Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.3.19.21

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.77249	0.265
27DAP/17DAP	2.1212	0.362
39DAP/27DAP	0.96439	0.7
41DAP/39DAP	0.94184	0.772
42DAP/41DAP	1.25346	0.691
43DAP/42DAP	1.22247	0.787
47DAP/43DAP	0.7553	0.319
52DAP/47DAP	1.22408	0.902
57DAP/52DAP	0.77804	0.759

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.80923	0.48
17DAP/reference	1.14634	0.051
27DAP/reference	1.09076	0.909
39DAP/reference	1.11548	0.413
41DAP/reference	1.34993	0.043
42DAP/reference	1.30121	0.001
43DAP/reference	1.03421	1
47DAP/reference	1.15613	0.052
52DAP/reference	1.10492	0.242
57DAP/reference	0.93586	0.308

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.14645	1
27DAP/17DAP	1.19999	0.426
39DAP/27DAP	0.98411	0.919
41DAP/39DAP	1.46136	0.098
42DAP/41DAP	0.82766	0.093
43DAP/42DAP	0.90149	0.466
47DAP/43DAP	1.10689	0.749
52DAP/47DAP	1.05878	0.831
57DAP/52DAP	1.50478	0.075
57DAP/7DAP	1.10612	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95475	0.445
17DAP/reference	0.9095	0.22
27DAP/reference	0.88361	0.082
39DAP/reference	0.94691	0.264
41DAP/reference	0.97621	0.489
42DAP/reference	1.04653	0.889
43DAP/reference	0.99359	0.608
47DAP/reference	1.37004	0.44
52DAP/reference	0.9773	0.523
57DAP/reference	1.20143	0.308

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.19639	0.19
17DAP/reference	1.41411	0.009
27DAP/reference	1.18706	0.188
39DAP/reference	1.30287	0.015
41DAP/reference	1.36728	0.058
42DAP/reference	1.25254	0.064
43DAP/reference	1.36933	0.122
47DAP/reference	1.06536	0.321
52DAP/reference	1.13899	0.279
57DAP/reference	1.27344	0.051

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.0153	1
17DAP/reference	0.98124	0.668
27DAP/reference	1.00053	0.843
39DAP/reference	0.92883	0.393
41DAP/reference	0.9915	0.682
42DAP/reference	1.09284	0.55
43DAP/reference	1.18148	0.154
47DAP/reference	1.1331	0.196
52DAP/reference	1.04035	0.876
57DAP/reference	1.36234	0.047

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.50035	0.752
26DAP/20DAP	1.19286	0.558
34DAP/26DAP	1.24424	1
51DAP/34DAP	1.37213	0.326
52DAP/51DAP	1.81959	0.396
53DAP/52DAP	0.80891	0.207
55DAP/53DAP	1.73615	0.452
57DAP/55DAP	0.99576	0.902
62DAP/57DAP	1.04848	1
68DAP/62DAP	0.68187	0.195
68DAP/14DAP	0.44682	0.09

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.95572	0.547

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.07714	0.287
Mature Green Tomato/Ripe Tomato	1.23863	0.523
Immature Eggplant/Mature Eggplant	1.25631	0.057
Ripe Pepper/Ripe Tomato	0.70496	0.293
Mature Eggplant/Ripe Tomato	2.06212	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	N/A	N/A
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	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	N/A	N/A
5-3/M82	N/A	N/A
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	1.26741	0.277
IL2-6/WTpooled	1.11789	0.788
IL7-5/WTpooled	0.99673	1
IL7-3/WTpooled	0.83525	0.31
IL12-4/WTpooled	1.01369	0.891
IL1-4/WTpooled	0.99827	1
WT/WTpooled	1.02793	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	0.93729	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.31718	0.75
DC3000/delta hrp 6h	1.04228	1
DC3000/delta hrp 12h	1.09984	1
DC3000/delta hrp 24h	1.50222	0.063

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.84613
DC3000 delta B/DC3000 delta AB	1.26846	0.198

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.02592	1
Exp 36h	1.00011	1
Exp 60h	1.20175	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	1.12433	1
Var 0h	1.14524	0.98
Var 12h I row2-row1	1.05138	0.58
Var 12h NI row2-row1	1.21094	1
Var 36h I row2-row1	1.25086	0.742
Var 36h NI row2-row1	0.92594	0.706
Var 60h I row2-row1	0.81836	0.285
Var 60h NI row2-row1	0.89366	0.756
Time course 0hI-0hNI	1.20641	0.377
Time course 12hI-12hNI	1.07535	0.204
Time course 36hI-36hNI	2.69802	0.004
Time course 60hI-60hNI	2.1906	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)	0.96414	0.485
transgenic ySAMdc/azygous control (breaker)	0.83951	0.251
transgenic ySAMdc/azygous control (red)	0.97271	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.00274	1

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.88765	0.255

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.14628	0.096
Manapal/WT (break)	1.3375	0.183
Manapal/WT (red)	0.95277	0.728