Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.2.1.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.68782	0.133
27DAP/17DAP	1.01053	0.932
39DAP/27DAP	0.77295	0.335
41DAP/39DAP	1.07262	0.921
42DAP/41DAP	0.84648	1
43DAP/42DAP	0.93063	0.827
47DAP/43DAP	1.26732	0.497
52DAP/47DAP	0.9481	0.761
57DAP/52DAP	1.08077	0.988

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02462	0.735
17DAP/reference	1.12793	0.045
27DAP/reference	1.04828	0.539
39DAP/reference	1.00914	0.842
41DAP/reference	0.9877	0.814
42DAP/reference	0.92723	0.078
43DAP/reference	1.0496	0.646
47DAP/reference	0.96305	0.106
52DAP/reference	1.06284	0.388
57DAP/reference	0.85853	0.051

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.43795	0.07
27DAP/17DAP	1.03377	0.938
39DAP/27DAP	0.75165	0.047
41DAP/39DAP	1.10778	0.921
42DAP/41DAP	1.11063	0.927
43DAP/42DAP	0.93895	0.415
47DAP/43DAP	0.85134	0.516
52DAP/47DAP	0.88361	0.702
57DAP/52DAP	1.11276	0.662
57DAP/7DAP	1.2421	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02507	1
17DAP/reference	1.25284	0.162
27DAP/reference	0.96955	0.462
39DAP/reference	0.90307	0.23
41DAP/reference	0.89153	0.09
42DAP/reference	1.01089	0.641
43DAP/reference	1.06217	0.873
47DAP/reference	0.89055	0.168
52DAP/reference	0.86966	0.077
57DAP/reference	0.87711	0.077

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.12091	0.151
17DAP/reference	0.98836	0.673
27DAP/reference	0.88915	0.15
39DAP/reference	0.90366	0.208
41DAP/reference	0.88556	0.083
42DAP/reference	0.84147	0.018
43DAP/reference	0.92162	0.328
47DAP/reference	0.91221	0.051
52DAP/reference	0.97634	0.433
57DAP/reference	1.09567	0.345

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.2462	0.162
17DAP/reference	1.23238	0.166
27DAP/reference	1.00021	0.691
39DAP/reference	1.11717	0.451
41DAP/reference	1.06985	0.796
42DAP/reference	1.00484	0.816
43DAP/reference	0.76597	0.036
47DAP/reference	0.97348	0.494
52DAP/reference	1.10752	0.917
57DAP/reference	0.66781	0.016

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.11661	0.752
26DAP/20DAP	0.6184	0.512
34DAP/26DAP	1.18094	0.126
51DAP/34DAP	0.89814	0.681
52DAP/51DAP	0.87626	1
53DAP/52DAP	1.33383
55DAP/53DAP	0.60474	0.075
57DAP/55DAP	1.03792	0.87
62DAP/57DAP	1.47231	0.445
68DAP/62DAP	0.8061	0.152
68DAP/14DAP	0.76745	0.121

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.92351	0.029

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	2.32475	0.095
Immature Eggplant/Mature Eggplant	1.18172	0.205
Ripe Pepper/Ripe Tomato	0.68724
Mature Eggplant/Ripe Tomato	1.21463

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	N/A	N/A
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	N/A	N/A
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	N/A	N/A
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.94382	0.321
IL2-6/WTpooled	1.48201	0.456
IL7-5/WTpooled	1.11686	1
IL7-3/WTpooled	0.97595	1
IL12-4/WTpooled	0.94456	1
IL1-4/WTpooled	1.12918	1
WT/WTpooled	0.96949	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	0.87907	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.04592	0.921
DC3000/delta hrp 6h	1.23694	1
DC3000/delta hrp 12h	1.1446	1
DC3000/delta hrp 24h	0.47719	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.8423	0.161
DC3000 delta B/DC3000 delta AB	1.11385	0.491

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.10847	1
Exp 36h	1.00811	1
Exp 60h	1.08059	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.97575	1
Var 0h	1.01279	1
Var 12h I row2-row1	0.84015	0.418
Var 12h NI row2-row1	1.60507	0.34
Var 36h I row2-row1	1.32722	0.742
Var 36h NI row2-row1	0.86851	0.61
Var 60h I row2-row1	1.00553	1
Var 60h NI row2-row1	0.8159	0.866
Time course 0hI-0hNI	1.06529	0.852
Time course 12hI-12hNI	1.0061	1
Time course 36hI-36hNI	1.11749	0.316
Time course 60hI-60hNI	0.46306	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)	0.89823	0.32
transgenic ySAMdc/azygous control (breaker)	1.36109	0.248
transgenic ySAMdc/azygous control (red)	1.13399	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.9676	0.136

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.09993	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.47709	0.307
Manapal/WT (break)	1.30866	0.14
Manapal/WT (red)	1.47099	0.222