Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.3.10.19

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	2.26464	0.033
27DAP/17DAP	1.17003	0.815
39DAP/27DAP	1.57446	0.256
41DAP/39DAP	0.54596	0.041
42DAP/41DAP	1.13038	0.913
43DAP/42DAP	1.03438	0.937
47DAP/43DAP	1.00919	0.934
52DAP/47DAP	0.79925	0.502
57DAP/52DAP	1.18749	0.904

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03143	0.679
17DAP/reference	1.57025	0.108
27DAP/reference	2.12796	0.01
39DAP/reference	1.70672	0.14
41DAP/reference	2.07853	0.029
42DAP/reference	3.08279	0.001
43DAP/reference	2.17683	0.007
47DAP/reference	3.63297	0.001
52DAP/reference	2.69132	0.007
57DAP/reference	2.43428	0.008

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	2.50369	0.041
27DAP/17DAP	1.13975	0.658
39DAP/27DAP	0.89027	0.412
41DAP/39DAP	1.50375	1
42DAP/41DAP	1.16573	0.81
43DAP/42DAP	0.76856	0.089
47DAP/43DAP	0.99368	0.933
52DAP/47DAP	1.08798	0.826
57DAP/52DAP	1.32085	0.253
57DAP/7DAP	2.10387	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.46241	0.049
17DAP/reference	1.31902	0.084
27DAP/reference	2.4431	0.007
39DAP/reference	3.14409	0.005
41DAP/reference	2.81051	0.008
42DAP/reference	2.90715	0.006
43DAP/reference	3.37326	0.006
47DAP/reference	4.19436	0.014
52DAP/reference	3.85677	0.007
57DAP/reference	3.36167	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.50681	0.007
17DAP/reference	1.19624	0.25
27DAP/reference	2.51797	0.012
39DAP/reference	2.43753	0.011
41DAP/reference	1.99044	0.005
42DAP/reference	2.54774	0.007
43DAP/reference	1.50738	0.368
47DAP/reference	2.67011	0.008
52DAP/reference	1.59131	0.006
57DAP/reference	1.26484	0.786

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.78272	0.082
17DAP/reference	0.8368	0.146
27DAP/reference	1.80332	0.015
39DAP/reference	2.14765	0.005
41DAP/reference	1.64441	0.006
42DAP/reference	2.63935	0.006
43DAP/reference	2.78332	0.006
47DAP/reference	2.44283	0.007
52DAP/reference	2.51958	0.027
57DAP/reference	3.70447	0.006

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.17028	0.966
26DAP/20DAP	2.08301	0.106
34DAP/26DAP	1.11675	1
51DAP/34DAP	0.88954	0.41
52DAP/51DAP	0.70659	0.151
53DAP/52DAP	1.03461	0.882
55DAP/53DAP	0.72845	0.021
57DAP/55DAP	1.29369	0.865
62DAP/57DAP	0.86511	0.681
68DAP/62DAP	0.80218	0.076
68DAP/14DAP	1.99574	0.311

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	2.621	0.061

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.89219	0.418
Mature Green Tomato/Ripe Tomato	0.84337
Immature Eggplant/Mature Eggplant	1.21375	0.058
Ripe Pepper/Ripe Tomato	1.22839	1
Mature Eggplant/Ripe Tomato	0.82902	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.79788	0.907
1-1-2/M82	1.21894	0.977
12-2/M82	0.94562	0.955
12-4/M82	1.42282	1
1-3/M82	2.6511	0.248
2-1-1/M82	0.96168	0.465
2-1/M82	0.83405	0.74
2-6/M82	0.94389	1
3-2/M82	1.14687	0.717
4-1-1/M82	1.09582	1
4-1/M82	2.76236	0.853
4-3-2/M82	1.19627	1
4-3/M82	1.12092	1
5-3/M82	0.96512	1
6-2/M82	1.25315	1
6-3/M82	0.96321	1
7-1/M82	1.0533	0.925
7-2/M82	1.34156	0.385
9-3-2/M82	1.23158	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.81982	0.247
IL2-6/WTpooled	1.02413	1
IL7-5/WTpooled	0.61997	1
IL7-3/WTpooled	1.03863	1
IL12-4/WTpooled	1.01546	1
IL1-4/WTpooled	0.93365	0.834
WT/WTpooled	0.98213	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	0.90058	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.18481	0.894
DC3000/delta hrp 6h	1.06458	1
DC3000/delta hrp 12h	1.0604	1
DC3000/delta hrp 24h	0.86755	0.198

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.00154	1
DC3000 delta B/DC3000 delta AB	1.09678	0.406

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.04773	1
Exp 36h	1.0867	1
Exp 60h	1.0049	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.03454	1
Var 0h	0.44567	0.933
Var 12h I row2-row1	1.1064	0.544
Var 12h NI row2-row1	0.99605	1
Var 36h I row2-row1	1.33749	0.489
Var 36h NI row2-row1	1.17746	1
Var 60h I row2-row1	0.76622	0.439
Var 60h NI row2-row1	0.97394	1
Time course 0hI-0hNI	1.07395	0.662
Time course 12hI-12hNI	0.98049	0.874
Time course 36hI-36hNI	1.06356	0.401
Time course 60hI-60hNI	1.03191	1

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)	1.05318	0.798
transgenic ySAMdc/azygous control (breaker)	1.02513	1
transgenic ySAMdc/azygous control (red)	0.98753	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.54756	0.092

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.28587	0.239

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.04898	1
Manapal/WT (break)	0.942	1
Manapal/WT (red)	1.38722	0.413