Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.3.16.19

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.0503	0.867
27DAP/17DAP	1.16674	1
39DAP/27DAP	2.15935	0.07
41DAP/39DAP	0.8966	0.412
42DAP/41DAP	0.89019	1
43DAP/42DAP	2.18121	0.793
47DAP/43DAP	1.0021	0.565
52DAP/47DAP	3.26047	0.327
57DAP/52DAP	1.32041	0.983

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93312	0.132
17DAP/reference	0.92391	0.06
27DAP/reference	0.99996	0.923
39DAP/reference	0.98462	0.691
41DAP/reference	0.88343	0.049
42DAP/reference	1.0338	0.231
43DAP/reference	0.98674	0.708
47DAP/reference	0.94707	0.025
52DAP/reference	0.99337	0.654
57DAP/reference	1.04973	0.643

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.62984	0.064
27DAP/17DAP	1.05174	0.932
39DAP/27DAP	1.30361	0.154
41DAP/39DAP	1.55315	0.024
42DAP/41DAP	0.73216	0.042
43DAP/42DAP	2.23023	0.013
47DAP/43DAP	1.1686	0.121
52DAP/47DAP	0.83919	0.233
57DAP/52DAP	2.2566	0.029
57DAP/7DAP	2.09609	0.249

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.09507	0.332
17DAP/reference	0.92	0.064
27DAP/reference	0.84692	0.016
39DAP/reference	0.98811	0.552
41DAP/reference	1.03116	0.836
42DAP/reference	1.03581	0.686
43DAP/reference	1.47627	0.008
47DAP/reference	1.11134	0.127
52DAP/reference	1.04788	0.526
57DAP/reference	1.09164	0.108

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98988	0.831
17DAP/reference	0.99636	0.766
27DAP/reference	0.8895	0.134
39DAP/reference	0.89758	0.076
41DAP/reference	1.01414	1
42DAP/reference	0.9363	0.15
43DAP/reference	1.10372	0.462
47DAP/reference	0.99547	0.695
52DAP/reference	1.01674	0.789
57DAP/reference	0.99255	0.789

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.05414	0.505
17DAP/reference	0.97742	0.624
27DAP/reference	0.96713	0.465
39DAP/reference	0.85084	0.019
41DAP/reference	0.87168	0.043
42DAP/reference	0.90178	0.071
43DAP/reference	0.85944	0.057
47DAP/reference	1.00387	0.731
52DAP/reference	0.98275	0.732
57DAP/reference	0.8333	0.078

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.95314	1
26DAP/20DAP	0.87654	0.512
34DAP/26DAP	0.93745	0.666
51DAP/34DAP	0.94197	0.722
52DAP/51DAP	1.19695	0.126
53DAP/52DAP	1.10742	0.444
55DAP/53DAP	1.04455	0.861
57DAP/55DAP	1.11462	0.865
62DAP/57DAP	1.10424	0.569
68DAP/62DAP	0.82153	0.109
68DAP/14DAP	0.68463	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	2.30929	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.97439
Mature Green Tomato/Ripe Tomato	0.20179	0.017
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.16003	0.224
Mature Eggplant/Ripe Tomato	0.19681	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.03627	0.944
1-1-2/M82	0.93978	1
12-2/M82	1.10161	1
12-4/M82	1.11108	1
1-3/M82	0.82503	0.501
2-1-1/M82	1.28667
2-1/M82	0.63462	0.74
2-6/M82	1.07142	0.695
3-2/M82	1.26099	0.419
4-1-1/M82	0.21078	0.985
4-1/M82	0.63122	0.998
4-3-2/M82	0.7452
4-3/M82	1.31239	1
5-3/M82	1.62462	1
6-2/M82	1.05715	1
6-3/M82	1.34805	1
7-1/M82	1.2181	1
7-2/M82	1.27566	1
9-3-2/M82	0.61232	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	1.44921	0.531
IL1-4/WTpooled	0.88204	0.415
WT/WTpooled	0.96633

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	1.91657

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.45606	0.921
DC3000/delta hrp 6h	0.79582	0.942
DC3000/delta hrp 12h	1.0706	1
DC3000/delta hrp 24h	0.86617	0.346

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	N/A
DC3000 delta B/DC3000 delta AB	0.97536	0.826

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.03044	1
Exp 36h	1.41194	0.409
Exp 60h	1.51724	0.221

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

hybridization	ratio	FDR (corrected p value)
self-self	0.9887
Var 0h	0.7969	0.457
Var 12h I row2-row1	1.05382	0.736
Var 12h NI row2-row1	1.02124	1
Var 36h I row2-row1	1.17026	1
Var 36h NI row2-row1	0.89561	0.706
Var 60h I row2-row1	1.1819	1
Var 60h NI row2-row1	1.14736	0.904
Time course 0hI-0hNI	1.14181	0.451
Time course 12hI-12hNI	1.03077	0.777
Time course 36hI-36hNI	1.00736	0.908
Time course 60hI-60hNI	1.23554	0.025

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)	1.39661	0.331
transgenic ySAMdc/azygous control (breaker)	0.82695	0.173
transgenic ySAMdc/azygous control (red)	0.9045	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.04619	0.077

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.94338	0.268

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.33416	0.09
Manapal/WT (break)	0.63903	0.333
Manapal/WT (red)	1.44426	0.413