Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-4.2.17.13

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	4.24006	0.018
27DAP/17DAP	1.99751	0.189
39DAP/27DAP	1.23695	0.548
41DAP/39DAP	1.22667	0.696
42DAP/41DAP	1.6194	0.049
43DAP/42DAP	1.51131	0.682
47DAP/43DAP	0.92563	0.699
52DAP/47DAP	0.97227	0.724
57DAP/52DAP	0.94506	0.94

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95491	0.442
17DAP/reference	0.8561	0.138
27DAP/reference	1.23747	0.054
39DAP/reference	1.01033	1
41DAP/reference	1.00929	1
42DAP/reference	1.41627	0.001
43DAP/reference	0.95228	0.377
47DAP/reference	1.45525	0.004
52DAP/reference	1.80153	0.01
57DAP/reference	1.42248	0.012

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.3858	0.036
27DAP/17DAP	1.29314	0.156
39DAP/27DAP	1.59681	0.078
41DAP/39DAP	0.71873	0.061
42DAP/41DAP	1.15976	0.334
43DAP/42DAP	1.45306	0.014
47DAP/43DAP	0.95982	0.787
52DAP/47DAP	1.34235	0.258
57DAP/52DAP	0.9614	0.716
57DAP/7DAP	1.97388	0.22

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.69968	0.091
17DAP/reference	0.92771	0.22
27DAP/reference	0.69895	0.01
39DAP/reference	1.43853	0.01
41DAP/reference	1.02831	0.677
42DAP/reference	1.26787	0.174
43DAP/reference	1.73436	0.039
47DAP/reference	2.05855	0.019
52DAP/reference	1.05947	0.941
57DAP/reference	1.30455	0.087

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98658	0.592
17DAP/reference	1.08716	0.874
27DAP/reference	0.92064	0.317
39DAP/reference	1.19705	0.128
41DAP/reference	1.08724	0.831
42DAP/reference	1.13399	0.398
43DAP/reference	0.90291	0.328
47DAP/reference	0.99561	0.66
52DAP/reference	1.42774	0.02
57DAP/reference	0.90056	0.259

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.44419	0.048
17DAP/reference	0.97713	0.55
27DAP/reference	0.75391	0.067
39DAP/reference	1.0168	0.962
41DAP/reference	1.21161	0.025
42DAP/reference	2.22956	0.006
43DAP/reference	1.59221	0.01
47DAP/reference	1.52994	0.011
52DAP/reference	1.08678	0.631
57DAP/reference	1.38235	0.274

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.88922	0.966
26DAP/20DAP	1.25733	0.77
34DAP/26DAP	1.46649	1
51DAP/34DAP	0.95917	0.747
52DAP/51DAP	1.49425	0.925
53DAP/52DAP	1.12404	0.738
55DAP/53DAP	0.92121	0.746
57DAP/55DAP	1.02767	1
62DAP/57DAP	1.33703	0.723
68DAP/62DAP	2.00959	0.878
68DAP/14DAP	1.19941	0.739

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	11.1798	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.80263	0.411
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.05662	N/A
Mature Eggplant/Ripe Tomato	0.12328	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.37076	0.742
1-1-2/M82	1.21744	1
12-2/M82	0.99668	N/A
12-4/M82	1.40811	1
1-3/M82	2.15558	0.26
2-1-1/M82	0.88736	0.465
2-1/M82	0.8096	0.345
2-6/M82	1.07626	0.695
3-2/M82	1.33877	0.717
4-1-1/M82	1.02053	1
4-1/M82	0.80479	N/A
4-3-2/M82	1.00583	N/A
4-3/M82	0.9319	0.72
5-3/M82	0.97278	1
6-2/M82	1.0697	1
6-3/M82	0.94623	1
7-1/M82	0.86491	0.452
7-2/M82	0.93358	0.881
9-3-2/M82	1.58176	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.91984	N/A
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	0.61121	1
IL7-3/WTpooled	0.71246	N/A
IL12-4/WTpooled	1.31647	0.785
IL1-4/WTpooled	0.60614	0.476
WT/WTpooled	1.19495	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	1.24056	0.222

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.02643	0.921
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	0.74771	1
DC3000/delta hrp 24h	1.08885	0.582

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	N/A
DC3000 delta B/DC3000 delta AB	2.58602	0.061

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	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
self-self	1.03054	1
Var 0h	0.51909	1
Var 12h I row2-row1	0.95435	0.856
Var 12h NI row2-row1	0.66022	0.627
Var 36h I row2-row1	0.72671	1
Var 36h NI row2-row1	0.8698	0.549
Var 60h I row2-row1	1.70834	0.562
Var 60h NI row2-row1	1.05532	1
Time course 0hI-0hNI	1.05624	0.603
Time course 12hI-12hNI	1.06287	0.493
Time course 36hI-36hNI	1.0458	0.513
Time course 60hI-60hNI	0.86949	0.011

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)	0.77712	0.567
transgenic ySAMdc/azygous control (breaker)	1.34409	0.248
transgenic ySAMdc/azygous control (red)	0.96344	1

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	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.73062	1
Manapal/WT (break)	0.73912	0.333
Manapal/WT (red)	0.52364	0.187