

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.6374	0.028
17DAP/reference	0.6933	0.043
27DAP/reference	0.69358	0.144
39DAP/reference	0.64712	0.119
41DAP/reference	0.48397	0.007
42DAP/reference	1.08481	0.482
43DAP/reference	0.77808	0.087
47DAP/reference	0.89769	0.368
52DAP/reference	0.64145	0.008
57DAP/reference	0.68845	0.054

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02893	0.505
17DAP/reference	0.98804	0.727
27DAP/reference	0.94901	0.49
39DAP/reference	0.95549	0.199
41DAP/reference	0.97739	0.371
42DAP/reference	0.90657	0.445
43DAP/reference	1.02303	1
47DAP/reference	0.76911	0.286
52DAP/reference	0.75587	0.22
57DAP/reference	1.00287	0.516

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.09187	0.966
26DAP/20DAP	1.23584	0.718
34DAP/26DAP	0.88144	0.816
51DAP/34DAP	0.91582	0.688
52DAP/51DAP	0.79643	1
53DAP/52DAP	0.9778	0.909
55DAP/53DAP	1.14485	0.82
57DAP/55DAP	1.77886	0.474
62DAP/57DAP	1.12494	0.098
68DAP/62DAP	1.09594	0.869
68DAP/14DAP	1.01947	0.915

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.2972	0.087

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.58771	0.153
Mature Green Tomato/Ripe Tomato	0.5002	0.022
Immature Eggplant/Mature Eggplant	0.96417	0.72
Ripe Pepper/Ripe Tomato	1.82695	0.235
Mature Eggplant/Ripe Tomato	1.61471	0.268

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.59631	0.742
1-1-2/M82	1.1691	1
12-2/M82	1.03075
12-4/M82	1.07589	1
1-3/M82	1.57391	1
2-1-1/M82	0.71046
2-1/M82	1.14337
2-6/M82	0.92191	1
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	1.0568	1
5-3/M82	1.02255	1
6-2/M82	1.20785
6-3/M82	0.98919	1
7-1/M82	1.27044	0.598
7-2/M82	0.82554	0.796
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.93196	0.321
IL2-6/WTpooled	1.2562	0.659
IL7-5/WTpooled	1.01056	1
IL7-3/WTpooled	0.61711	0.293
IL12-4/WTpooled	0.90805	1
IL1-4/WTpooled	0.93037	0.834
WT/WTpooled	0.97252	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	0.94393	0.341

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.99839	1
DC3000/delta hrp 6h	0.92683	0.95
DC3000/delta hrp 12h	1.12649	1
DC3000/delta hrp 24h	0.85	0.145

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	N/A
DC3000 delta B/DC3000 delta AB	0.42174	0.103

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.88908	1
Exp 36h	0.98891	0.943
Exp 60h	0.89395	0.664

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00691	1
Var 0h	0.75858	1
Var 12h I row2-row1	1.21906	0.242
Var 12h NI row2-row1	0.8797	0.394
Var 36h I row2-row1	0.85356	0.438
Var 36h NI row2-row1	1.43677	0.253
Var 60h I row2-row1	0.80529
Var 60h NI row2-row1	1.1879	0.904
Time course 0hI-0hNI	0.88538	0.325
Time course 12hI-12hNI	0.86553	0.147
Time course 36hI-36hNI	0.81184	0.035
Time course 60hI-60hNI	0.28997	0.006

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)	1.10981	0.261
transgenic ySAMdc/azygous control (breaker)	0.89089	0.49
transgenic ySAMdc/azygous control (red)	0.88747	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	3.64466	0.036

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.91107	0.083
Manapal/WT (break)	1.35303	0.381
Manapal/WT (red)	1.41981	0.133