Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.4.11.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.75708	0.085
27DAP/17DAP	1.10539	0.872
39DAP/27DAP	0.8025	0.41
41DAP/39DAP	1.32951	0.426
42DAP/41DAP	1.09614	0.994
43DAP/42DAP	0.86378	0.554
47DAP/43DAP	1.24852	0.469
52DAP/47DAP	1.57661	0.307
57DAP/52DAP	1.04511	0.969

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03236	0.788
17DAP/reference	0.96149	0.104
27DAP/reference	1.00478	0.934
39DAP/reference	1.00059	1
41DAP/reference	1.01061	1
42DAP/reference	0.93439	0.02
43DAP/reference	0.98904	0.728
47DAP/reference	0.89053	0.004
52DAP/reference	0.9985	0.654
57DAP/reference	0.8457	0.022

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.92263	0.211
27DAP/17DAP	0.99494	0.969
39DAP/27DAP	1.06929	0.553
41DAP/39DAP	0.99901	1
42DAP/41DAP	1.0552	0.795
43DAP/42DAP	0.98174	0.854
47DAP/43DAP	1.03009	0.88
52DAP/47DAP	1.02666	0.919
57DAP/52DAP	1.00666	1
57DAP/7DAP	1.11035	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91971	0.108
17DAP/reference	0.91513	0.018
27DAP/reference	0.8843	0.01
39DAP/reference	0.93493	0.023
41DAP/reference	0.92929	0.018
42DAP/reference	0.96842	0.436
43DAP/reference	0.91377	0.076
47DAP/reference	0.87568	0.034
52DAP/reference	0.86644	0.028
57DAP/reference	0.90268	0.144

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04361	0.41
17DAP/reference	1.00053	0.851
27DAP/reference	0.95219	0.423
39DAP/reference	0.96077	0.178
41DAP/reference	0.88864	0.052
42DAP/reference	0.93789	0.135
43DAP/reference	1.03789	0.673
47DAP/reference	0.89915	0.013
52DAP/reference	0.95596	0.131
57DAP/reference	1.0417	0.626

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91104	0.098
17DAP/reference	0.96261	0.462
27DAP/reference	0.89091	0.038
39DAP/reference	0.92495	0.092
41DAP/reference	0.91821	0.07
42DAP/reference	0.89191	0.059
43DAP/reference	0.83477	0.049
47DAP/reference	0.97577	0.452
52DAP/reference	0.97661	0.69
57DAP/reference	0.758	0.022

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.9462	0.787
26DAP/20DAP	0.92536	1
34DAP/26DAP	0.97841	0.909
51DAP/34DAP	0.97021	0.77
52DAP/51DAP	1.04641	0.454
53DAP/52DAP	0.9864	0.983
55DAP/53DAP	0.96117	0.852
57DAP/55DAP	0.98704	0.875
62DAP/57DAP	1.00155	1
68DAP/62DAP	0.88825	0.668
68DAP/14DAP	0.98668	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.01253	0.855

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.62381
Mature Green Tomato/Ripe Tomato	1.25192	0.237
Immature Eggplant/Mature Eggplant	1.19222	0.13
Ripe Pepper/Ripe Tomato	2.58625
Mature Eggplant/Ripe Tomato	N/A	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.05775	1
1-1-2/M82	0.95894	1
12-2/M82	1.08084	1
12-4/M82	0.90656	0.619
1-3/M82	0.9441	1
2-1-1/M82	1.1941	0.457
2-1/M82	N/A	N/A
2-6/M82	0.99358	1
3-2/M82	0.93098
4-1-1/M82	1.00368	1
4-1/M82	0.92419
4-3-2/M82	0.86911	1
4-3/M82	0.93604	1
5-3/M82	1.00917	1
6-2/M82	0.93878	1
6-3/M82	1.10328
7-1/M82	0.81413	0.803
7-2/M82	1.04806	1
9-3-2/M82	0.82071	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.77413	0.247
IL2-6/WTpooled	1.87891	0.427
IL7-5/WTpooled	1.16746	1
IL7-3/WTpooled	0.57479	0.294
IL12-4/WTpooled	0.8	0.71
IL1-4/WTpooled	0.8402	0.699
WT/WTpooled	1.03652	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	0.77742	0.341

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.07682	0.692
DC3000/delta hrp 6h	1.13287	1
DC3000/delta hrp 12h	1.25262	1
DC3000/delta hrp 24h	1.02023	1

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.0826	0.208
DC3000 delta B/DC3000 delta AB	1.04139	0.544

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.07787	1
Exp 36h	1.45726	1
Exp 60h	1.05114	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98521	1
Var 0h	1.02841	1
Var 12h I row2-row1	1.28453	0.235
Var 12h NI row2-row1	1.10474	1
Var 36h I row2-row1	0.92892	1
Var 36h NI row2-row1	0.80627	0.421
Var 60h I row2-row1	1.0342	1
Var 60h NI row2-row1	1.15439	0.904
Time course 0hI-0hNI	1.06246	0.833
Time course 12hI-12hNI	1.0008	1
Time course 36hI-36hNI	0.94744	0.206
Time course 60hI-60hNI	1.86697	0.009

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)	1.11059	0.218
transgenic ySAMdc/azygous control (breaker)	1.74314	1
transgenic ySAMdc/azygous control (red)	1.24844	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.09162	0.069

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.10268	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.88691	1
Manapal/WT (break)	0.87874	1
Manapal/WT (red)	N/A	N/A