Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.3.15.4

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.09238	0.827
27DAP/17DAP	1.09478	0.852
39DAP/27DAP	0.80851	0.482
41DAP/39DAP	1.365	0.323
42DAP/41DAP	0.88232	1
43DAP/42DAP	1.04692	1
47DAP/43DAP	1.16736	0.474
52DAP/47DAP	1.15226	0.699
57DAP/52DAP	1.08215	0.806

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87237	0.071
17DAP/reference	0.94954	0.278
27DAP/reference	1.00959	0.934
39DAP/reference	0.98012	0.651
41DAP/reference	1.00726	1
42DAP/reference	0.89532	0.003
43DAP/reference	0.88931	0.073
47DAP/reference	0.9527	0.137
52DAP/reference	1.06699	0.354
57DAP/reference	1.04376	0.27

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.97803	0.732
27DAP/17DAP	0.99756	0.969
39DAP/27DAP	1.05151	0.575
41DAP/39DAP	0.94118	0.764
42DAP/41DAP	0.99058	0.841
43DAP/42DAP	1.04467	0.324
47DAP/43DAP	1.00244	1
52DAP/47DAP	1.00758	0.979
57DAP/52DAP	0.96907	0.657
57DAP/7DAP	1.01603	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00266	1
17DAP/reference	1.07207	0.054
27DAP/reference	1.01107	1
39DAP/reference	1.14365	0.069
41DAP/reference	1.15832	0.101
42DAP/reference	1.19333	0.1
43DAP/reference	1.18566	0.05
47DAP/reference	1.05116	0.717
52DAP/reference	1.00589	1
57DAP/reference	1.10214	0.41

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9681	0.58
17DAP/reference	0.91677	0.139
27DAP/reference	0.89075	0.139
39DAP/reference	0.87009	0.074
41DAP/reference	0.9044	0.053
42DAP/reference	0.94345	0.189
43DAP/reference	0.85502	0.039
47DAP/reference	0.99165	0.643
52DAP/reference	0.93782	0.086
57DAP/reference	0.85987	0.026

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94526	0.197
17DAP/reference	1.02621	0.72
27DAP/reference	1.08211	0.207
39DAP/reference	0.99204	0.693
41DAP/reference	1.0442	1
42DAP/reference	0.95	0.361
43DAP/reference	0.97345	0.449
47DAP/reference	0.90261	0.145
52DAP/reference	0.96336	0.562
57DAP/reference	1.08504	0.452

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.99274	1
26DAP/20DAP	0.90816	0.317
34DAP/26DAP	0.93028	0.735
51DAP/34DAP	0.99758	0.946
52DAP/51DAP	1.0596	0.606
53DAP/52DAP	1.06259	0.83
55DAP/53DAP	0.80623	0.144
57DAP/55DAP	1.03488	0.975
62DAP/57DAP	1.09511	0.902
68DAP/62DAP	1.10654	0.481
68DAP/14DAP	1.22477	0.504

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.88084	0.062

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.93761	0.591
Mature Green Tomato/Ripe Tomato	0.79407	0.182
Immature Eggplant/Mature Eggplant	1.26719
Ripe Pepper/Ripe Tomato	1.45474	1
Mature Eggplant/Ripe Tomato	0.82705	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.03625	1
1-1-2/M82	0.99627	1
12-2/M82	1.03243	1
12-4/M82	0.95915	1
1-3/M82	0.99134	1
2-1-1/M82	1.16812	0.439
2-1/M82	N/A	N/A
2-6/M82	0.99864	1
3-2/M82	0.96562
4-1-1/M82	1.01142	1
4-1/M82	1.16916
4-3-2/M82	0.91972	1
4-3/M82	0.92218	1
5-3/M82	1.02569	1
6-2/M82	0.94109	0.497
6-3/M82	0.96379	1
7-1/M82	1.06794	1
7-2/M82	1.01247	1
9-3-2/M82	0.84988	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.93817	1
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	1.25146
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	1.29433
IL1-4/WTpooled	0.84175	0.415
WT/WTpooled	0.80958	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	0.75908	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.99743	1
DC3000/delta hrp 6h	1.02283	0.95
DC3000/delta hrp 12h	1.19951	1
DC3000/delta hrp 24h	0.96547	0.794

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.02691	0.476
DC3000 delta B/DC3000 delta AB	1.01772	0.714

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	1.34764	0.693
Exp 60h	1.27064	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	0.95786	1
Var 0h	1.76495	0.98
Var 12h I row2-row1	1.08576	0.379
Var 12h NI row2-row1	0.9331	0.494
Var 36h I row2-row1	0.79386	0.805
Var 36h NI row2-row1	0.76994	0.61
Var 60h I row2-row1	1.37057	1
Var 60h NI row2-row1	1.18557	0.904
Time course 0hI-0hNI	1.03309	1
Time course 12hI-12hNI	1.07975	0.55
Time course 36hI-36hNI	0.93831	0.175
Time course 60hI-60hNI	1.20471	0.013

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)	1.05596	0.297
transgenic ySAMdc/azygous control (breaker)	1.29374	0.248
transgenic ySAMdc/azygous control (red)	1.01944	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.01002	0.372

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.99878	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.91255	1
Manapal/WT (break)	0.80927	0.333
Manapal/WT (red)	0.79666	0.183