Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.2.6.13

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.87905	0.436
27DAP/17DAP	1.02562	1
39DAP/27DAP	1.53857	0.073
41DAP/39DAP	0.94859	0.772
42DAP/41DAP	1.18315	0.868
43DAP/42DAP	0.98935	0.937
47DAP/43DAP	0.88162	0.603
52DAP/47DAP	1.33214	0.559
57DAP/52DAP	0.88989	0.772

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87138	0.048
17DAP/reference	0.81876	0.24
27DAP/reference	0.96132	0.406
39DAP/reference	0.97253	0.704
41DAP/reference	0.97167	0.667
42DAP/reference	0.93913	0.103
43DAP/reference	0.99877	0.84
47DAP/reference	0.99327	0.602
52DAP/reference	1.08139	0.8
57DAP/reference	0.89746	0.101

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.93053	0.35
27DAP/17DAP	1.02378	0.945
39DAP/27DAP	1.04358	0.659
41DAP/39DAP	1.10943	0.603
42DAP/41DAP	1.06694	0.824
43DAP/42DAP	1.0119	0.83
47DAP/43DAP	1.00716	0.951
52DAP/47DAP	0.97503	0.902
57DAP/52DAP	0.89658	0.346
57DAP/7DAP	1.19319	0.22

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93196	0.088
17DAP/reference	0.87219	0.253
27DAP/reference	1.12877	1
39DAP/reference	1.05884	0.511
41DAP/reference	0.92395	0.174
42DAP/reference	0.93014	0.178
43DAP/reference	0.9328	0.403
47DAP/reference	1.09959	0.48
52DAP/reference	1.47761	0.055
57DAP/reference	1.04483	0.799

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99548	0.831
17DAP/reference	0.88953	0.12
27DAP/reference	0.77155	0.022
39DAP/reference	0.7833	0.037
41DAP/reference	0.81028	0.078
42DAP/reference	0.87634	0.135
43DAP/reference	1.00058	0.736
47DAP/reference	0.94214	0.214
52DAP/reference	0.74345	0.06
57DAP/reference	1.03102	1

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.08535	0.939
17DAP/reference	1.05255	0.767
27DAP/reference	1.03287	0.644
39DAP/reference	1.14358	0.596
41DAP/reference	1.55667	0.174
42DAP/reference	1.22868	0.175
43DAP/reference	1.13256	0.58
47DAP/reference	1.28293	0.11
52DAP/reference	1.03295	0.952
57DAP/reference	0.89272	0.225

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.9243	1
26DAP/20DAP	0.98177	1
34DAP/26DAP	1.1473	0.542
51DAP/34DAP	0.94297	0.606
52DAP/51DAP	1.0327	0.676
53DAP/52DAP	0.95449	0.758
55DAP/53DAP	1.04951	0.748
57DAP/55DAP	1.01307	0.953
62DAP/57DAP	1.15944
68DAP/62DAP	0.95074	0.885
68DAP/14DAP	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.29652	0.036

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	7.01233	0.058
Mature Green Tomato/Ripe Tomato	1.30539	0.478
Immature Eggplant/Mature Eggplant	0.26974	0.058
Ripe Pepper/Ripe Tomato	0.8367	1
Mature Eggplant/Ripe Tomato	2.7711	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.9325	0.944
1-1-2/M82	1.02741	1
12-2/M82	1.0832	1
12-4/M82	1.11528	1
1-3/M82	0.98487	1
2-1-1/M82	0.8992	0.565
2-1/M82	0.96217	0.519
2-6/M82	1.02148	1
3-2/M82	1.07537
4-1-1/M82	0.94391	1
4-1/M82	1.41073	0.512
4-3-2/M82	1.15041	0.284
4-3/M82	1.18025	1
5-3/M82	0.9847	1
6-2/M82	0.96575	1
6-3/M82	1.01884	1
7-1/M82	0.96312	1
7-2/M82	1.07677	1
9-3-2/M82	1.08025	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.98955	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.99901	1
IL12-4/WTpooled	0.9638	1
IL1-4/WTpooled	1.10349	0.426
WT/WTpooled	1.00345	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	1.01265	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.00319	1
DC3000/delta hrp 6h	1.20205	1
DC3000/delta hrp 12h	1.00024	1
DC3000/delta hrp 24h	1.09223	0.453

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.9746	0.955
DC3000 delta B/DC3000 delta AB	1.03062	0.614

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.04647	1
Exp 36h	1.89595	0.693
Exp 60h	1.81759	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	0.9744	1
Var 0h	1.05754	0.936
Var 12h I row2-row1	0.94241	0.363
Var 12h NI row2-row1	1.00663	1
Var 36h I row2-row1	1.02706	0.368
Var 36h NI row2-row1	0.99838	1
Var 60h I row2-row1	0.86132	0.439
Var 60h NI row2-row1	1.03356	0.793
Time course 0hI-0hNI	0.96065	0.763
Time course 12hI-12hNI	1.00448	1
Time course 36hI-36hNI	1.05001	0.166
Time course 60hI-60hNI	1.27096	0.009

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)	0.88542	0.251
transgenic ySAMdc/azygous control (breaker)	1.92383	0.178
transgenic ySAMdc/azygous control (red)	1.65493	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.03088	0.223

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.06276	0.105
Manapal/WT (break)	2.656	0.183
Manapal/WT (red)	1.08945	1