Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.4.7.14

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.12702	0.697
27DAP/17DAP	0.55193	0.029
39DAP/27DAP	0.62043	0.255
41DAP/39DAP	0.63183	0.068
42DAP/41DAP	0.83437	0.774
43DAP/42DAP	1.06821	1
47DAP/43DAP	0.74007	0.266
52DAP/47DAP	1.82566	0.226
57DAP/52DAP	0.96183	0.957

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.6537	0.007
17DAP/reference	1.34687	0.034
27DAP/reference	1.04633	0.831
39DAP/reference	0.95415	0.611
41DAP/reference	0.89415	0.154
42DAP/reference	0.80031	0.05
43DAP/reference	0.74188	0.073
47DAP/reference	0.41067	0.002
52DAP/reference	0.53394	0.017
57DAP/reference	0.66062	0.065

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.59767	0.054
27DAP/17DAP	0.85594	0.537
39DAP/27DAP	0.50298	0.031
41DAP/39DAP	1.17143	0.362
42DAP/41DAP	0.92435	0.515
43DAP/42DAP	0.67923	0.022
47DAP/43DAP	0.86555	0.045
52DAP/47DAP	0.92602	0.807
57DAP/52DAP	1.01025	1
57DAP/7DAP	0.49965	0.219

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.43933	0.028
17DAP/reference	1.03946	0.18
27DAP/reference	0.89812	0.062
39DAP/reference	0.86769	0.073
41DAP/reference	0.73514	0.011
42DAP/reference	0.69889	0.011
43DAP/reference	0.69702	0.011
47DAP/reference	0.54235	0.026
52DAP/reference	0.73387	0.013
57DAP/reference	0.76949	0.007

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.26208	0.404
17DAP/reference	1.83102	0.007
27DAP/reference	1.72966	0.018
39DAP/reference	0.74052	0.074
41DAP/reference	1.10058	0.862
42DAP/reference	0.94583	0.534
43DAP/reference	0.75062	0.082
47DAP/reference	0.66678	0.064
52DAP/reference	0.64337	0.005
57DAP/reference	0.79534	0.079

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.38471	0.015
17DAP/reference	2.41198	0.048
27DAP/reference	1.71452	0.015
39DAP/reference	1.43117	0.007
41DAP/reference	1.13506	0.093
42DAP/reference	1.01609	1
43DAP/reference	1.03528	0.88
47DAP/reference	0.82204	0.076
52DAP/reference	0.67529	0.134
57DAP/reference	1.28036	0.126

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.62454	0.966
26DAP/20DAP	0.92465	0.512
34DAP/26DAP	0.98366	0.988
51DAP/34DAP	0.8292	0.158
52DAP/51DAP	1.03614	0.616
53DAP/52DAP	1.07744	0.58
55DAP/53DAP	1.06443	0.782
57DAP/55DAP	0.86273	0.458
62DAP/57DAP	0.97656	0.994
68DAP/62DAP	1.39569	0.869
68DAP/14DAP	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.1566	0.212

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	7.61384	0.015
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	15.5125
Mature Eggplant/Ripe Tomato	12.3241	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.84236	0.934
1-1-2/M82	N/A	N/A
12-2/M82	0.81642	0.955
12-4/M82	1.15363
1-3/M82	0.87992	0.501
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	1.17826
3-2/M82	1.19019
4-1-1/M82	1.40214	1
4-1/M82	0.79943
4-3-2/M82	1.11121	0.508
4-3/M82	1.26757
5-3/M82	1.40309	0.572
6-2/M82	0.95379
6-3/M82	N/A	N/A
7-1/M82	1.2233	0.992
7-2/M82	1.19101	0.385
9-3-2/M82	1.0024

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.83091
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	1.46627
IL7-3/WTpooled	1.63954	1
IL12-4/WTpooled	0.89125	0.539
IL1-4/WTpooled	0.86783
WT/WTpooled	1.00802	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	0.97265	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.82075	0.463
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	0.61864
DC3000/delta hrp 24h	0.96116	0.736

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.7992
DC3000 delta B/DC3000 delta AB	0.53224	0.022

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	N/A	N/A
Exp 60h	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
self-self	0.96231	1
Var 0h	1.68752	0.421
Var 12h I row2-row1	0.99185	1
Var 12h NI row2-row1	0.98545	0.906
Var 36h I row2-row1	0.78851	1
Var 36h NI row2-row1	0.93785	0.478
Var 60h I row2-row1	1.14414	0.562
Var 60h NI row2-row1	0.98842	1
Time course 0hI-0hNI	0.97225	0.821
Time course 12hI-12hNI	0.98724	0.909
Time course 36hI-36hNI	0.9993	0.811
Time course 60hI-60hNI	0.84291	0.319

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)	N/A	N/A
transgenic ySAMdc/azygous control (breaker)	N/A	N/A
transgenic ySAMdc/azygous control (red)	N/A	N/A

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.6637	0.186

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	N/A	N/A
Manapal/WT (break)	N/A	N/A
Manapal/WT (red)	14.085	0.142