Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.3.1.2

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.42162	0.315
27DAP/17DAP	0.96672	0.973
39DAP/27DAP	1.0633	1
41DAP/39DAP	0.71728	0.145
42DAP/41DAP	0.95344	1
43DAP/42DAP	1.19135	0.722
47DAP/43DAP	1.01634	1
52DAP/47DAP	0.69501	0.271
57DAP/52DAP	1.26616	0.894

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.71002	0.05
17DAP/reference	1.00173	0.819
27DAP/reference	0.86655	0.059
39DAP/reference	0.66677	0.018
41DAP/reference	0.92719	0.434
42DAP/reference	1.24248	0.084
43DAP/reference	0.91405	0.03
47DAP/reference	0.91334	0.038
52DAP/reference	0.77959	0.043
57DAP/reference	1.12156	0.186

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.16355	0.093
27DAP/17DAP	0.9004	0.724
39DAP/27DAP	0.90883	0.437
41DAP/39DAP	1.00177	1
42DAP/41DAP	0.99881	0.892
43DAP/42DAP	0.96602	0.831
47DAP/43DAP	0.91363	0.111
52DAP/47DAP	1.27997	0.324
57DAP/52DAP	1.36033	0.695
57DAP/7DAP	0.52057	0.186

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.34339	0.286
17DAP/reference	0.93714	0.338
27DAP/reference	1.34143	0.371
39DAP/reference	0.70915	0.016
41DAP/reference	0.91954	0.213
42DAP/reference	0.85786	0.189
43DAP/reference	0.94043	0.44
47DAP/reference	1.03438	1
52DAP/reference	0.75774	0.077
57DAP/reference	1.65702	0.046

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.89469	0.261
17DAP/reference	2.79346	0.007
27DAP/reference	2.39303	0.015
39DAP/reference	1.44184	0.097
41DAP/reference	1.99064	0.008
42DAP/reference	1.95765	0.007
43DAP/reference	0.97239	0.507
47DAP/reference	1.36281	0.009
52DAP/reference	0.84808	0.01
57DAP/reference	1.00155	0.549

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.18823	0.347
17DAP/reference	1.16932	0.595
27DAP/reference	0.8604
39DAP/reference	1.03445	0.792
41DAP/reference	0.79508	0.459
42DAP/reference	1.49246	0.6
43DAP/reference	1.89343	0.547
47DAP/reference	0.59009	0.013
52DAP/reference	0.74646	0.277
57DAP/reference	1.1008	0.827

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.66689
26DAP/20DAP	0.87845	1
34DAP/26DAP	1.15826	1
51DAP/34DAP	1.04952	0.946
52DAP/51DAP	2.25669	0.087
53DAP/52DAP	0.61359	0.049
55DAP/53DAP	1.72748	0.047
57DAP/55DAP	0.88695	0.41
62DAP/57DAP	0.99584
68DAP/62DAP	0.92408	0.787
68DAP/14DAP	0.61043	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.59804	0.033

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.08863	0.417
Mature Green Tomato/Ripe Tomato	1.55681	0.086
Immature Eggplant/Mature Eggplant	0.77111	0.081
Ripe Pepper/Ripe Tomato	0.76599	0.224
Mature Eggplant/Ripe Tomato	1.85062

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	2.42778
12-2/M82	N/A	N/A
12-4/M82	1.04489	1
1-3/M82	0.80491
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	0.95033
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	3.44785
4-3-2/M82	1.42555	0.508
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	0.95561
7-2/M82	N/A	N/A
9-3-2/M82	1.37758	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.97395
IL2-6/WTpooled	0.28847
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	1.37772
IL1-4/WTpooled	1.24185
WT/WTpooled	1.0737	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	0.99855	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.90583	1
DC3000/delta hrp 6h	0.98544	0.95
DC3000/delta hrp 12h	1.90487	1
DC3000/delta hrp 24h	0.90394	0.447

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.11549	0.476
DC3000 delta B/DC3000 delta AB	1.08298	0.516

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.12961	1
Exp 36h	1.23664	0.693
Exp 60h	1.49045	0.283

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99125	1
Var 0h	1.22715	0.936
Var 12h I row2-row1	0.74973	0.39
Var 12h NI row2-row1	0.97024	0.906
Var 36h I row2-row1	0.98782	1
Var 36h NI row2-row1	1.12656	0.276
Var 60h I row2-row1	0.85391	0.439
Var 60h NI row2-row1	0.98129	1
Time course 0hI-0hNI	0.93053	0.415
Time course 12hI-12hNI	0.96855	0.759
Time course 36hI-36hNI	0.87521	0.048
Time course 60hI-60hNI	0.38476	0.005

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)	1.1811	0.372
transgenic ySAMdc/azygous control (breaker)	1.11041	1
transgenic ySAMdc/azygous control (red)	1.54452	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.25958	0.223

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.0081	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.27328	0.105
Manapal/WT (break)	0.96651	1
Manapal/WT (red)	0.85731	0.181