Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.3.8.1

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.20778	0.646
27DAP/17DAP	1.10438	0.92
39DAP/27DAP	1.06028	0.876
41DAP/39DAP	1.28007	0.197
42DAP/41DAP	1.04778	0.978
43DAP/42DAP	1.07714	1
47DAP/43DAP	0.7678	0.263
52DAP/47DAP	1.22925	0.915
57DAP/52DAP	1.3378	1

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.85075	0.03
17DAP/reference	1.15771	0.08
27DAP/reference	1.04029	0.782
39DAP/reference	0.96397	0.455
41DAP/reference	1.11575	0.241
42DAP/reference	0.88946	0.02
43DAP/reference	0.98406	0.745
47DAP/reference	0.88768	0.014
52DAP/reference	0.98511	0.546
57DAP/reference	0.89019	0.112

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.98919	0.763
27DAP/17DAP	1.149	0.747
39DAP/27DAP	1.00675	0.844
41DAP/39DAP	1.12732	0.612
42DAP/41DAP	1.03663	0.934
43DAP/42DAP	1.26855	0.052
47DAP/43DAP	1.0157	0.973
52DAP/47DAP	1.06125	0.826
57DAP/52DAP	1.1013	0.874
57DAP/7DAP	0.97328	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.05854	0.524
17DAP/reference	1.07055	0.971
27DAP/reference	0.98482	0.53
39DAP/reference	0.89302	0.17
41DAP/reference	0.81864	0.058
42DAP/reference	0.80804	0.027
43DAP/reference	0.9633	0.334
47DAP/reference	1.07032	1
52DAP/reference	0.83968	0.137
57DAP/reference	1.00637	0.831

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.09525	0.767
17DAP/reference	0.99465	0.747
27DAP/reference	0.91545	0.269
39DAP/reference	0.96583	0.381
41DAP/reference	1.24945	0.642
42DAP/reference	0.91292	0.15
43DAP/reference	1.07073	0.647
47DAP/reference	0.89317	0.058
52DAP/reference	0.92774	0.239
57DAP/reference	1.01068	1

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.14601	0.212
17DAP/reference	0.91431	0.292
27DAP/reference	1.13069	0.552
39DAP/reference	0.81595	0.046
41DAP/reference	0.84483	0.185
42DAP/reference	0.97356	0.671
43DAP/reference	0.7361	0.102
47DAP/reference	1.08459	0.519
52DAP/reference	1.29688	0.583
57DAP/reference	0.84049	0.059

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.1199	1
26DAP/20DAP	0.74023	0.317
34DAP/26DAP	1.85849
51DAP/34DAP	1.24393	0.627
52DAP/51DAP	0.86202	1
53DAP/52DAP	0.94931	0.783
55DAP/53DAP	1.63884	0.494
57DAP/55DAP	1.16948
62DAP/57DAP	1.13575	0.868
68DAP/62DAP	0.81269	0.505
68DAP/14DAP	0.64445	0.121

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.96946	0.099

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.68511	0.063
Mature Green Tomato/Ripe Tomato	2.04541	0.237
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	2.04655	1
Mature Eggplant/Ripe Tomato	0.44084	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.86774
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	0.77029	0.282
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	1.13039
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	1.07862	1
6-2/M82	N/A	N/A
6-3/M82	1.19392
7-1/M82	1.00583
7-2/M82	N/A	N/A
9-3-2/M82	1.11265

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.26899
IL2-6/WTpooled	1.33098
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.98753
IL12-4/WTpooled	0.92029	1
IL1-4/WTpooled	0.93839	0.834
WT/WTpooled	0.90513	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	0.96126	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.09958	0.921
DC3000/delta hrp 6h	0.91205	0.95
DC3000/delta hrp 12h	1.17556	1
DC3000/delta hrp 24h	1.12729	0.553

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	3.13742
DC3000 delta B/DC3000 delta AB	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.031	1
Exp 36h	1.6613	0.693
Exp 60h	1.20274	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.05536	1
Var 0h	0.80898	1
Var 12h I row2-row1	0.99244	1
Var 12h NI row2-row1	1.01762	1
Var 36h I row2-row1	0.91215	1
Var 36h NI row2-row1	1.16708	1
Var 60h I row2-row1	0.93063	0.439
Var 60h NI row2-row1	0.89842	0.977
Time course 0hI-0hNI	0.97649	0.917
Time course 12hI-12hNI	1.08146	0.19
Time course 36hI-36hNI	1.24097	0.008
Time course 60hI-60hNI	1.27279	0.013

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)	0.89846	0.409
transgenic ySAMdc/azygous control (breaker)	0.80956	0.251
transgenic ySAMdc/azygous control (red)	0.86599	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.09679	0.034

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.75231	0.238

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)	N/A	N/A
Manapal/WT (red)	1.15849	0.142