Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.3.15.13

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.55249	0.075
27DAP/17DAP	1.39494	0.723
39DAP/27DAP	0.73267	0.382
41DAP/39DAP	1.26818	0.164
42DAP/41DAP	1.16018	0.871
43DAP/42DAP	0.93148	0.822
47DAP/43DAP	1.11919	0.668
52DAP/47DAP	0.89067	0.673
57DAP/52DAP	0.98991	0.983

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93255	0.177
17DAP/reference	0.93468	0.091
27DAP/reference	0.99567	0.822
39DAP/reference	0.97026	0.575
41DAP/reference	0.91664	0.085
42DAP/reference	0.9475	0.05
43DAP/reference	0.99924	0.942
47DAP/reference	0.97545	0.258
52DAP/reference	1.05263	0.663
57DAP/reference	1.1067	0.043

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.90598	0.26
27DAP/17DAP	1.05424	0.811
39DAP/27DAP	1.14157	0.331
41DAP/39DAP	1.08993	0.861
42DAP/41DAP	0.93288	0.548
43DAP/42DAP	1.04804	0.446
47DAP/43DAP	1.01424	0.941
52DAP/47DAP	1.02715	0.868
57DAP/52DAP	1.02173	0.891
57DAP/7DAP	0.9389	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.17256	0.181
17DAP/reference	1.23024	0.123
27DAP/reference	1.33414	0.107
39DAP/reference	1.06349	0.705
41DAP/reference	0.99859	0.741
42DAP/reference	0.95424	0.304
43DAP/reference	1.38255	0.045
47DAP/reference	1.24072	0.259
52DAP/reference	1.27468	0.401
57DAP/reference	1.27666	0.1

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92944	0.164
17DAP/reference	0.95575	0.239
27DAP/reference	0.94922	0.203
39DAP/reference	1.00993	0.769
41DAP/reference	0.99872	0.683
42DAP/reference	0.94983	0.014
43DAP/reference	1.0056	1
47DAP/reference	0.94714	0.069
52DAP/reference	0.96311	0.143
57DAP/reference	0.93231	0.208

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04561	0.918
17DAP/reference	1.0478	0.934
27DAP/reference	1.67129	0.02
39DAP/reference	1.48102	0.017
41DAP/reference	1.14639	0.777
42DAP/reference	1.01746	0.979
43DAP/reference	0.96116	0.449
47DAP/reference	1.047	0.585
52DAP/reference	1.43974	0.198
57DAP/reference	1.27254	0.018

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.96817	1
26DAP/20DAP	0.79935	0.228
34DAP/26DAP	0.96446	0.917
51DAP/34DAP	1.09732	0.303
52DAP/51DAP	1.02515	0.722
53DAP/52DAP	0.94671	0.75
55DAP/53DAP	0.83817	0.21
57DAP/55DAP	0.90167	0.508
62DAP/57DAP	1.00633	1
68DAP/62DAP	1.03641	0.944
68DAP/14DAP	1.57827	0.236

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.90099	0.304

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.30486	0.063
Mature Green Tomato/Ripe Tomato	1.33671	0.237
Immature Eggplant/Mature Eggplant	1.04503	0.379
Ripe Pepper/Ripe Tomato	0.79244	1
Mature Eggplant/Ripe Tomato	0.99321	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.97694	0.944
1-1-2/M82	0.98509	1
12-2/M82	1.20215	0.61
12-4/M82	1.0303	1
1-3/M82	0.82475	0.378
2-1-1/M82	1.0757
2-1/M82	N/A	N/A
2-6/M82	1.08982	0.425
3-2/M82	0.8642
4-1-1/M82	0.91803	1
4-1/M82	0.88286	1
4-3-2/M82	0.76821
4-3/M82	0.9313	1
5-3/M82	0.98651	1
6-2/M82	0.94388	1
6-3/M82	1.03537	1
7-1/M82	N/A	N/A
7-2/M82	1.00535	1
9-3-2/M82	0.86379	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.17386	0.277
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	0.74093	0.559
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	1.17185	0.891
IL1-4/WTpooled	0.9299	0.834
WT/WTpooled	1.06889

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	1.29714	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.04623	0.921
DC3000/delta hrp 6h	1.03976	1
DC3000/delta hrp 12h	0.90757	1
DC3000/delta hrp 24h	1.0681	0.516

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.30965	0.183
DC3000 delta B/DC3000 delta AB	1.14975	0.274

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.94663	1
Exp 36h	1.04763	1
Exp 60h	1.22323	0.283

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

hybridization	ratio	FDR (corrected p value)
self-self	0.92888	1
Var 0h	1.03857	1
Var 12h I row2-row1	1.12976	0.348
Var 12h NI row2-row1	0.90997	0.627
Var 36h I row2-row1	1.17337	0.742
Var 36h NI row2-row1	1.01809	1
Var 60h I row2-row1	1.22061	0.562
Var 60h NI row2-row1	1.23255	0.904
Time course 0hI-0hNI	1.07662	0.833
Time course 12hI-12hNI	1.01299	0.88
Time course 36hI-36hNI	1.19637	0.005
Time course 60hI-60hNI	1.33461	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)	0.99597	0.931
transgenic ySAMdc/azygous control (breaker)	1.27356	0.248
transgenic ySAMdc/azygous control (red)	1.18815	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.01353	0.317

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.98544	0.789

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.85921	1
Manapal/WT (break)	1.08959	0.183
Manapal/WT (red)	1.20515	0.222