Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.3.4.1

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.70617	0.105
27DAP/17DAP	1.07361	1
39DAP/27DAP	0.86767	0.631
41DAP/39DAP	1.04199	0.964
42DAP/41DAP	0.97851	1
43DAP/42DAP	1.02255	0.937
47DAP/43DAP	1.55334	0.316
52DAP/47DAP	1.28839	0.818
57DAP/52DAP	1.31998	0.912

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.66971	0.028
17DAP/reference	0.87046	0.194
27DAP/reference	1.07976	0.405
39DAP/reference	0.88679	0.124
41DAP/reference	0.75581	0.01
42DAP/reference	0.83208	0.008
43DAP/reference	0.80354	0.021
47DAP/reference	1.05965	1
52DAP/reference	1.82304	0.038
57DAP/reference	1.73183	0.011

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.9987	0.847
27DAP/17DAP	0.93876	0.724
39DAP/27DAP	1.09859	0.57
41DAP/39DAP	0.88861	0.481
42DAP/41DAP	1.06032	0.675
43DAP/42DAP	0.90621	0.415
47DAP/43DAP	0.97199	0.857
52DAP/47DAP	1.37503	0.351
57DAP/52DAP	1.15108	0.421
57DAP/7DAP	1.27044	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02154	1
17DAP/reference	1.61892	0.038
27DAP/reference	1.15213	0.107
39DAP/reference	1.39917	0.186
41DAP/reference	1.18597	0.336
42DAP/reference	1.11468	1
43DAP/reference	1.01334	1
47DAP/reference	0.97985	0.671
52DAP/reference	1.05096	0.832
57DAP/reference	1.2502	0.356

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.88295	0.214
17DAP/reference	0.77299	0.011
27DAP/reference	0.91608	0.257
39DAP/reference	1.02603	1
41DAP/reference	0.99883	0.649
42DAP/reference	0.88944	0.098
43DAP/reference	0.7071	0.028
47DAP/reference	0.88909	0.039
52DAP/reference	0.9436	0.259
57DAP/reference	0.70835	0.021

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.74828	0.054
17DAP/reference	1.10628	0.585
27DAP/reference	1.30386	0.031
39DAP/reference	1.14465	0.633
41DAP/reference	1.04001	1
42DAP/reference	0.9385	0.361
43DAP/reference	1.13095	0.679
47DAP/reference	1.00761	0.731
52DAP/reference	1.59604	0.216
57DAP/reference	1.20561	0.104

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.00807	1
26DAP/20DAP	1.55283	0.164
34DAP/26DAP	0.8516	0.682
51DAP/34DAP	1.11307	0.473
52DAP/51DAP	1.14736	0.503
53DAP/52DAP	1.39875	0.738
55DAP/53DAP	0.83445	0.489
57DAP/55DAP	1.07114	0.915
62DAP/57DAP	0.99167	1
68DAP/62DAP	1.25398	0.582
68DAP/14DAP	1.71355	0.039

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.94993	0.547

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.03346	1
Mature Green Tomato/Ripe Tomato	1.25975	0.835
Immature Eggplant/Mature Eggplant	1.03691	0.528
Ripe Pepper/Ripe Tomato	1.59234	0.256
Mature Eggplant/Ripe Tomato	1.22854	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.94377
1-1-2/M82	0.89738
12-2/M82	N/A	N/A
12-4/M82	0.74238	0.33
1-3/M82	N/A	N/A
2-1-1/M82	1.00626	1
2-1/M82	0.76612	0.322
2-6/M82	0.77965	1
3-2/M82	1.11737
4-1-1/M82	1.08285	1
4-1/M82	N/A	N/A
4-3-2/M82	0.86158	0.698
4-3/M82	0.91782	1
5-3/M82	1.20199	1
6-2/M82	0.79498	0.481
6-3/M82	1.14578
7-1/M82	1.03734	1
7-2/M82	N/A	N/A
9-3-2/M82	1.2635	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.10013	0.441
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.91208
IL12-4/WTpooled	1.00323	1
IL1-4/WTpooled	1.14371
WT/WTpooled	0.96867	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	1.07052	0.479

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.59716
DC3000/delta hrp 6h	1.05799	1
DC3000/delta hrp 12h	0.92878	1
DC3000/delta hrp 24h	1.44413	0.065

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.41865	0.076
DC3000 delta B/DC3000 delta AB	0.84843	0.261

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.93792	1
Exp 36h	1.25427	1
Exp 60h	1.06325	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01199	1
Var 0h	0.67956	1
Var 12h I row2-row1	0.96851	0.948
Var 12h NI row2-row1	0.84071	0.627
Var 36h I row2-row1	0.99073	1
Var 36h NI row2-row1	1.10163
Var 60h I row2-row1	1.26682	1
Var 60h NI row2-row1	1.05651	0.904
Time course 0hI-0hNI	1.06237	0.799
Time course 12hI-12hNI	0.90953	0.312
Time course 36hI-36hNI	0.61681	0.023
Time course 60hI-60hNI	0.10452	0.006

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)	0.96643	0.338
transgenic ySAMdc/azygous control (breaker)	1.23829	0.248
transgenic ySAMdc/azygous control (red)	1.13331	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.27346	0.042

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.94278	0.789

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.84026	1
Manapal/WT (break)	1.07688	0.381
Manapal/WT (red)	1.0805	1