Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.4.4.14

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.37361	0.014
27DAP/17DAP	0.33193	0.027
39DAP/27DAP	0.70531	0.414
41DAP/39DAP	0.53226	0.049
42DAP/41DAP	0.75781	0.774
43DAP/42DAP	1.11319	0.937
47DAP/43DAP	0.95004	0.799
52DAP/47DAP	0.88945	0.702
57DAP/52DAP	0.97574	0.957

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.54804	0.015
17DAP/reference	0.58651	0.007
27DAP/reference	0.76815	0.03
39DAP/reference	0.45066	0.005
41DAP/reference	0.36237	0.008
42DAP/reference	0.46242	0.001
43DAP/reference	0.40891	0.012
47DAP/reference	0.4305	0.001
52DAP/reference	0.40613	0.013
57DAP/reference	0.53538	0.009

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.33129	0.033
27DAP/17DAP	1.57441	0.045
39DAP/27DAP	0.68771	0.082
41DAP/39DAP	0.56342	0.013
42DAP/41DAP	0.85042	0.25
43DAP/42DAP	0.83819	0.235
47DAP/43DAP	0.94899	0.781
52DAP/47DAP	0.92446	0.763
57DAP/52DAP	1.07444	0.732
57DAP/7DAP	0.20289	0.219

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.29635	0.055
17DAP/reference	1.26229	0.023
27DAP/reference	1.17918	0.041
39DAP/reference	1.17365	0.036
41DAP/reference	1.64352	0.09
42DAP/reference	1.50437	0.009
43DAP/reference	1.25066	0.212
47DAP/reference	0.61324	0.168
52DAP/reference	0.90134	0.213
57DAP/reference	0.82356	0.057

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.06659	0.903
17DAP/reference	0.61838	0.012
27DAP/reference	0.5151	0.006
39DAP/reference	0.26323	0.007
41DAP/reference	0.61433	0.027
42DAP/reference	0.51986	0.011
43DAP/reference	0.35117	0.002
47DAP/reference	0.50686	0.009
52DAP/reference	0.38522	0.004
57DAP/reference	0.42039	0.004

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	3.46852	0.03
17DAP/reference	1.06335	0.934
27DAP/reference	1.28423	0.07
39DAP/reference	0.90885	0.328
41DAP/reference	0.82717	0.055
42DAP/reference	3.49689	0.142
43DAP/reference	1.02155	0.365
47DAP/reference	0.22242	0.004
52DAP/reference	2.20343	0.851
57DAP/reference	0.69056	0.048

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.00008	1
26DAP/20DAP	1.74892	0.098
34DAP/26DAP	1.19	0.819
51DAP/34DAP	0.68874	0.06
52DAP/51DAP	1.06275	0.565
53DAP/52DAP	0.60099	0.055
55DAP/53DAP	0.61368	0.056
57DAP/55DAP	0.74515	0.141
62DAP/57DAP	0.72664	0.162
68DAP/62DAP	1.11083	0.89
68DAP/14DAP	0.59888	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.11333	0.019

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	3.60144	0.058
Mature Green Tomato/Ripe Tomato	12.769	0.015
Immature Eggplant/Mature Eggplant	0.41674	0.058
Ripe Pepper/Ripe Tomato	21.9134	0.256
Mature Eggplant/Ripe Tomato	78.8279	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.00909
1-1-2/M82	1.03799
12-2/M82	N/A	N/A
12-4/M82	1.11044
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	0.9852
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	0.84271	0.364
6-2/M82	0.54793
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	0.91219

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.90435	1
IL2-6/WTpooled	1.24243	0.584
IL7-5/WTpooled	1.40174	1
IL7-3/WTpooled	0.97176	1
IL12-4/WTpooled	1.0965	0.785
IL1-4/WTpooled	1.01489	1
WT/WTpooled	0.97633	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	0.83481	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.94725	0.734
DC3000/delta hrp 6h	0.9295	0.95
DC3000/delta hrp 12h	0.90043	1
DC3000/delta hrp 24h	1.11784	0.502

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.10824
DC3000 delta B/DC3000 delta AB	0.87376	0.195

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.14562	1
Exp 36h	0.83606	0.623
Exp 60h	0.75907	0.266

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	1.05639	0.259
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)	0.7068	0.33
transgenic ySAMdc/azygous control (breaker)	1.19035	1
transgenic ySAMdc/azygous control (red)	1.71586	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.79279	0.092

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	4.33531	0.233

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	2.08764	0.084
Manapal/WT (break)	3.37024	0.13
Manapal/WT (red)	2.14306	0.134