Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.3.1.6

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.92406	0.568
27DAP/17DAP	0.84854	0.558
39DAP/27DAP	1.44792	0.344
41DAP/39DAP	0.89176	0.571
42DAP/41DAP	0.95545	1
43DAP/42DAP	1.3521	0.69
47DAP/43DAP	0.73114	0.25
52DAP/47DAP	1.35243	0.48
57DAP/52DAP	1.38996	0.638

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.70893	0.025
17DAP/reference	0.7578	0.008
27DAP/reference	1.0784	0.446
39DAP/reference	0.79411	0.019
41DAP/reference	0.7101	0.011
42DAP/reference	1.29894	0.005
43DAP/reference	0.86372	0.019
47DAP/reference	1.17239	0.035
52DAP/reference	1.62387	0.008
57DAP/reference	1.19109	0.026

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.91736	0.613
27DAP/17DAP	1.58947	0.353
39DAP/27DAP	0.95649	0.859
41DAP/39DAP	0.93726	0.822
42DAP/41DAP	0.9538	0.637
43DAP/42DAP	1.18853	0.25
47DAP/43DAP	1.16356	0.63
52DAP/47DAP	2.12596	0.048
57DAP/52DAP	6.97491	0.058
57DAP/7DAP	0.87759	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.44173	0.054
17DAP/reference	1.30839	0.054
27DAP/reference	1.24135	0.041
39DAP/reference	1.00697	0.745
41DAP/reference	1.5646	0.03
42DAP/reference	1.43352	0.076
43DAP/reference	1.49901	0.023
47DAP/reference	1.50619	0.079
52DAP/reference	1.13951	0.352
57DAP/reference	1.64802	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.88618	0.277
17DAP/reference	0.86712	0.139
27DAP/reference	1.1446	0.373
39DAP/reference	1.17714	0.17
41DAP/reference	1.27175	0.199
42DAP/reference	1.15956	0.126
43DAP/reference	0.84753	0.17
47DAP/reference	0.80541	0.015
52DAP/reference	1.0548	0.838
57DAP/reference	0.78774	0.004

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.0258	0.918
17DAP/reference	1.04767	0.784
27DAP/reference	1.36952	0.04
39DAP/reference	1.0401	0.451
41DAP/reference	1.00479	0.754
42DAP/reference	1.6131	0.008
43DAP/reference	1.25047	0.111
47DAP/reference	1.04434	0.847
52DAP/reference	1.49218	0.061
57DAP/reference	1.67209	0.006

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.25639	0.966
26DAP/20DAP	1.23005	0.415
34DAP/26DAP	0.93559	0.92
51DAP/34DAP	1.21007	0.416
52DAP/51DAP	1.19492	0.04
53DAP/52DAP	1.36593	0.678
55DAP/53DAP	0.92177	0.698
57DAP/55DAP	0.69171	0.084
62DAP/57DAP	1.1906	0.002
68DAP/62DAP	2.12948	0.028
68DAP/14DAP	2.92862	0.017

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.1638	0.591

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.79691	0.251
Mature Green Tomato/Ripe Tomato	1.21285	0.363
Immature Eggplant/Mature Eggplant	1.07038	1
Ripe Pepper/Ripe Tomato	3.06783	0.256
Mature Eggplant/Ripe Tomato	1.90333	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	1.48722	1
12-2/M82	N/A	N/A
12-4/M82	2.48526
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
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	1.08366
5-3/M82	1.49319	0.37
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.11769	0.277
IL2-6/WTpooled	1.15414	0.659
IL7-5/WTpooled	0.87509	1
IL7-3/WTpooled	1.0946	1
IL12-4/WTpooled	1.15397	0.595
IL1-4/WTpooled	0.95987	0.834
WT/WTpooled	0.99602	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	1.0898	0.167

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.13617	0.724
DC3000/delta hrp 6h	0.91692	0.95
DC3000/delta hrp 12h	1.00463	1
DC3000/delta hrp 24h	1.17713	0.356

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.30645	0.121
DC3000 delta B/DC3000 delta AB	1.113	0.429

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.89492	1
Exp 36h	1.46025	1
Exp 60h	1.3096	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	0.85987	1
Var 0h	0.89897	1
Var 12h I row2-row1	0.96294	0.856
Var 12h NI row2-row1	1.19985	0.281
Var 36h I row2-row1	1.28037	0.298
Var 36h NI row2-row1	0.83837	0.421
Var 60h I row2-row1	1.20361
Var 60h NI row2-row1	0.82884	0.818
Time course 0hI-0hNI	0.89395	0.367
Time course 12hI-12hNI	0.98462	0.924
Time course 36hI-36hNI	1.33944	0.015
Time course 60hI-60hNI	0.86972	0.026

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)	1.38627	0.326
transgenic ySAMdc/azygous control (breaker)	1.41203	1
transgenic ySAMdc/azygous control (red)	1.01135	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.26925	0.035

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.62902	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.17006	0.14
Manapal/WT (break)	1.70242	1
Manapal/WT (red)	1.32845	0.133