Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.1.19.19

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.9322	0.617
27DAP/17DAP	1.19409	0.844
39DAP/27DAP	0.95724	0.733
41DAP/39DAP	1.00572	1
42DAP/41DAP	0.8559	0.774
43DAP/42DAP	0.79966	0.483
47DAP/43DAP	0.90537	0.66
52DAP/47DAP	0.94463	0.8
57DAP/52DAP	0.87176	0.784

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93545	0.39
17DAP/reference	0.86357	0.021
27DAP/reference	0.87128	0.444
39DAP/reference	0.88759	0.141
41DAP/reference	0.95266	0.542
42DAP/reference	0.91615	0.059
43DAP/reference	0.89183	0.08
47DAP/reference	1.12572	0.264
52DAP/reference	0.99508	0.654
57DAP/reference	1.04806	0.564

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.10781	0.593
27DAP/17DAP	1.10694	0.719
39DAP/27DAP	1.03563	0.824
41DAP/39DAP	0.98726	1
42DAP/41DAP	1.00678	0.91
43DAP/42DAP	1.09411	0.176
47DAP/43DAP	1.07238	0.906
52DAP/47DAP	0.97755	0.905
57DAP/52DAP	1.10739	0.772
57DAP/7DAP	0.78085	0.186

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87046	0.129
17DAP/reference	0.96522	0.389
27DAP/reference	1.06801	0.804
39DAP/reference	0.76453	0.073
41DAP/reference	0.68627	0.062
42DAP/reference	0.89877	0.304
43DAP/reference	1.06469	0.873
47DAP/reference	0.98979	1
52DAP/reference	0.84326	0.097
57DAP/reference	1.05566	0.966

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93415	0.353
17DAP/reference	1.03882	0.739
27DAP/reference	0.94224	0.249
39DAP/reference	1.10828	0.164
41DAP/reference	0.87707	0.218
42DAP/reference	0.95374	0.321
43DAP/reference	1.42582	0.199
47DAP/reference	0.90896	0.123
52DAP/reference	1.07943	0.747
57DAP/reference	1.01843	0.789

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90836	0.311
17DAP/reference	0.92045	0.433
27DAP/reference	1.26898	0.26
39DAP/reference	0.93054	0.246
41DAP/reference	1.12196	0.369
42DAP/reference	1.00064	1
43DAP/reference	0.99023	0.66
47DAP/reference	0.88063	0.174
52DAP/reference	1.1119	0.821
57DAP/reference	0.91364	0.394

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.98603	1
26DAP/20DAP	1.00564	1
34DAP/26DAP	1.1783	0.819
51DAP/34DAP	1.10059	0.565
52DAP/51DAP	0.87894	1
53DAP/52DAP	0.97841	0.882
55DAP/53DAP	0.77185	0.053
57DAP/55DAP	1.22496	0.793
62DAP/57DAP	0.98078	0.994
68DAP/62DAP	1.65484	0.455
68DAP/14DAP	1.04652

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.76573	0.145

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.90331	0.491
Mature Green Tomato/Ripe Tomato	1.09477	0.898
Immature Eggplant/Mature Eggplant	1.2541	0.105
Ripe Pepper/Ripe Tomato	0.73101	1
Mature Eggplant/Ripe Tomato	0.95446	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.01326	1
1-1-2/M82	N/A	N/A
12-2/M82	0.97406
12-4/M82	0.94575
1-3/M82	0.94175
2-1-1/M82	0.86736
2-1/M82	0.87723
2-6/M82	0.81764	0.501
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	1.13665
5-3/M82	1.05728	1
6-2/M82	N/A	N/A
6-3/M82	1.06298
7-1/M82	N/A	N/A
7-2/M82	0.81942
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.32547	0.277
IL2-6/WTpooled	1.02809	1
IL7-5/WTpooled	2.17451	0.722
IL7-3/WTpooled	1.16812	1
IL12-4/WTpooled	1.37965	0.516
IL1-4/WTpooled	1.12573	1
WT/WTpooled	0.93993	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	0.8757	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.04498	0.921
DC3000/delta hrp 6h	1.06175	1
DC3000/delta hrp 12h	0.94893	1
DC3000/delta hrp 24h	1.06679	0.69

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	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.92862	1
Exp 36h	0.951	0.699
Exp 60h	0.81004	0.266

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

hybridization	ratio	FDR (corrected p value)
self-self	1.02593	1
Var 0h	0.59327	0.933
Var 12h I row2-row1	1.06563	0.406
Var 12h NI row2-row1	1.75146	0.649
Var 36h I row2-row1	1.04212	1
Var 36h NI row2-row1	0.94551	0.645
Var 60h I row2-row1	0.88262	0.439
Var 60h NI row2-row1	0.91772	0.756
Time course 0hI-0hNI	1.02371	1
Time course 12hI-12hNI	1.16842	0.033
Time course 36hI-36hNI	1.16324	0.07
Time course 60hI-60hNI	1.48344	0.011

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)	0.96579	0.614
transgenic ySAMdc/azygous control (breaker)	0.75513	0.142
transgenic ySAMdc/azygous control (red)	0.94379	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.1126	0.049

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.89019	0.255

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.20962	0.307
Manapal/WT (break)	0.82326	0.333
Manapal/WT (red)	0.77809	0.181