Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.2.17.3

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.95028	0.689
27DAP/17DAP	0.79949	0.452
39DAP/27DAP	1.49073	0.382
41DAP/39DAP	0.80035	0.271
42DAP/41DAP	1.62669	0.286
43DAP/42DAP	1.15879	0.91
47DAP/43DAP	0.7818	0.366
52DAP/47DAP	0.96851	0.781
57DAP/52DAP	1.00777	0.996

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.89412	0.194
17DAP/reference	0.98818	0.777
27DAP/reference	0.92023	0.182
39DAP/reference	1.12799	0.045
41DAP/reference	1.04406	0.667
42DAP/reference	0.99779	0.531
43DAP/reference	0.93723	0.191
47DAP/reference	0.94134	0.279
52DAP/reference	0.89695	0.162
57DAP/reference	0.90116	0.147

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.97976	0.75
27DAP/17DAP	1.01115	1
39DAP/27DAP	1.25692	0.135
41DAP/39DAP	1.63441	0.115
42DAP/41DAP	0.91372	0.436
43DAP/42DAP	1.08691	0.297
47DAP/43DAP	1.25266	0.175
52DAP/47DAP	0.80366	0.192
57DAP/52DAP	1.01322	1
57DAP/7DAP	1.24904	0.168

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.77139	0.076
17DAP/reference	0.80833	0.019
27DAP/reference	1.03599	0.804
39DAP/reference	0.89513	0.023
41DAP/reference	0.89405	0.049
42DAP/reference	0.95703	0.178
43DAP/reference	0.88592	0.072
47DAP/reference	0.93834	0.293
52DAP/reference	0.91538	0.196
57DAP/reference	0.93492	0.28

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.11462	0.373
17DAP/reference	1.1823	0.07
27DAP/reference	1.19144	0.136
39DAP/reference	1.13044	0.366
41DAP/reference	1.01414	1
42DAP/reference	1.09476	0.233
43DAP/reference	1.59828	0.012
47DAP/reference	1.20884	0.074
52DAP/reference	1.43289	0.006
57DAP/reference	1.40257	0.022

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.76101	0.035
17DAP/reference	1.01763	0.825
27DAP/reference	0.70738	0.047
39DAP/reference	0.79408	0.031
41DAP/reference	0.99849	0.682
42DAP/reference	0.96935	0.671
43DAP/reference	0.85666	0.106
47DAP/reference	1.15683	0.171
52DAP/reference	0.90194	0.455
57DAP/reference	1.05361	0.717

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.94674	1
26DAP/20DAP	0.85274	0.512
34DAP/26DAP	0.63739	0.394
51DAP/34DAP	1.05637	0.816
52DAP/51DAP	0.86066
53DAP/52DAP	1.00532	0.897
55DAP/53DAP	1.22983	0.504
57DAP/55DAP	1.00046	0.968
62DAP/57DAP	1.36572	0.081
68DAP/62DAP	0.7791	0.152
68DAP/14DAP	0.69095	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.30298	0.246

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.37002	0.058
Mature Green Tomato/Ripe Tomato	N/A	N/A
Immature Eggplant/Mature Eggplant	0.66147	0.062
Ripe Pepper/Ripe Tomato	1.03153	1
Mature Eggplant/Ripe Tomato	0.9565	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.79694
1-1-2/M82	1.34017	1
12-2/M82	0.99858
12-4/M82	0.67386	0.282
1-3/M82	0.78091	0.378
2-1-1/M82	0.69261	0.465
2-1/M82	0.71299
2-6/M82	0.614	0.501
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	0.62434	0.578
5-3/M82	1.22089	0.455
6-2/M82	N/A	N/A
6-3/M82	1.13719	1
7-1/M82	N/A	N/A
7-2/M82	0.86273	0.881
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.70682	0.277
IL2-6/WTpooled	0.57926	0.473
IL7-5/WTpooled	0.73041	1
IL7-3/WTpooled	1.89121	1
IL12-4/WTpooled	1.13707	0.839
IL1-4/WTpooled	1.44311	0.426
WT/WTpooled	1.00114	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	1.67062	0.309

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.07687	0.875
DC3000/delta hrp 6h	1.06374	1
DC3000/delta hrp 12h	1.04908	1
DC3000/delta hrp 24h	1.06294	0.567

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	3.17669
DC3000 delta B/DC3000 delta AB	2.15211	0.079

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.38672	1
Exp 36h	2.50761	0.693
Exp 60h	2.09422	0.237

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

hybridization	ratio	FDR (corrected p value)
self-self	0.96679	1
Var 0h	0.51229	1
Var 12h I row2-row1	1.13929	0.613
Var 12h NI row2-row1	1.76898	0.649
Var 36h I row2-row1	0.99018	1
Var 36h NI row2-row1	0.81584	0.522
Var 60h I row2-row1	0.65656	0.293
Var 60h NI row2-row1	0.72064	0.335
Time course 0hI-0hNI	0.9837	0.95
Time course 12hI-12hNI	2.56596	0.005
Time course 36hI-36hNI	5.13664	0.004
Time course 60hI-60hNI	12.8085	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)	0.97631	0.722
transgenic ySAMdc/azygous control (breaker)	0.93145	0.49
transgenic ySAMdc/azygous control (red)	1.36689	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.86906	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.90707	0.307
Manapal/WT (break)	0.60569	0.333
Manapal/WT (red)	1.09136	1