Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.3.17.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.13025	0.812
27DAP/17DAP	1.13097	0.86
39DAP/27DAP	1.09393	0.882
41DAP/39DAP	1.04486	0.758
42DAP/41DAP	1.248	0.556
43DAP/42DAP	1.03955	1
47DAP/43DAP	1.20971	0.285
52DAP/47DAP	0.96338	0.884
57DAP/52DAP	0.98065	0.971

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.21108	0.132
17DAP/reference	1.17672	0.653
27DAP/reference	1.03998	1
39DAP/reference	1.0905	1
41DAP/reference	1.50229	0.012
42DAP/reference	1.38727	0.001
43DAP/reference	0.96768	0.691
47DAP/reference	1.16112	0.728
52DAP/reference	0.98056	0.58
57DAP/reference	0.94207	0.395

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.98141	0.732
27DAP/17DAP	0.9854	0.919
39DAP/27DAP	1.2051	0.154
41DAP/39DAP	0.94739	0.849
42DAP/41DAP	0.99803	0.899
43DAP/42DAP	1.10718	0.122
47DAP/43DAP	1.01342	0.906
52DAP/47DAP	1.07321	0.734
57DAP/52DAP	0.95547	0.494
57DAP/7DAP	1.11902	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.17001	0.876
17DAP/reference	0.86046	0.144
27DAP/reference	0.97487	0.462
39DAP/reference	0.97878	0.474
41DAP/reference	0.93198	0.311
42DAP/reference	1.08789	0.889
43DAP/reference	0.90846	0.241
47DAP/reference	1.02639	1
52DAP/reference	1.30635	0.024
57DAP/reference	1.05844	0.966

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97484	0.756
17DAP/reference	1.43164	0.013
27DAP/reference	1.31721	0.23
39DAP/reference	1.31614	0.046
41DAP/reference	1.1191	0.45
42DAP/reference	1.06916	0.697
43DAP/reference	1.38745	0.097
47DAP/reference	1.22729	0.291
52DAP/reference	1.21674	0.156
57DAP/reference	1.4226	0.068

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.21101	0.397
17DAP/reference	1.25292	0.135
27DAP/reference	1.08116	0.34
39DAP/reference	1.27177	0.104
41DAP/reference	1.26881	0.093
42DAP/reference	1.12891	0.589
43DAP/reference	1.52304	0.079
47DAP/reference	1.13389	0.207
52DAP/reference	0.87686	0.415
57DAP/reference	1.04677	0.581

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.35105	0.966
26DAP/20DAP	1.10314	0.931
34DAP/26DAP	1.057	1
51DAP/34DAP	1.06611	0.473
52DAP/51DAP	1.05836	0.704
53DAP/52DAP	1.08951	0.83
55DAP/53DAP	1.1033	0.527
57DAP/55DAP	1.1858	0.818
62DAP/57DAP	1.19317	0.902
68DAP/62DAP	0.93509	0.722
68DAP/14DAP	1.2075	0.504

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.92851	0.129

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.06159	0.752
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	1.74578
Mature Eggplant/Ripe Tomato	0.68569	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.246	0.877
1-1-2/M82	1.25057	1
12-2/M82	1.02815
12-4/M82	0.99152
1-3/M82	1.1432
2-1-1/M82	0.89351	0.784
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	0.8799
4-1/M82	N/A	N/A
4-3-2/M82	1.21602	0.284
4-3/M82	0.83622
5-3/M82	1.06564	1
6-2/M82	1.27566
6-3/M82	0.97016	1
7-1/M82	N/A	N/A
7-2/M82	0.92493	0.434
9-3-2/M82	1.12213	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.05344	0.788
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.08403	1
IL12-4/WTpooled	0.9031	0.71
IL1-4/WTpooled	0.97638	1
WT/WTpooled	1.04058	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	1.08244	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.94563	1
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	0.80725	1
DC3000/delta hrp 24h	1.12517	0.553

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.13192	0.081
DC3000 delta B/DC3000 delta AB	1.17624	0.308

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	N/A	N/A
Exp 60h	1.19178	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.97456	1
Var 0h	0.95707	1
Var 12h I row2-row1	1.06462	0.544
Var 12h NI row2-row1	0.98248	1
Var 36h I row2-row1	1.11458	0.908
Var 36h NI row2-row1	0.89916	0.522
Var 60h I row2-row1	0.83056	0.439
Var 60h NI row2-row1	1.01354	1
Time course 0hI-0hNI	1.02229	0.799
Time course 12hI-12hNI	1.11891	0.077
Time course 36hI-36hNI	1.22286	0.218
Time course 60hI-60hNI	1.92278	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)	N/A	N/A
transgenic ySAMdc/azygous control (breaker)	N/A	N/A
transgenic ySAMdc/azygous control (red)	0.6807	0.485

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.25085	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	N/A	N/A
Manapal/WT (break)	1.11947	1
Manapal/WT (red)	0.75982	0.229