Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.2.3.2

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.00414	0.728
27DAP/17DAP	0.78074	0.406
39DAP/27DAP	0.81329	0.522
41DAP/39DAP	0.74028	0.17
42DAP/41DAP	1.39689	0.573
43DAP/42DAP	1.14661	0.787
47DAP/43DAP	0.8229	0.455
52DAP/47DAP	1.28463	0.75
57DAP/52DAP	1.04547	0.977

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.32719	0.018
17DAP/reference	1.11256	0.086
27DAP/reference	1.03848	0.894
39DAP/reference	1.0273	1
41DAP/reference	0.96747	0.814
42DAP/reference	0.95879	0.372
43DAP/reference	0.77023
47DAP/reference	0.72901	0.005
52DAP/reference	0.66656	0.042
57DAP/reference	0.03141

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.94954	0.595
27DAP/17DAP	0.92109	0.782
39DAP/27DAP	0.54318	0.029
41DAP/39DAP	1.12632	0.663
42DAP/41DAP	0.86611	0.167
43DAP/42DAP	0.62058	0.022
47DAP/43DAP	0.91319	0.677
52DAP/47DAP	0.76813	0.372
57DAP/52DAP	0.98234	0.793
57DAP/7DAP	0.43527

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.64505	0.028
17DAP/reference	1.21439	0.084
27DAP/reference	1.36975	0.01
39DAP/reference	1.26809	1
41DAP/reference	1.26151	0.171
42DAP/reference	1.75221	0.007
43DAP/reference	1.38934	0.026
47DAP/reference	1.19932	0.45
52DAP/reference	2.09246	0.007
57DAP/reference	1.90253	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.29073	0.141
17DAP/reference	1.16498	0.396
27DAP/reference	0.83072	0.134
39DAP/reference	0.91862	0.298
41DAP/reference	0.90649	0.256
42DAP/reference	0.89519	0.212
43DAP/reference	0.80207	0.108
47DAP/reference	0.86226	0.023
52DAP/reference	0.84986	0.101
57DAP/reference	0.5745	0.014

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.28181	0.027
17DAP/reference	1.59481	0.074
27DAP/reference	1.2045	0.092
39DAP/reference	1.32983	0.013
41DAP/reference	1.07159	0.637
42DAP/reference	1.32907	0.097
43DAP/reference	1.1461	0.09
47DAP/reference	1.30339	0.027
52DAP/reference	1.16729	0.324
57DAP/reference	1.36984	0.015

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.09008	1
26DAP/20DAP	1.06348	0.865
34DAP/26DAP	0.90432	0.741
51DAP/34DAP	1.18943	0.164
52DAP/51DAP	1.17356	0.588
53DAP/52DAP	0.71214	0.073
55DAP/53DAP	0.88922	0.203
57DAP/55DAP	0.81155	0.309
62DAP/57DAP	0.89109	0.28
68DAP/62DAP	1.15421	0.869
68DAP/14DAP	0.42001	0.086

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.59007	0.052

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.14758	0.058
Mature Green Tomato/Ripe Tomato	5.70459	0.015
Immature Eggplant/Mature Eggplant	0.31142	0.064
Ripe Pepper/Ripe Tomato	3.45966	1
Mature Eggplant/Ripe Tomato	5.23582	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.92093
12-2/M82	N/A	N/A
12-4/M82	N/A	N/A
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	0.93722
3-2/M82	1.0276
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	N/A	N/A
5-3/M82	0.97391	1
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	1.30481
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.00598	1
IL2-6/WTpooled	1.35629
IL7-5/WTpooled	1.55416	0.792
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	0.63731
IL1-4/WTpooled	0.9441	1
WT/WTpooled	0.92007

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	0.86123	0.341

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	N/A	N/A
DC3000/delta hrp 6h	0.96649	0.95
DC3000/delta hrp 12h	N/A	N/A
DC3000/delta hrp 24h	0.46677	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.4909	0.025
DC3000 delta B/DC3000 delta AB	0.50315	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.9019	1
Exp 36h	0.89599	0.449
Exp 60h	0.76395	0.343

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	1.03627	1
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)	1.17687	0.331
transgenic ySAMdc/azygous control (breaker)	1.90124	0.178
transgenic ySAMdc/azygous control (red)	1.63824	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.86601	0.083

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.87485	0.233

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	2.93921	0.083
Manapal/WT (break)	5.63998	0.123
Manapal/WT (red)	9.46174	0.15