Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.1.10.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.03123	0.951
27DAP/17DAP	1.05192	1
39DAP/27DAP	1.18935	0.725
41DAP/39DAP	0.88656	0.561
42DAP/41DAP	1.183	0.92
43DAP/42DAP	1.32199	0.728
47DAP/43DAP	0.87474	0.599
52DAP/47DAP	0.82521	0.543
57DAP/52DAP	1.08552	0.983

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02331	0.9
17DAP/reference	0.93155	0.321
27DAP/reference	1.16498	0.264
39DAP/reference	0.95898	0.513
41DAP/reference	1.01482	1
42DAP/reference	0.92831	0.124
43DAP/reference	1.04543	0.942
47DAP/reference	1.02558	1
52DAP/reference	1.18641	0.096
57DAP/reference	1.1511	0.136

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.85374	0.428
27DAP/17DAP	1.04265	0.909
39DAP/27DAP	1.87029	0.079
41DAP/39DAP	3.34286	0.005
42DAP/41DAP	0.60844	0.007
43DAP/42DAP	0.49936	0.02
47DAP/43DAP	1.00357	0.998
52DAP/47DAP	1.34367	0.63
57DAP/52DAP	0.52094	0.137
57DAP/7DAP	0.79802	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04382	0.6
17DAP/reference	0.94202	0.072
27DAP/reference	0.86345	0.01
39DAP/reference	0.99734	0.745
41DAP/reference	1.09479	0.097
42DAP/reference	1.04424	0.534
43DAP/reference	0.93524	0.061
47DAP/reference	0.99893	1
52DAP/reference	0.98235	0.571
57DAP/reference	0.97598	0.458

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.1377	0.106
17DAP/reference	1.128	0.21
27DAP/reference	1.18118	0.192
39DAP/reference	1.27885	0.182
41DAP/reference	1.36361	0.025
42DAP/reference	1.01057	0.723
43DAP/reference	1.1213	0.392
47DAP/reference	0.93137	0.214
52DAP/reference	1.20952	0.259
57DAP/reference	1.07665	0.64

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93814	0.098
17DAP/reference	1.04967	0.627
27DAP/reference	0.93715	0.286
39DAP/reference	0.95057	0.393
41DAP/reference	0.90455	0.077
42DAP/reference	0.97594	0.671
43DAP/reference	0.9736	0.545
47DAP/reference	1.06356	0.655
52DAP/reference	0.84689	0.296
57DAP/reference	1.40478	0.044

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.00406	1
26DAP/20DAP	0.91466	1
34DAP/26DAP	1.29456	1
51DAP/34DAP	1.32255	0.496
52DAP/51DAP	0.76447	1
53DAP/52DAP	1.06397	0.998
55DAP/53DAP	1.09673	0.861
57DAP/55DAP	1.03266	1
62DAP/57DAP	0.6981	0.466
68DAP/62DAP	1.42188	0.682
68DAP/14DAP	1.03132	0.889

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.74165	0.015

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.72083	0.215
Mature Green Tomato/Ripe Tomato	2.40421	0.016
Immature Eggplant/Mature Eggplant	0.72021	0.096
Ripe Pepper/Ripe Tomato	1.85426	0.258
Mature Eggplant/Ripe Tomato	1.19391	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.81368	0.841
1-1-2/M82	1.15334	1
12-2/M82	0.93737	1
12-4/M82	1.12085	1
1-3/M82	0.9235	1
2-1-1/M82	0.91587
2-1/M82	0.93041
2-6/M82	0.93464	0.501
3-2/M82	1.10309
4-1-1/M82	1.05986	0.968
4-1/M82	N/A	N/A
4-3-2/M82	0.86143
4-3/M82	0.828	0.72
5-3/M82	1.20924	0.378
6-2/M82	0.85931
6-3/M82	0.97469	1
7-1/M82	1.74895
7-2/M82	0.88747	0.881
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.95177	1
IL2-6/WTpooled	1.29867	0.419
IL7-5/WTpooled	0.93882	1
IL7-3/WTpooled	1.32612	1
IL12-4/WTpooled	0.91068	1
IL1-4/WTpooled	0.9701	1
WT/WTpooled	1.21237	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	1.28726	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.01385	1
DC3000/delta hrp 6h	1.0804	0.95
DC3000/delta hrp 12h	1.17088	1
DC3000/delta hrp 24h	1.093	0.502

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.9913	0.042
DC3000 delta B/DC3000 delta AB	3.27954	0.031

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.00306	1
Exp 36h	0.84858	0.449
Exp 60h	0.82746	0.278

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99685	1
Var 0h	1.00247	1
Var 12h I row2-row1	0.76048	0.565
Var 12h NI row2-row1	2.21468	0.34
Var 36h I row2-row1	1.38301	0.742
Var 36h NI row2-row1	0.56274	0.522
Var 60h I row2-row1	0.84122	0.582
Var 60h NI row2-row1	0.67829	0.458
Time course 0hI-0hNI	1.3004	0.603
Time course 12hI-12hNI	1.19145	0.785
Time course 36hI-36hNI	3.86607	0.004
Time course 60hI-60hNI	11.2304	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)	0.93021	0.338
transgenic ySAMdc/azygous control (breaker)	0.87446	0.251
transgenic ySAMdc/azygous control (red)	0.84582	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.97339	0.418

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.07399	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.41203	0.096
Manapal/WT (break)	0.97275	1
Manapal/WT (red)	0.85361	0.188