Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.3.2.6

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.05225	0.961
27DAP/17DAP	1.16111	0.849
39DAP/27DAP	0.7621	0.402
41DAP/39DAP	0.99289	0.946
42DAP/41DAP	0.7804	0.774
43DAP/42DAP	0.98571	0.931
47DAP/43DAP	1.09308	0.538
52DAP/47DAP	0.64434	0.174
57DAP/52DAP	0.86826	0.666

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.0082	1
17DAP/reference	1.00985	0.907
27DAP/reference	1.03563	0.648
39DAP/reference	1.06402	0.108
41DAP/reference	1.01275	0.808
42DAP/reference	0.94776	0.115
43DAP/reference	0.98631	0.675
47DAP/reference	0.93859	0.083
52DAP/reference	0.86114	0.121
57DAP/reference	1.00779	1

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.93945	0.442
27DAP/17DAP	1.07795	0.761
39DAP/27DAP	1.04827	0.611
41DAP/39DAP	1.09611	0.763
42DAP/41DAP	1.0085	0.934
43DAP/42DAP	0.77777	0.032
47DAP/43DAP	1.079	0.844
52DAP/47DAP	0.93533	0.624
57DAP/52DAP	0.86588	0.163
57DAP/7DAP	1.09742	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91326	0.402
17DAP/reference	0.72387	0.025
27DAP/reference	0.70315	0.016
39DAP/reference	0.82091	0.015
41DAP/reference	0.85775	0.16
42DAP/reference	0.74534	0.01
43DAP/reference	0.70902	0.019
47DAP/reference	0.82606	0.222
52DAP/reference	0.59671	0.012
57DAP/reference	0.78291	0.018

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00125	0.993
17DAP/reference	0.9556	0.347
27DAP/reference	1.0162	1
39DAP/reference	1.0168	1
41DAP/reference	0.97994	0.472
42DAP/reference	1.04346	0.777
43DAP/reference	1.25634	0.208
47DAP/reference	1.0479	0.164
52DAP/reference	1.0619	0.322
57DAP/reference	1.01638	0.908

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96933	0.566
17DAP/reference	1.01255	1
27DAP/reference	0.74948	0.035
39DAP/reference	0.74388	0.029
41DAP/reference	0.74394	0.028
42DAP/reference	0.63502	0.019
43DAP/reference	0.78057	0.029
47DAP/reference	0.92796	0.24
52DAP/reference	0.63017	0.089
57DAP/reference	0.74255	0.032

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.04964	0.966
26DAP/20DAP	0.9088	1
34DAP/26DAP	0.94554	0.879
51DAP/34DAP	0.94763	0.727
52DAP/51DAP	1.06906	0.708
53DAP/52DAP	1.04877	0.806
55DAP/53DAP	1.15219	0.429
57DAP/55DAP	0.98823	0.88
62DAP/57DAP	1.16976	0.723
68DAP/62DAP	0.95167	0.787
68DAP/14DAP	0.88669	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.86175	0.05

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	16.0972	0.068
Mature Green Tomato/Ripe Tomato	5.57702	0.015
Immature Eggplant/Mature Eggplant	0.6211	0.068
Ripe Pepper/Ripe Tomato	0.38789	0.293
Mature Eggplant/Ripe Tomato	2.98229	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.78395	0.605
1-1-2/M82	0.92485	1
12-2/M82	0.67352
12-4/M82	0.91078	1
1-3/M82	0.74065	0.501
2-1-1/M82	1.05471
2-1/M82	N/A	N/A
2-6/M82	0.99468	1
3-2/M82	0.73597
4-1-1/M82	1.20819	0.968
4-1/M82	1.2077
4-3-2/M82	1.16571	0.508
4-3/M82	1.29548	1
5-3/M82	0.94148	1
6-2/M82	0.65702	0.481
6-3/M82	1.17349	1
7-1/M82	1.32361	0.556
7-2/M82	0.92683	0.881
9-3-2/M82	0.67115	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	1.42884
IL7-3/WTpooled	1.08832
IL12-4/WTpooled	1.16494
IL1-4/WTpooled	0.94902
WT/WTpooled	1.10455	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	0.56419	0.341

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.98317	1
DC3000/delta hrp 6h	0.85539	0.95
DC3000/delta hrp 12h	1.13664	1
DC3000/delta hrp 24h	0.78797	0.035

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.09886	0.441
DC3000 delta B/DC3000 delta AB	0.92833	0.406

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.06371	1
Exp 36h	0.99149	0.943
Exp 60h	0.82242	0.664

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

hybridization	ratio	FDR (corrected p value)
self-self	0.9776	1
Var 0h	1.12232	0.421
Var 12h I row2-row1	1.13428	0.254
Var 12h NI row2-row1	1.00587	1
Var 36h I row2-row1	0.85604	1
Var 36h NI row2-row1	0.98339	0.852
Var 60h I row2-row1	1.3321	0.562
Var 60h NI row2-row1	1.22948	0.904
Time course 0hI-0hNI	0.90221	0.226
Time course 12hI-12hNI	0.74644	0.034
Time course 36hI-36hNI	0.7855	0.023
Time course 60hI-60hNI	0.6165	0.006

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)	0.90986	0.314
transgenic ySAMdc/azygous control (breaker)	1.29863	0.248
transgenic ySAMdc/azygous control (red)	1.0094	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.00543	0.811

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.28493	0.231

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.01632	1
Manapal/WT (break)	1.26773	0.381
Manapal/WT (red)	1.0951	1