Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.2.14.19

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.06938	0.798
27DAP/17DAP	1.18352	0.819
39DAP/27DAP	0.75441	0.414
41DAP/39DAP	1.25131	0.535
42DAP/41DAP	1.03358	0.994
43DAP/42DAP	1.07342	1
47DAP/43DAP	1.07746	0.733
52DAP/47DAP	1.22422	0.597
57DAP/52DAP	1.02284	1

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94502	0.205
17DAP/reference	0.98152	0.664
27DAP/reference	1.00754	0.934
39DAP/reference	0.95393	0.315
41DAP/reference	0.91561	0.434
42DAP/reference	0.87824	0.017
43DAP/reference	0.97162	0.464
47DAP/reference	0.96878	0.148
52DAP/reference	0.96187	0.382
57DAP/reference	0.94971	0.21

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.00092	1
27DAP/17DAP	0.98893	0.943
39DAP/27DAP	1.06633	0.496
41DAP/39DAP	1.05226	0.807
42DAP/41DAP	0.98123	0.777
43DAP/42DAP	0.99609	1
47DAP/43DAP	0.9818	0.902
52DAP/47DAP	0.99122	0.941
57DAP/52DAP	0.99483	0.862
57DAP/7DAP	1.08952	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04184	0.705
17DAP/reference	1.10688	0.049
27DAP/reference	1.01651	0.974
39DAP/reference	1.10127	0.04
41DAP/reference	1.14911	0.022
42DAP/reference	1.10725	0.1
43DAP/reference	1.12331	0.148
47DAP/reference	1.05907	0.304
52DAP/reference	1.11122	0.092
57DAP/reference	1.06799	0.746

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96722	0.592
17DAP/reference	0.92454	0.223
27DAP/reference	1.10631	1
39DAP/reference	0.89676	0.038
41DAP/reference	1.11298	0.781
42DAP/reference	0.87186	0.073
43DAP/reference	0.86203	0.135
47DAP/reference	0.96667	0.4
52DAP/reference	0.95156	0.131
57DAP/reference	0.96077	0.384

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04954	0.56
17DAP/reference	1.12582	0.578
27DAP/reference	1.24264	0.027
39DAP/reference	1.17979	0.069
41DAP/reference	1.09439	0.383
42DAP/reference	0.97068	0.552
43DAP/reference	1.03421	0.744
47DAP/reference	0.93944	0.231
52DAP/reference	1.12492	0.405
57DAP/reference	0.99229	0.682

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.03102	0.966
26DAP/20DAP	0.89326	0.228
34DAP/26DAP	0.94978	0.777
51DAP/34DAP	0.89005	0.213
52DAP/51DAP	0.97487	1
53DAP/52DAP	1.0858	0.643
55DAP/53DAP	0.91363	0.462
57DAP/55DAP	1.16229	0.492
62DAP/57DAP	0.99396	0.994
68DAP/62DAP	1.1011	1
68DAP/14DAP	1.12462	0.578

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.97192	0.547

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.90412	0.411
Immature Eggplant/Mature Eggplant	0.96982
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	1.93235

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.99619	1
1-1-2/M82	0.9968	1
12-2/M82	1.16911	1
12-4/M82	1.01425	1
1-3/M82	0.97126	1
2-1-1/M82	1.05704	1
2-1/M82	1.57147	1
2-6/M82	1.02712	0.695
3-2/M82	0.96849	1
4-1-1/M82	0.90954	1
4-1/M82	1.05551
4-3-2/M82	0.96037	0.698
4-3/M82	0.99651	1
5-3/M82	1.00699	1
6-2/M82	1.00679	1
6-3/M82	0.99881	1
7-1/M82	1.05667
7-2/M82	0.9775	1
9-3-2/M82	0.7991	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.31061
IL2-6/WTpooled	0.94488	1
IL7-5/WTpooled	1.47147
IL7-3/WTpooled	0.99652	1
IL12-4/WTpooled	1.03311	0.646
IL1-4/WTpooled	0.9588	1
WT/WTpooled	0.99609	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	1.36644	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.99071	1
DC3000/delta hrp 6h	1.00695	0.95
DC3000/delta hrp 12h	0.98673	1
DC3000/delta hrp 24h	1.03712	0.633

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.18014	0.042
DC3000 delta B/DC3000 delta AB	1.10142	0.358

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.93145	1
Exp 36h	0.66654	0.449
Exp 60h	0.68158	0.29

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00418	1
Var 0h	0.53825	1
Var 12h I row2-row1	1.11716	0.473
Var 12h NI row2-row1	1.04072	0.649
Var 36h I row2-row1	1.00961	1
Var 36h NI row2-row1	0.8846	0.61
Var 60h I row2-row1	1.05481	1
Var 60h NI row2-row1	1.03775	0.904
Time course 0hI-0hNI	1.03137	0.867
Time course 12hI-12hNI	1.10274	0.26
Time course 36hI-36hNI	1.03403	0.58
Time course 60hI-60hNI	1.11964	0.017

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)	1.04461	0.748
transgenic ySAMdc/azygous control (breaker)	1.16896	1
transgenic ySAMdc/azygous control (red)	1.0062	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.99318	0.568

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.30317	0.237

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	N/A	N/A
Manapal/WT (break)	1.02575	1
Manapal/WT (red)	0.47052	0.181