Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.3.13.4

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.18178	0.498
27DAP/17DAP	1.0184	1
39DAP/27DAP	0.88687	0.512
41DAP/39DAP	1.20872	0.372
42DAP/41DAP	1.0212	1
43DAP/42DAP	1.11161	0.985
47DAP/43DAP	0.96363	0.84
52DAP/47DAP	1.18993	0.588
57DAP/52DAP	1.00355	0.992

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91724	0.465
17DAP/reference	1.01519	0.546
27DAP/reference	1.06696	0.291
39DAP/reference	0.979	0.901
41DAP/reference	1.03807	0.48
42DAP/reference	0.94843	0.085
43DAP/reference	0.96737	0.611
47DAP/reference	1.00275	1
52DAP/reference	0.93845	0.382
57DAP/reference	0.96587	0.435

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.99185	0.801
27DAP/17DAP	0.98895	0.854
39DAP/27DAP	0.98341	0.932
41DAP/39DAP	1.01114	0.895
42DAP/41DAP	0.98103	0.791
43DAP/42DAP	1.00972	0.699
47DAP/43DAP	1.01129	0.941
52DAP/47DAP	1.03686	0.835
57DAP/52DAP	0.95848	0.524
57DAP/7DAP	1.03345	0.249

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02642	0.91
17DAP/reference	0.9576	0.124
27DAP/reference	0.94269	0.101
39DAP/reference	0.98666	0.474
41DAP/reference	0.98852	0.412
42DAP/reference	0.9991	0.791
43DAP/reference	0.94108	0.126
47DAP/reference	0.99147	1
52DAP/reference	0.97159	0.398
57DAP/reference	1.03885	0.907

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01881	0.832
17DAP/reference	0.99126	0.673
27DAP/reference	0.9875	0.598
39DAP/reference	0.96387	0.33
41DAP/reference	0.94736	0.373
42DAP/reference	1.00637	1
43DAP/reference	0.94767	0.37
47DAP/reference	1.12043	0.065
52DAP/reference	0.9643	0.259
57DAP/reference	0.96435	0.433

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98238	0.455
17DAP/reference	0.98296	0.647
27DAP/reference	0.99729	0.805
39DAP/reference	0.92481	0.035
41DAP/reference	0.94194	0.032
42DAP/reference	0.87252	0.028
43DAP/reference	0.93481	0.068
47DAP/reference	0.95493	0.278
52DAP/reference	0.88631	0.186
57DAP/reference	0.92595	0.051

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.01897	0.966
26DAP/20DAP	1.01128	1
34DAP/26DAP	1.03158	0.819
51DAP/34DAP	0.96925	0.66
52DAP/51DAP	0.97622	1
53DAP/52DAP	1.02183	0.91
55DAP/53DAP	0.86089	0.169
57DAP/55DAP	1.01473	1
62DAP/57DAP	0.99835	1
68DAP/62DAP	1.37127	0.259
68DAP/14DAP	0.96586	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.02199	0.865

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.21429	0.068
Mature Green Tomato/Ripe Tomato	0.82604	0.411
Immature Eggplant/Mature Eggplant	15.2795	0.05
Ripe Pepper/Ripe Tomato	1.56257	0.258
Mature Eggplant/Ripe Tomato	1.06678	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.10074	0.551
1-1-2/M82	0.9651	1
12-2/M82	1.04387	1
12-4/M82	0.90074	0.619
1-3/M82	1.21623	0.255
2-1-1/M82	0.98372	1
2-1/M82	1.23005	1
2-6/M82	0.97085	1
3-2/M82	0.85456	1
4-1-1/M82	1.07805	1
4-1/M82	0.97415	1
4-3-2/M82	1.27068	0.253
4-3/M82	1.10252	1
5-3/M82	1.01461	1
6-2/M82	1.06279	1
6-3/M82	1.06794	1
7-1/M82	0.96295	1
7-2/M82	1.52482	0.385
9-3-2/M82	1.33895	0.196

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.1222	0.395
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.09598	0.362
IL12-4/WTpooled	1.07105	0.695
IL1-4/WTpooled	1.01617
WT/WTpooled	0.95791	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	1.69581	0.309

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.93655	1
DC3000/delta hrp 6h	1.27848	0.978
DC3000/delta hrp 12h	1.01788	1
DC3000/delta hrp 24h	1.07018	0.283

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.09013	0.102
DC3000 delta B/DC3000 delta AB	1.17078	0.225

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.20043	1
Exp 36h	1.76728	0.693
Exp 60h	1.48385	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98527	1
Var 0h	0.49487	1
Var 12h I row2-row1	1.03354	0.654
Var 12h NI row2-row1	1.52135	0.649
Var 36h I row2-row1	1.15222	1
Var 36h NI row2-row1	0.76181	0.522
Var 60h I row2-row1	1.03941	1
Var 60h NI row2-row1	0.7037	0.458
Time course 0hI-0hNI	1.06326	0.662
Time course 12hI-12hNI	1.29809	0.134
Time course 36hI-36hNI	4.20166	0.004
Time course 60hI-60hNI	6.90576	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)	0.88547	0.567
transgenic ySAMdc/azygous control (breaker)	0.43422	0.142
transgenic ySAMdc/azygous control (red)	1.01182	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.99663	0.832

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.44059	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	11.6298	0.096
Manapal/WT (break)	6.91977	0.14
Manapal/WT (red)	5.41703	0.164