Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.1.4.16

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.95216	0.64
27DAP/17DAP	1.00674	1
39DAP/27DAP	1.12052	0.774
41DAP/39DAP	1.00148	0.887
42DAP/41DAP	0.94155	1
43DAP/42DAP	1.02602	0.937
47DAP/43DAP	1.00067	0.876
52DAP/47DAP	1.34401	0.463
57DAP/52DAP	1.02875	1

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.08626	0.147
17DAP/reference	1.05146	0.08
27DAP/reference	0.99563	0.847
39DAP/reference	1.02628	0.771
41DAP/reference	1.03834	0.759
42DAP/reference	1.08856	0.144
43DAP/reference	1.08798	0.089
47DAP/reference	0.96889	0.242
52DAP/reference	0.89218	0.049
57DAP/reference	0.87428	0.049

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.97944	0.732
27DAP/17DAP	1.00895	0.98
39DAP/27DAP	0.98206	0.87
41DAP/39DAP	1.03772	0.88
42DAP/41DAP	1.02213	0.872
43DAP/42DAP	1.00753	1
47DAP/43DAP	1.0163	0.951
52DAP/47DAP	0.98527	0.925
57DAP/52DAP	0.99259	0.838
57DAP/7DAP	1.17736	0.204

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02936	0.761
17DAP/reference	1.02592	0.147
27DAP/reference	1.02979	0.551
39DAP/reference	0.96144	0.015
41DAP/reference	0.96294	0.223
42DAP/reference	0.92259	0.022
43DAP/reference	0.91654	0.023
47DAP/reference	1.0713	0.659
52DAP/reference	0.97355	0.363
57DAP/reference	0.97261	0.093

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.11544	0.172
17DAP/reference	1.1026	0.089
27DAP/reference	1.02978	0.769
39DAP/reference	1.03061	0.935
41DAP/reference	0.9987	0.735
42DAP/reference	0.89019	0.032
43DAP/reference	1.14894	0.047
47DAP/reference	0.96557	0.359
52DAP/reference	0.98232	0.5
57DAP/reference	1.1155	0.094

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03922	0.433
17DAP/reference	1.05108	0.365
27DAP/reference	1.01859	0.749
39DAP/reference	1.00536	0.962
41DAP/reference	1.04562	0.439
42DAP/reference	1.3024	0.022
43DAP/reference	1.08931	0.452
47DAP/reference	1.04516	0.388
52DAP/reference	1.03552	0.876
57DAP/reference	0.85769	0.03

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.90899	0.915
26DAP/20DAP	0.92652	1
34DAP/26DAP	0.82177	0.44
51DAP/34DAP	1.11207	0.746
52DAP/51DAP	0.95086	1
53DAP/52DAP	1.05952	0.489
55DAP/53DAP	1.03938	0.911
57DAP/55DAP	0.99922	0.914
62DAP/57DAP	1.05922	0.569
68DAP/62DAP	0.78284	0.044
68DAP/14DAP	0.8374	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.29289	0.015

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.23961	0.287
Mature Green Tomato/Ripe Tomato	1.28058	0.095
Immature Eggplant/Mature Eggplant	1.17	0.074
Ripe Pepper/Ripe Tomato	0.78625	0.224
Mature Eggplant/Ripe Tomato	2.42286	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.01409	1
1-1-2/M82	1.10276	1
12-2/M82	1.15176	0.61
12-4/M82	0.95151	0.619
1-3/M82	1.05899	1
2-1-1/M82	1.01022	1
2-1/M82	1.07713	1
2-6/M82	0.96477	1
3-2/M82	0.87954	0.451
4-1-1/M82	1.27584	1
4-1/M82	1.09441	1
4-3-2/M82	1.24806	1
4-3/M82	1.2727	1
5-3/M82	1.09098	0.572
6-2/M82	0.9155	0.497
6-3/M82	1.00493	1
7-1/M82	1.0845	0.87
7-2/M82	1.14316	1
9-3-2/M82	1.05753	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.93243	1
IL2-6/WTpooled	0.99561	1
IL7-5/WTpooled	0.69623	1
IL7-3/WTpooled	0.83433	0.418
IL12-4/WTpooled	1.01473	1
IL1-4/WTpooled	1.01682	1
WT/WTpooled	1.03037	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	1.05203	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.04166	0.823
DC3000/delta hrp 6h	1.01593	1
DC3000/delta hrp 12h	1.10455	1
DC3000/delta hrp 24h	1.05859	0.535

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.07082	0.313
DC3000 delta B/DC3000 delta AB	1.01933	0.677

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.99772	1
Exp 36h	1.17025	1
Exp 60h	1.06239	1

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	N/A	N/A
Var 12h I row2-row1	N/A	N/A
Var 12h NI row2-row1	N/A	N/A
Var 36h I row2-row1	N/A	N/A
Var 36h NI row2-row1	N/A	N/A
Var 60h I row2-row1	N/A	N/A
Var 60h NI row2-row1	N/A	N/A
Time course 0hI-0hNI	N/A	N/A
Time course 12hI-12hNI	N/A	N/A
Time course 36hI-36hNI	N/A	N/A
Time course 60hI-60hNI	N/A	N/A

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)	0.93107	0.314
transgenic ySAMdc/azygous control (breaker)	1.54076	0.172
transgenic ySAMdc/azygous control (red)	1.17867	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.06528	0.08

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.93322	0.284

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.76253	1
Manapal/WT (break)	0.83106	0.333
Manapal/WT (red)	1.20546	0.222