Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.4.9.9

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.75773	0.226
27DAP/17DAP	0.91776	0.8
39DAP/27DAP	1.76429	0.47
41DAP/39DAP	1.54059	0.408
42DAP/41DAP	0.9532	1
43DAP/42DAP	0.80465	0.699
47DAP/43DAP	0.69123	0.228
52DAP/47DAP	3.40773	0.256
57DAP/52DAP	0.8246	0.783

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.62296	0.027
17DAP/reference	0.66213	0.007
27DAP/reference	0.76141	0.012
39DAP/reference	0.7973	0.023
41DAP/reference	0.74551	0.011
42DAP/reference	0.8341	0.001
43DAP/reference	0.90049	0.143
47DAP/reference	0.74623	0.002
52DAP/reference	0.77999	0.022
57DAP/reference	0.91623	0.118

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.82277	0.164
27DAP/17DAP	1.04105	0.957
39DAP/27DAP	1.12061	0.512
41DAP/39DAP	1.08418	0.799
42DAP/41DAP	0.92498	0.503
43DAP/42DAP	1.22172	0.176
47DAP/43DAP	1.06024	0.827
52DAP/47DAP	0.93996	0.814
57DAP/52DAP	1.0126	1
57DAP/7DAP	1.3171	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.7288	0.059
17DAP/reference	0.76441	0.015
27DAP/reference	0.90997	0.159
39DAP/reference	0.75991	0.011
41DAP/reference	0.741	0.01
42DAP/reference	0.74183	0.01
43DAP/reference	0.70246	0.013
47DAP/reference	0.73366	0.032
52DAP/reference	0.66923	0.031
57DAP/reference	0.66291	0.008

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.72687	0.026
17DAP/reference	0.62119	0.003
27DAP/reference	0.64671	0.02
39DAP/reference	0.53153	0.008
41DAP/reference	0.62856	0.018
42DAP/reference	0.94738	0.392
43DAP/reference	0.8806	0.147
47DAP/reference	1.05634	0.454
52DAP/reference	0.50115	0.003
57DAP/reference	0.61584	0.003

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.69042	0.026
17DAP/reference	0.88058	0.389
27DAP/reference	0.71753	0.038
39DAP/reference	0.67436	0.008
41DAP/reference	0.74165	0.032
42DAP/reference	0.93175	0.361
43DAP/reference	0.70249	0.035
47DAP/reference	0.65684	0.004
52DAP/reference	0.82469	0.169
57DAP/reference	0.71296	0.03

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.88072	0.566
26DAP/20DAP	0.95155	1
34DAP/26DAP	1.04708	1
51DAP/34DAP	0.96635	0.807
52DAP/51DAP	1.04301	0.836
53DAP/52DAP	1.19731	0.47
55DAP/53DAP	1.08625	0.813
57DAP/55DAP	0.93421	0.703
62DAP/57DAP	1.09033	0.767
68DAP/62DAP	0.86259	0.543
68DAP/14DAP	0.77552	0.121

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.20863	0.558

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.9441
Mature Green Tomato/Ripe Tomato	0.92126	0.487
Immature Eggplant/Mature Eggplant	0.83874	0.651
Ripe Pepper/Ripe Tomato	0.54158	0.293
Mature Eggplant/Ripe Tomato	0.56569	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.04032	0.591
1-1-2/M82	0.81082	1
12-2/M82	1.10744	1
12-4/M82	0.95915	1
1-3/M82	1.21327	1
2-1-1/M82	1.37596
2-1/M82	1.05845	1
2-6/M82	0.92902	1
3-2/M82	0.90505	0.455
4-1-1/M82	0.97326	1
4-1/M82	0.75753	1
4-3-2/M82	1.0023	1
4-3/M82	0.90954	1
5-3/M82	1.06134	1
6-2/M82	0.99446	1
6-3/M82	0.96256	1
7-1/M82	1.01942	1
7-2/M82	0.95339	0.565
9-3-2/M82	0.94483	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.73343	0.247
IL2-6/WTpooled	1.59119	0.419
IL7-5/WTpooled	0.93011	1
IL7-3/WTpooled	0.69647	0.31
IL12-4/WTpooled	1.07369	0.891
IL1-4/WTpooled	1.18707	1
WT/WTpooled	1.07281	0.957

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	1.08438	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.06651	0.894
DC3000/delta hrp 6h	0.86683	0.95
DC3000/delta hrp 12h	0.94578	1
DC3000/delta hrp 24h	1.08882	0.483

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.80154	0.056
DC3000 delta B/DC3000 delta AB	1.13124	0.484

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.28956	1
Exp 36h	1.56361	0.693
Exp 60h	1.3537	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00089	1
Var 0h	0.98773	1
Var 12h I row2-row1	1.02445	0.736
Var 12h NI row2-row1	1.33349	0.266
Var 36h I row2-row1	1.2333	0.742
Var 36h NI row2-row1	0.59373	0.478
Var 60h I row2-row1	1.29988	0.562
Var 60h NI row2-row1	0.71932	0.292
Time course 0hI-0hNI	1.12267	0.719
Time course 12hI-12hNI	1.05381	0.892
Time course 36hI-36hNI	2.35638	0.004
Time course 60hI-60hNI	8.29465	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)	1.16966	0.699
transgenic ySAMdc/azygous control (breaker)	2.93058	0.248
transgenic ySAMdc/azygous control (red)	0.78906	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.98567	0.694

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.76825	0.284

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.13874	1
Manapal/WT (break)	0.99826	1
Manapal/WT (red)	0.26693	0.181