Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.2.7.17

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.23711	0.414
27DAP/17DAP	1.11304	0.852
39DAP/27DAP	0.92225	0.482
41DAP/39DAP	1.02136	0.925
42DAP/41DAP	1.09031	0.992
43DAP/42DAP	1.07144	1
47DAP/43DAP	1.11358	0.733
52DAP/47DAP	0.79387	0.502
57DAP/52DAP	1.18311	0.963

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.83893	0.162
17DAP/reference	1.03893	0.874
27DAP/reference	0.80768	0.011
39DAP/reference	1.04611	0.639
41DAP/reference	0.86806	0.341
42DAP/reference	0.91085	0.103
43DAP/reference	1.12963	0.36
47DAP/reference	0.88443	0.065
52DAP/reference	0.88821	0.215
57DAP/reference	1.03161	0.927

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.14344
27DAP/17DAP	1.04796	0.842
39DAP/27DAP	0.98127	0.852
41DAP/39DAP	1.05632	0.817
42DAP/41DAP	0.96225	0.641
43DAP/42DAP	1.06321	0.042
47DAP/43DAP	1.01324	0.951
52DAP/47DAP	1.00864	0.991
57DAP/52DAP	0.92286	0.213
57DAP/7DAP	0.95446	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.68319	0.095
17DAP/reference	1.08416	1
27DAP/reference	0.81615	0.125
39DAP/reference	1.07053	1
41DAP/reference	1.18533	0.593
42DAP/reference	0.91546	0.32
43DAP/reference	1.00742	0.764
47DAP/reference	1.0703	0.901
52DAP/reference	0.95525	0.679
57DAP/reference	1.15894	0.438

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9099	0.487
17DAP/reference	0.90557	0.189
27DAP/reference	1.01368	1
39DAP/reference	0.90537	0.214
41DAP/reference	0.99282	0.557
42DAP/reference	1.10344	0.433
43DAP/reference	1.02209	0.875
47DAP/reference	0.91219	0.221
52DAP/reference	1.03447	0.938
57DAP/reference	1.06783	0.93

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.86365	0.23
17DAP/reference	0.88758	0.328
27DAP/reference	1.008	1
39DAP/reference	0.95695	0.299
41DAP/reference	1.53278	0.031
42DAP/reference	0.92977	0.552
43DAP/reference	1.67211	0.259
47DAP/reference	0.98434	0.593
52DAP/reference	1.69667	0.088
57DAP/reference	1.1332	0.592

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.24773	0.85
26DAP/20DAP	0.97945	1
34DAP/26DAP	1.00606	1
51DAP/34DAP	1.03691	0.719
52DAP/51DAP	1.05898	0.454
53DAP/52DAP	1.19113
55DAP/53DAP	0.89431
57DAP/55DAP	1.15631	0.906
62DAP/57DAP	0.94673	0.994
68DAP/62DAP	0.5992
68DAP/14DAP	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.96626	0.576

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.38248	0.267
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	1.70011
Mature Eggplant/Ripe Tomato	1.01579	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.11832	0.551
1-1-2/M82	0.96169	1
12-2/M82	1.01035	1
12-4/M82	1.0406	1
1-3/M82	1.00633	1
2-1-1/M82	1.02198	1
2-1/M82	1.14417	1
2-6/M82	1.01265	1
3-2/M82	0.99275	1
4-1-1/M82	1.02625	1
4-1/M82	0.86489	0.737
4-3-2/M82	0.98403	1
4-3/M82	1.01895	1
5-3/M82	0.93744	1
6-2/M82	1.03352	1
6-3/M82	0.98821	1
7-1/M82	1.00367	1
7-2/M82	1.03091	1
9-3-2/M82	0.94926	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.56647	0.358
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	2.04266	1
IL12-4/WTpooled	1.13569	0.785
IL1-4/WTpooled	1.13601
WT/WTpooled	0.99613	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	0.87445	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.95231	1
DC3000/delta hrp 6h	1.1162	0.95
DC3000/delta hrp 12h	1.03831	1
DC3000/delta hrp 24h	1.05161	0.633

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.05102	0.441
DC3000 delta B/DC3000 delta AB	1.07799	0.42

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	1.10763	1
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	0.98921	1
Var 0h	0.54429	0.933
Var 12h I row2-row1	1.16878	0.22
Var 12h NI row2-row1	0.91365	0.713
Var 36h I row2-row1	0.99444	1
Var 36h NI row2-row1	0.83784	0.421
Var 60h I row2-row1	1.13478	0.562
Var 60h NI row2-row1	1.18098	0.904
Time course 0hI-0hNI	1.05099	0.867
Time course 12hI-12hNI	1.02213	0.836
Time course 36hI-36hNI	1.01294	0.975
Time course 60hI-60hNI	1.30003	0.008

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)	1.0537	0.3
transgenic ySAMdc/azygous control (breaker)	0.80135	0.15
transgenic ySAMdc/azygous control (red)	1.03676	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.99569	0.832

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.6163	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.70629	1
Manapal/WT (break)	1.05842	1
Manapal/WT (red)	1.23288	0.413