Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.1.13.15

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.98362	0.847
27DAP/17DAP	1.11581	0.847
39DAP/27DAP	1.02624	1
41DAP/39DAP	1.0119	0.921
42DAP/41DAP	1.02277	0.978
43DAP/42DAP	0.95948	0.867
47DAP/43DAP	0.92007	0.705
52DAP/47DAP	1.06781	0.847
57DAP/52DAP	1.03602	0.969

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00462	1
17DAP/reference	0.99199	0.858
27DAP/reference	0.98233	0.471
39DAP/reference	0.97451	0.541
41DAP/reference	0.99808	1
42DAP/reference	0.99443	0.484
43DAP/reference	0.98188	0.653
47DAP/reference	1.01726	0.666
52DAP/reference	0.962	0.33
57DAP/reference	1.08611	0.153

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.0246	0.63
27DAP/17DAP	0.97708	0.508
39DAP/27DAP	0.97669	0.721
41DAP/39DAP	0.95735	0.839
42DAP/41DAP	1.01731	0.947
43DAP/42DAP	0.98374	0.729
47DAP/43DAP	1.00968	0.941
52DAP/47DAP	0.98691	0.925
57DAP/52DAP	0.95854	0.598
57DAP/7DAP	0.99814	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95192	0.27
17DAP/reference	0.95249	0.012
27DAP/reference	0.98939	0.43
39DAP/reference	1.00242	1
41DAP/reference	0.97907	0.431
42DAP/reference	1.01209	0.889
43DAP/reference	1.0219	0.637
47DAP/reference	0.91878	0.044
52DAP/reference	0.99909	0.802
57DAP/reference	0.97954	0.569

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99853	0.97
17DAP/reference	1.03793	0.508
27DAP/reference	1.01299	1
39DAP/reference	0.94719	0.126
41DAP/reference	0.95252	0.237
42DAP/reference	1.00362	1
43DAP/reference	1.11554	0.331
47DAP/reference	1.0273	0.311
52DAP/reference	0.97075	0.239
57DAP/reference	1.00809	1

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94528	0.047
17DAP/reference	0.97003	0.313
27DAP/reference	0.9832	0.397
39DAP/reference	1.04112	0.67
41DAP/reference	1.01434	0.818
42DAP/reference	0.91973	0.134
43DAP/reference	0.97725	0.432
47DAP/reference	0.97012	0.421
52DAP/reference	1.00551	1
57DAP/reference	1.05151	0.481

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.04789	0.916
26DAP/20DAP	1.05804	0.77
34DAP/26DAP	0.9989	1
51DAP/34DAP	1.06172	0.524
52DAP/51DAP	1.02823	0.758
53DAP/52DAP	0.97376	0.882
55DAP/53DAP	1.0039	1
57DAP/55DAP	1.23792	0.805
62DAP/57DAP	1.15385	0.833
68DAP/62DAP	0.94393	0.769
68DAP/14DAP	1.0307	0.785

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.99196	0.696

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.93988	0.618
Mature Green Tomato/Ripe Tomato	1.13671	0.363
Immature Eggplant/Mature Eggplant	1.0712	0.507
Ripe Pepper/Ripe Tomato	0.88891	1
Mature Eggplant/Ripe Tomato	0.60429	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.92318	0.907
1-1-2/M82	0.89766	1
12-2/M82	0.91806	0.955
12-4/M82	0.99762	1
1-3/M82	0.99777	1
2-1-1/M82	0.89999	0.683
2-1/M82	0.95218	0.519
2-6/M82	0.97514	1
3-2/M82	0.98665	1
4-1-1/M82	0.9299	1
4-1/M82	0.99438	1
4-3-2/M82	0.79342	0.487
4-3/M82	0.95861	1
5-3/M82	0.98604	1
6-2/M82	1.01942	1
6-3/M82	1.05125	1
7-1/M82	0.97667	1
7-2/M82	0.93699	0.881
9-3-2/M82	0.99663	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.99256	1
IL7-5/WTpooled	0.79629
IL7-3/WTpooled	0.97145	1
IL12-4/WTpooled	0.89813	0.566
IL1-4/WTpooled	0.93999	0.834
WT/WTpooled	0.93649	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	1.3203	0.479

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.96085	1
DC3000/delta hrp 6h	1.32739	1
DC3000/delta hrp 12h	0.91314	1
DC3000/delta hrp 24h	1.02296	0.743

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.00054	1
DC3000 delta B/DC3000 delta AB	0.9342	0.347

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	1.30791	0.371
Exp 60h	1.32693	0.227

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00682	1
Var 0h	0.47438	0.457
Var 12h I row2-row1	1.1328	0.296
Var 12h NI row2-row1	0.99387	1
Var 36h I row2-row1	1.04213	1
Var 36h NI row2-row1	0.9739	0.61
Var 60h I row2-row1	1.11247	0.562
Var 60h NI row2-row1	1.06497	1
Time course 0hI-0hNI	1.0211	1
Time course 12hI-12hNI	1.01262	0.892
Time course 36hI-36hNI	0.94668	0.295
Time course 60hI-60hNI	0.95476	0.319

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)	0.96074	0.567
transgenic ySAMdc/azygous control (breaker)	0.92619	1
transgenic ySAMdc/azygous control (red)	1.20794	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.95256	0.11

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.16433	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.85149	0.172
Manapal/WT (break)	0.82138	1
Manapal/WT (red)	0.93901	0.607