Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.4.16.19

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.05103	0.975
27DAP/17DAP	0.91565	0.783
39DAP/27DAP	1.06529	0.995
41DAP/39DAP	1.00812	0.978
42DAP/41DAP	1.08901	0.997
43DAP/42DAP	1.13443	1
47DAP/43DAP	1.13902	0.972
52DAP/47DAP	0.7858	0.499
57DAP/52DAP	1.23139	0.952

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01135	0.9
17DAP/reference	1.01268	0.631
27DAP/reference	1.02969	0.285
39DAP/reference	0.9886	0.816
41DAP/reference	0.99335	0.814
42DAP/reference	0.95367	0.078
43DAP/reference	0.97666	0.611
47DAP/reference	0.9752	0.279
52DAP/reference	0.91926	0.162
57DAP/reference	0.96414	0.395

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.96019	0.509
27DAP/17DAP	0.97387	0.614
39DAP/27DAP	0.98846	0.932
41DAP/39DAP	1.04679	0.781
42DAP/41DAP	0.96398	0.644
43DAP/42DAP	0.9571	0.447
47DAP/43DAP	1.00395	0.973
52DAP/47DAP	1.00738	0.986
57DAP/52DAP	1.02304	0.941
57DAP/7DAP	0.91289	0.219

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01368	1
17DAP/reference	0.67756	0.014
27DAP/reference	1.28	0.015
39DAP/reference	0.90953	0.23
41DAP/reference	1.02304	1
42DAP/reference	1.22022	0.132
43DAP/reference	1.02435	1
47DAP/reference	1.02497	0.885
52DAP/reference	0.93547	0.232
57DAP/reference	0.59229	0.019

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97172	0.532
17DAP/reference	0.92269	0.099
27DAP/reference	1.0231	0.917
39DAP/reference	0.93342	0.235
41DAP/reference	0.99434	0.601
42DAP/reference	0.97065	0.482
43DAP/reference	1.03269	0.719
47DAP/reference	1.0414	0.658
52DAP/reference	0.96257	0.239
57DAP/reference	0.9901	0.72

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87907	0.087
17DAP/reference	0.8116	0.144
27DAP/reference	0.81082	0.05
39DAP/reference	0.775	0.012
41DAP/reference	0.80563	0.05
42DAP/reference	0.95143	0.445
43DAP/reference	0.85044	0.051
47DAP/reference	1.00781	1
52DAP/reference	1.46688	0.118
57DAP/reference	1.16996	0.909

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.98921	1
26DAP/20DAP	0.96887	1
34DAP/26DAP	1.02082	1
51DAP/34DAP	0.95291	0.681
52DAP/51DAP	0.98981	1
53DAP/52DAP	0.97701	0.854
55DAP/53DAP	0.94019	0.592
57DAP/55DAP	1.07271	0.955
62DAP/57DAP	0.92353	0.466
68DAP/62DAP	0.9724	0.787
68DAP/14DAP	1.02141	0.802

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.95936	0.253

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.09726	0.176
Mature Green Tomato/Ripe Tomato	1.43944	0.04
Immature Eggplant/Mature Eggplant	1.31296	0.19
Ripe Pepper/Ripe Tomato	0.42808	0.224
Mature Eggplant/Ripe Tomato	0.64844	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.04492	1
1-1-2/M82	1.02485	1
12-2/M82	0.9456	0.955
12-4/M82	1.01847	1
1-3/M82	0.94657	0.378
2-1-1/M82	0.99169	1
2-1/M82	1.13029	1
2-6/M82	0.94578	1
3-2/M82	1.29639
4-1-1/M82	0.86607	0.962
4-1/M82	0.88663
4-3-2/M82	0.7612
4-3/M82	0.8952	1
5-3/M82	0.89004	0.447
6-2/M82	0.99531	1
6-3/M82	1.03709	1
7-1/M82	1.06488
7-2/M82	0.9727	1
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.08477	0.277
IL2-6/WTpooled	0.61406	0.473
IL7-5/WTpooled	0.95966	1
IL7-3/WTpooled	1.84793	0.362
IL12-4/WTpooled	1.04038	1
IL1-4/WTpooled	1.07	1
WT/WTpooled	1.17433	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	0.68056	0.226

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.1015	0.692
DC3000/delta hrp 6h	1.1092	0.95
DC3000/delta hrp 12h	0.93872	1
DC3000/delta hrp 24h	0.95999	0.598

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.05009	0.333
DC3000 delta B/DC3000 delta AB	1.11359	0.386

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.06248	1
Exp 36h	1.20392	1
Exp 60h	0.85724	0.586

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00901	1
Var 0h	1.04444	0.98
Var 12h I row2-row1	1.30001	0.196
Var 12h NI row2-row1	0.9279	0.82
Var 36h I row2-row1	1.01351	1
Var 36h NI row2-row1	0.92733	0.645
Var 60h I row2-row1	1.15004	1
Var 60h NI row2-row1	1.23746	0.904
Time course 0hI-0hNI	1.06595	0.852
Time course 12hI-12hNI	0.99499	0.994
Time course 36hI-36hNI	1.22097	0.355
Time course 60hI-60hNI	2.38634	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)	1.15272	0.261
transgenic ySAMdc/azygous control (breaker)	0.98888	1
transgenic ySAMdc/azygous control (red)	1.03669	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.0607	0.155

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.70963	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.79937	1
Manapal/WT (break)	0.86516	1
Manapal/WT (red)	0.98245	0.863