Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.4.16.2

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.8959	0.278
27DAP/17DAP	1.02898	1
39DAP/27DAP	0.99429	0.782
41DAP/39DAP	1.79909	0.211
42DAP/41DAP	0.99321	1
43DAP/42DAP	0.96138	0.887
47DAP/43DAP	0.86665	0.58
52DAP/47DAP	1.42234	0.385
57DAP/52DAP	1.00162	0.983

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99926	0.824
17DAP/reference	0.93694	0.06
27DAP/reference	0.88556	0.023
39DAP/reference	0.99735	0.975
41DAP/reference	0.96949	0.341
42DAP/reference	1.00072	0.707
43DAP/reference	0.94235	0.191
47DAP/reference	0.98369	0.392
52DAP/reference	1.029	0.663
57DAP/reference	0.93613	0.124

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.91826	0.496
27DAP/17DAP	0.98771	0.919
39DAP/27DAP	1.05805	0.611
41DAP/39DAP	0.98756	0.997
42DAP/41DAP	1.02494	0.991
43DAP/42DAP	0.97028	0.709
47DAP/43DAP	1.03778	0.817
52DAP/47DAP	1.03823	0.862
57DAP/52DAP	1.07051	0.596
57DAP/7DAP	1.14482	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91691	0.246
17DAP/reference	0.93861	0.013
27DAP/reference	0.88608	0.016
39DAP/reference	0.9319	0.043
41DAP/reference	0.93034	0.184
42DAP/reference	0.94717	0.178
43DAP/reference	0.90922	0.016
47DAP/reference	0.91112	0.066
52DAP/reference	0.93258	0.163
57DAP/reference	0.94626	0.27

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04271	0.501
17DAP/reference	1.00904	1
27DAP/reference	0.9832	0.519
39DAP/reference	0.98973	0.569
41DAP/reference	0.96742	0.307
42DAP/reference	0.93397	0.135
43DAP/reference	1.02885	0.835
47DAP/reference	0.9978	0.73
52DAP/reference	1.03823	0.528
57DAP/reference	1.06566	0.286

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87188	0.039
17DAP/reference	0.97156	0.335
27DAP/reference	0.9143	0.03
39DAP/reference	0.89949	0.008
41DAP/reference	0.95036	0.185
42DAP/reference	0.89023	0.028
43DAP/reference	0.92965	0.051
47DAP/reference	0.9408	0.103
52DAP/reference	0.87403	0.238
57DAP/reference	0.76894	0.023

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.00851	1
26DAP/20DAP	1.08534	0.762
34DAP/26DAP	0.98333	0.954
51DAP/34DAP	0.9559	0.611
52DAP/51DAP	1.10015	0.218
53DAP/52DAP	0.93205	0.572
55DAP/53DAP	0.99404	0.908
57DAP/55DAP	1.01133	0.938
62DAP/57DAP	1.00906	0.935
68DAP/62DAP	0.87681	0.345
68DAP/14DAP	0.95904	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.1129	0.415

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.61699
Mature Green Tomato/Ripe Tomato	0.99603	0.898
Immature Eggplant/Mature Eggplant	2.17587	0.05
Ripe Pepper/Ripe Tomato	1.80769
Mature Eggplant/Ripe Tomato	4.73556	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.01224	1
1-1-2/M82	0.82688	1
12-2/M82	0.97353	0.955
12-4/M82	1.00516	1
1-3/M82	1.05043
2-1-1/M82	0.87578
2-1/M82	N/A	N/A
2-6/M82	0.9189	1
3-2/M82	0.9837	1
4-1-1/M82	0.88669	1
4-1/M82	0.64392	0.737
4-3-2/M82	0.91473	0.698
4-3/M82	0.67291
5-3/M82	1.14709	1
6-2/M82	1.08022
6-3/M82	N/A	N/A
7-1/M82	0.95465
7-2/M82	1.02329	1
9-3-2/M82	0.85982	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.35787
IL2-6/WTpooled	1.20837	0.584
IL7-5/WTpooled	0.58204
IL7-3/WTpooled	1.25763	1
IL12-4/WTpooled	1.1124	0.595
IL1-4/WTpooled	1.08834	1
WT/WTpooled	1.01234	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	0.93563	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.0245	0.921
DC3000/delta hrp 6h	1.15019	1
DC3000/delta hrp 12h	1.01116	1
DC3000/delta hrp 24h	0.96416	0.782

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.09757	0.052
DC3000 delta B/DC3000 delta AB	1.15012	0.259

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.03671	1
Exp 36h	1.14721	0.693
Exp 60h	1.14107	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99595	1
Var 0h	1.03987	0.98
Var 12h I row2-row1	1.0821	0.348
Var 12h NI row2-row1	1.0468	1
Var 36h I row2-row1	1.08121	1
Var 36h NI row2-row1	0.94611	0.743
Var 60h I row2-row1	0.93908	0.285
Var 60h NI row2-row1	0.96008	1
Time course 0hI-0hNI	1.08253	0.833
Time course 12hI-12hNI	1.03509	0.827
Time course 36hI-36hNI	1.0957	0.147
Time course 60hI-60hNI	1.8682	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)	1.28437	0.277
transgenic ySAMdc/azygous control (breaker)	0.68709	0.173
transgenic ySAMdc/azygous control (red)	1.45683	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.98104	0.334

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.23707	0.239

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.7675	1
Manapal/WT (break)	0.63681	0.255
Manapal/WT (red)	0.98217	0.863