Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.3.3.2

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.90091	0.511
27DAP/17DAP	0.94004	0.894
39DAP/27DAP	1.62115	0.135
41DAP/39DAP	1.14684	0.758
42DAP/41DAP	0.97202	1
43DAP/42DAP	1.38214	0.772
47DAP/43DAP	0.64951	0.102
52DAP/47DAP	1.26341	0.718
57DAP/52DAP	0.98296	0.971

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.83669	0.132
17DAP/reference	0.70444	0.025
27DAP/reference	0.6659	0.013
39DAP/reference	0.52122	0.01
41DAP/reference	0.48765	0.008
42DAP/reference	0.85045	0.085
43DAP/reference	0.89616	0.302
47DAP/reference	1.13424	0.295
52DAP/reference	0.66468	0.014
57DAP/reference	N/A	N/A

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.03087	0.975
27DAP/17DAP	0.90325	0.854
39DAP/27DAP	1.23547	0.117
41DAP/39DAP	1.03358	1
42DAP/41DAP	1.01766	0.841
43DAP/42DAP	1.69288	0.019
47DAP/43DAP	1.1528	0.581
52DAP/47DAP	0.80858	0.389
57DAP/52DAP	1.25549	0.124
57DAP/7DAP	1.1332

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99895	0.758
17DAP/reference	0.68189	0.049
27DAP/reference	0.55179	0.035
39DAP/reference	1.00918	0.474
41DAP/reference	1.01427	0.589
42DAP/reference	0.89269	0.275
43DAP/reference	1.22013	0.14
47DAP/reference	0.87008	0.168
52DAP/reference	1.22809	0.149
57DAP/reference	0.95159	0.353

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.69866	0.041
17DAP/reference	0.75499	0.03
27DAP/reference	0.90821	0.269
39DAP/reference	0.77769	0.067
41DAP/reference	0.8147	0.058
42DAP/reference	0.72796	0.015
43DAP/reference	0.57655	0.009
47DAP/reference	0.70678	0.009
52DAP/reference	0.63644	0.01
57DAP/reference	0.63687	0.011

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.752	0.127
17DAP/reference	1.46628	0.059
27DAP/reference	1.16167
39DAP/reference	0.73828	0.023
41DAP/reference	0.92164	0.459
42DAP/reference	0.87277	0.445
43DAP/reference	1.33934	0.056
47DAP/reference	0.80674	0.013
52DAP/reference	1.17245	0.457
57DAP/reference	1.06267	0.604

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.09998	0.966
26DAP/20DAP	0.9473	1
34DAP/26DAP	0.91002	0.917
51DAP/34DAP	1.11851	0.898
52DAP/51DAP	0.79957	1
53DAP/52DAP	1.9516	0.03
55DAP/53DAP	0.89948	0.445
57DAP/55DAP	0.96464	0.823
62DAP/57DAP	1.23454	0.868
68DAP/62DAP	0.98464	0.81
68DAP/14DAP	0.80805	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	2.3105	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.50028	0.097
Mature Green Tomato/Ripe Tomato	0.27579	0.033
Immature Eggplant/Mature Eggplant	1.2003	0.051
Ripe Pepper/Ripe Tomato	0.5091	0.224
Mature Eggplant/Ripe Tomato	0.25607	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.06562	1
1-1-2/M82	1.35824	1
12-2/M82	0.99028	0.955
12-4/M82	0.64532	0.619
1-3/M82	1.85041	0.277
2-1-1/M82	0.82611	0.683
2-1/M82	0.85194	0.74
2-6/M82	0.97373	1
3-2/M82	N/A	N/A
4-1-1/M82	0.89042	1
4-1/M82	0.81936
4-3-2/M82	1.42246
4-3/M82	1.02473	1
5-3/M82	1.22317	0.572
6-2/M82	1.63269	0.235
6-3/M82	1.09241	1
7-1/M82	N/A	N/A
7-2/M82	1.21819	0.385
9-3-2/M82	1.34774	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.04138	1
IL2-6/WTpooled	1.13875	0.46
IL7-5/WTpooled	0.97767	1
IL7-3/WTpooled	0.94355	0.418
IL12-4/WTpooled	0.94267	0.71
IL1-4/WTpooled	0.97622	1
WT/WTpooled	0.89231	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	1.38735	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.97736	1
DC3000/delta hrp 6h	0.90643	0.95
DC3000/delta hrp 12h	1.18037	1
DC3000/delta hrp 24h	0.87444	0.136

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.46435
DC3000 delta B/DC3000 delta AB	1.11573	0.462

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.95407	1
Exp 36h	0.80075	0.471
Exp 60h	0.76524	0.251

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

hybridization	ratio	FDR (corrected p value)
self-self	N/A	N/A
Var 0h	N/A	N/A
Var 12h I row2-row1	N/A	N/A
Var 12h NI row2-row1	N/A	N/A
Var 36h I row2-row1	N/A	N/A
Var 36h NI row2-row1	N/A	N/A
Var 60h I row2-row1	N/A	N/A
Var 60h NI row2-row1	N/A	N/A
Time course 0hI-0hNI	N/A	N/A
Time course 12hI-12hNI	N/A	N/A
Time course 36hI-36hNI	N/A	N/A
Time course 60hI-60hNI	N/A	N/A

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)	1.05625	0.699
transgenic ySAMdc/azygous control (breaker)	0.88998	0.173
transgenic ySAMdc/azygous control (red)	1.12047	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.35368	0.163

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.27993	0.233

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	2.22758	0.086
Manapal/WT (break)	1.45728	0.123
Manapal/WT (red)	0.85639	0.36