Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.3.13.5

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.91407	0.652
27DAP/17DAP	0.98391	1
39DAP/27DAP	1.30995	0.857
41DAP/39DAP	1.24446	0.619
42DAP/41DAP	1.27159	0.882
43DAP/42DAP	0.90443	0.851
47DAP/43DAP	0.73816	0.234
52DAP/47DAP	1.94068	0.156
57DAP/52DAP	0.86294	0.827

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.85779	0.046
17DAP/reference	1.06368	0.675
27DAP/reference	0.94341	0.163
39DAP/reference	1.05323	0.706
41DAP/reference	0.86452	0.085
42DAP/reference	0.94746	0.099
43DAP/reference	1.02581	0.838
47DAP/reference	0.91687	0.046
52DAP/reference	0.89367	0.223
57DAP/reference	0.96876	0.435

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.95571	0.629
27DAP/17DAP	1.03623	0.954
39DAP/27DAP	1.02023	0.811
41DAP/39DAP	1.23263	0.735
42DAP/41DAP	0.9983	0.83
43DAP/42DAP	0.96983	0.774
47DAP/43DAP	1.04371	0.92
52DAP/47DAP	0.96231	0.876
57DAP/52DAP	0.99439	0.852
57DAP/7DAP	1.21992	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.79253	0.07
17DAP/reference	0.80613	0.024
27DAP/reference	0.81783	0.014
39DAP/reference	0.91717	0.17
41DAP/reference	0.83078	0.029
42DAP/reference	0.81861	0.01
43DAP/reference	0.778	0.012
47DAP/reference	0.87893	0.293
52DAP/reference	0.75958	0.028
57DAP/reference	0.73923	0.01

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04664	0.679
17DAP/reference	0.89772	0.109
27DAP/reference	0.85932	0.15
39DAP/reference	0.88105	0.099
41DAP/reference	0.9264	0.262
42DAP/reference	0.9251	0.108
43DAP/reference	1.00428	0.846
47DAP/reference	1.02947	0.751
52DAP/reference	0.84159	0.02
57DAP/reference	1.05741	0.353

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92553	0.335
17DAP/reference	0.98542	0.709
27DAP/reference	0.82797	0.048
39DAP/reference	0.8114	0.018
41DAP/reference	0.83351	0.058
42DAP/reference	0.84882	0.108
43DAP/reference	0.80204	0.022
47DAP/reference	1.02299	1
52DAP/reference	0.79914	0.153
57DAP/reference	0.95694	0.416

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.13276	0.966
26DAP/20DAP	0.8551	0.317
34DAP/26DAP	1.34145	0.819
51DAP/34DAP	0.8116	0.059
52DAP/51DAP	1.16544	0.186
53DAP/52DAP	1.00871	1
55DAP/53DAP	1.14723	0.229
57DAP/55DAP	0.9723	0.821
62DAP/57DAP	1.14755	0.622
68DAP/62DAP	1.03887	1
68DAP/14DAP	0.71747	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.98419	0.635

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.76737	0.107
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.99773
Mature Eggplant/Ripe Tomato	0.31089	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.88781	0.934
1-1-2/M82	0.93769	1
12-2/M82	1.40219	0.405
12-4/M82	1.02311	1
1-3/M82	0.99864	1
2-1-1/M82	1.10363
2-1/M82	1.12224
2-6/M82	1.07115	1
3-2/M82	0.8433
4-1-1/M82	1.09099	1
4-1/M82	0.95845	1
4-3-2/M82	1.08346	1
4-3/M82	0.90129	1
5-3/M82	0.85058	0.49
6-2/M82	0.87071	0.497
6-3/M82	1.12746	1
7-1/M82	N/A	N/A
7-2/M82	1.05572	1
9-3-2/M82	1.09465	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.79648	1
IL2-6/WTpooled	0.95327	1
IL7-5/WTpooled	1.78951
IL7-3/WTpooled	1.19778	1
IL12-4/WTpooled	1.14553	0.695
IL1-4/WTpooled	0.86366	0.699
WT/WTpooled	1.01257	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	1.13789	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.0738	0.921
DC3000/delta hrp 6h	1.27464	1
DC3000/delta hrp 12h	1.50159	1
DC3000/delta hrp 24h	1.07636	0.553

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	N/A
DC3000 delta B/DC3000 delta AB	0.96791	0.729

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.02464	1
Exp 36h	N/A	N/A
Exp 60h	1.42121	0.283

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

hybridization	ratio	FDR (corrected p value)
self-self	0.96234	1
Var 0h	0.83921	1
Var 12h I row2-row1	1.09365	0.473
Var 12h NI row2-row1	0.86314	0.627
Var 36h I row2-row1	0.98506	1
Var 36h NI row2-row1	0.83643	0.584
Var 60h I row2-row1	1.235	0.562
Var 60h NI row2-row1	1.24994	0.904
Time course 0hI-0hNI	1.17319	0.537
Time course 12hI-12hNI	1.18401	0.073
Time course 36hI-36hNI	1.0849	0.881
Time course 60hI-60hNI	1.8053	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)	0.89561	0.409
transgenic ySAMdc/azygous control (breaker)	0.83289	0.49
transgenic ySAMdc/azygous control (red)	1.19071	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.02081	0.135

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.77251	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.80895	1
Manapal/WT (break)	0.85064	0.333
Manapal/WT (red)	1.0291	1