Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.1.1.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.53261	0.224
27DAP/17DAP	2.14438	0.159
39DAP/27DAP	1.27655	0.44
41DAP/39DAP	1.05495	0.938
42DAP/41DAP	1.0303	1
43DAP/42DAP	1.02031	1
47DAP/43DAP	0.81826	0.449
52DAP/47DAP	1.39032	0.462
57DAP/52DAP	0.94537	0.927

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.83693	0.045
17DAP/reference	1.04323	0.282
27DAP/reference	1.03543	0.599
39DAP/reference	0.92822	0.2
41DAP/reference	0.91666	0.201
42DAP/reference	0.95806	0.211
43DAP/reference	1.00464	0.957
47DAP/reference	0.9783	0.418
52DAP/reference	1.02923	0.991
57DAP/reference	0.93149	0.186

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.19047	0.058
27DAP/17DAP	1.33813	0.045
39DAP/27DAP	1.02519	1
41DAP/39DAP	0.89014	0.547
42DAP/41DAP	0.87615	0.362
43DAP/42DAP	1.22385	0.079
47DAP/43DAP	0.8845	0.163
52DAP/47DAP	1.15432	0.498
57DAP/52DAP	0.89281	0.384
57DAP/7DAP	1.05925	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.85321	0.072
17DAP/reference	0.87159	0.016
27DAP/reference	0.87937	0.01
39DAP/reference	0.82927	0.021
41DAP/reference	0.77904	0.016
42DAP/reference	0.89552	0.338
43DAP/reference	0.79434	0.022
47DAP/reference	0.85957	0.168
52DAP/reference	0.70994	0.03
57DAP/reference	0.79526	0.026

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94075	0.286
17DAP/reference	0.98497	0.611
27DAP/reference	1.00674	0.79
39DAP/reference	1.07623	0.725
41DAP/reference	0.99993	0.666
42DAP/reference	0.90072	0.081
43DAP/reference	0.93972	0.361
47DAP/reference	0.83291	0.011
52DAP/reference	0.88688	0.047
57DAP/reference	0.93823	0.298

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.88412	0.052
17DAP/reference	0.93514	0.275
27DAP/reference	0.9103	0.036
39DAP/reference	0.91106	0.122
41DAP/reference	0.9223	0.119
42DAP/reference	0.96006	0.552
43DAP/reference	1.01574	1
47DAP/reference	1.22147	0.044
52DAP/reference	0.84372	0.128
57DAP/reference	1.47197	0.063

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.04812	0.966
26DAP/20DAP	0.98255	1
34DAP/26DAP	1.03246	1
51DAP/34DAP	0.97852	0.816
52DAP/51DAP	1.0531	0.722
53DAP/52DAP	1.06484	0.678
55DAP/53DAP	1.05101	0.608
57DAP/55DAP	1.03426	0.997
62DAP/57DAP	1.53517
68DAP/62DAP	0.86098	0.037
68DAP/14DAP	1.00233	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	2.83886	0.015

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.83851	0.295
Mature Green Tomato/Ripe Tomato	1.44785	0.267
Immature Eggplant/Mature Eggplant	0.78171	0.062
Ripe Pepper/Ripe Tomato	2.16587	1
Mature Eggplant/Ripe Tomato	2.28455	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.95904	0.841
1-1-2/M82	1.06361	1
12-2/M82	1.11146	1
12-4/M82	1.14325	1
1-3/M82	0.88971	0.501
2-1-1/M82	1.22041	1
2-1/M82	1.24154	1
2-6/M82	0.96026	0.501
3-2/M82	0.98567	1
4-1-1/M82	0.93259	0.959
4-1/M82	1.00647	1
4-3-2/M82	0.91711	0.698
4-3/M82	0.67358	0.72
5-3/M82	1.03263	1
6-2/M82	0.88021	1
6-3/M82	0.89379	0.715
7-1/M82	0.85931	0.803
7-2/M82	1.02604	1
9-3-2/M82	1.01268	1

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	1.59351	1
IL12-4/WTpooled	0.79965
IL1-4/WTpooled	1.25385	1
WT/WTpooled	0.39765

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	0.92383	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.06609	0.921
DC3000/delta hrp 6h	1.0447	1
DC3000/delta hrp 12h	1.0176	1
DC3000/delta hrp 24h	1.02381	0.604

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.86832	0.597
DC3000 delta B/DC3000 delta AB	1.08204	0.394

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.18563	1
Exp 36h	0.78676	0.661
Exp 60h	0.8087	0.586

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98938	1
Var 0h	1.02241	1
Var 12h I row2-row1	1.04347	0.692
Var 12h NI row2-row1	0.93792	0.906
Var 36h I row2-row1	1.02397	1
Var 36h NI row2-row1	0.9701	0.791
Var 60h I row2-row1	1.02911	0.562
Var 60h NI row2-row1	1.03059	1
Time course 0hI-0hNI	0.9555	0.698
Time course 12hI-12hNI	0.97227	0.814
Time course 36hI-36hNI	1.05302	0.401
Time course 60hI-60hNI	1.56165	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)	0.91989	0.289
transgenic ySAMdc/azygous control (breaker)	1.2529	0.248
transgenic ySAMdc/azygous control (red)	1.36364	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.10875	0.11

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.60204	0.237

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.70829	0.096
Manapal/WT (break)	1.4198	0.381
Manapal/WT (red)	1.59632	0.222