Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.4.9.8

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.88657	0.464
27DAP/17DAP	1.39482	0.646
39DAP/27DAP	3.12973	0.025
41DAP/39DAP	1.6076	0.334
42DAP/41DAP	1.00229	1
43DAP/42DAP	1.35709	0.587
47DAP/43DAP	1.62579	0.215
52DAP/47DAP	0.80654	0.502
57DAP/52DAP	1.6501	0.264

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.7851	0.03
17DAP/reference	0.89252	0.074
27DAP/reference	0.85641	0.031
39DAP/reference	1.35757	0.286
41DAP/reference	1.18202	0.03
42DAP/reference	1.44883	0.005
43DAP/reference	1.38693	0.007
47DAP/reference	2.30227	0.001
52DAP/reference	1.23174	0.195
57DAP/reference	1.19962	0.379

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.0761	0.5
27DAP/17DAP	1.03477	0.909
39DAP/27DAP	1.35618	0.067
41DAP/39DAP	0.71171	0.028
42DAP/41DAP	1.15976	0.651
43DAP/42DAP	1.27647	0.112
47DAP/43DAP	1.24794	0.138
52DAP/47DAP	1.01208	0.962
57DAP/52DAP	1.17689	0.627
57DAP/7DAP	1.64943	0.23

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.60977	0.058
17DAP/reference	0.67781	0.039
27DAP/reference	1.22109	1
39DAP/reference	1.22052	0.186
41DAP/reference	1.7968	0.008
42DAP/reference	1.72874	0.012
43DAP/reference	1.32871	0.087
47DAP/reference	1.20888	0.21
52DAP/reference	1.95658	0.008
57DAP/reference	3.2217	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.68709	0.017
17DAP/reference	0.73719	0.007
27DAP/reference	0.85745	0.119
39DAP/reference	0.76038	0.012
41DAP/reference	0.99308	0.584
42DAP/reference	1.06998	0.455
43DAP/reference	1.23038	0.503
47DAP/reference	2.64733	0.008
52DAP/reference	1.26142	0.007
57DAP/reference	1.79162	0.007

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.56105	0.036
17DAP/reference	0.72943	0.146
27DAP/reference	1.00711	1
39DAP/reference	1.62789	0.008
41DAP/reference	1.27814	0.028
42DAP/reference	1.62279	0.017
43DAP/reference	1.38816	0.037
47DAP/reference	2.53655	0.005
52DAP/reference	3.14201	0.027
57DAP/reference	1.34766	0.339

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.0105	1
26DAP/20DAP	1.2142	0.33
34DAP/26DAP	1.20289	0.542
51DAP/34DAP	2.33418	0.026
52DAP/51DAP	0.80437	1
53DAP/52DAP	1.6707	0.261
55DAP/53DAP	0.56919	0.016
57DAP/55DAP	0.95911	0.804
62DAP/57DAP	1.65612	0.004
68DAP/62DAP	0.77543	0.152
68DAP/14DAP	0.78679	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.9358	0.422

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.06401	0.039
Mature Green Tomato/Ripe Tomato	0.31477	0.021
Immature Eggplant/Mature Eggplant	12.5516	0.05
Ripe Pepper/Ripe Tomato	1.71065	0.256
Mature Eggplant/Ripe Tomato	0.43022	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.00532	1
1-1-2/M82	1.3895	1
12-2/M82	0.94922	0.955
12-4/M82	0.99494	1
1-3/M82	1.24362	0.479
2-1-1/M82	0.94044	0.465
2-1/M82	1.00136	1
2-6/M82	0.94567	1
3-2/M82	1.19146	0.717
4-1-1/M82	1.06822	1
4-1/M82	2.15159	0.853
4-3-2/M82	1.51595	0.241
4-3/M82	0.91329	1
5-3/M82	0.84991	1
6-2/M82	0.95606	1
6-3/M82	1.07767	1
7-1/M82	0.99131	1
7-2/M82	1.24195	1
9-3-2/M82	2.19045	0.196

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.75929	0.247
IL2-6/WTpooled	0.82533	0.473
IL7-5/WTpooled	0.92747	1
IL7-3/WTpooled	0.97986	1
IL12-4/WTpooled	0.80825	0.71
IL1-4/WTpooled	0.95097	1
WT/WTpooled	1.03789	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	1.26053	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.91444	0.868
DC3000/delta hrp 6h	1.1106	0.562
DC3000/delta hrp 12h	1.08568	1
DC3000/delta hrp 24h	1.02799	0.62

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.96805	1
DC3000 delta B/DC3000 delta AB	1.89987	0.088

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.09743	1
Exp 36h	1.12449	1
Exp 60h	0.98951	0.994

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

hybridization	ratio	FDR (corrected p value)
self-self	1.03624	1
Var 0h	1.93444	0.98
Var 12h I row2-row1	0.89134	0.565
Var 12h NI row2-row1	1.70848	0.34
Var 36h I row2-row1	0.96654	1
Var 36h NI row2-row1	1.43086	1
Var 60h I row2-row1	0.53195	0.285
Var 60h NI row2-row1	0.67655	0.306
Time course 0hI-0hNI	1.03324	0.764
Time course 12hI-12hNI	1.29022	0.075
Time course 36hI-36hNI	2.89254	0.005
Time course 60hI-60hNI	10.059	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)	0.58378	0.314
transgenic ySAMdc/azygous control (breaker)	1.02863	1
transgenic ySAMdc/azygous control (red)	1.11298	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.55569	0.05

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.867	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	3.60307	0.096
Manapal/WT (break)	2.33469	0.183
Manapal/WT (red)	1.3877	0.134