Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.3.15.7

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.76776	0.032
27DAP/17DAP	0.99646	1
39DAP/27DAP	1.04375	0.992
41DAP/39DAP	1.12509	0.619
42DAP/41DAP	1.16544	0.886
43DAP/42DAP	1.04482	1
47DAP/43DAP	1.16704	0.463
52DAP/47DAP	0.78168	0.476
57DAP/52DAP	1.01071	0.992

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91151	0.125
17DAP/reference	1.0107	0.843
27DAP/reference	1.06142	0.446
39DAP/reference	1.06785	0.089
41DAP/reference	1.07647	0.287
42DAP/reference	0.96395	0.176
43DAP/reference	1.04436	0.646
47DAP/reference	0.98238	0.445
52DAP/reference	1.0594	0.407
57DAP/reference	1.09638	0.032

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.01949	0.871
27DAP/17DAP	0.83551	0.446
39DAP/27DAP	1.14886	0.663
41DAP/39DAP	1.13288	0.336
42DAP/41DAP	1.01107	0.887
43DAP/42DAP	0.99223	0.991
47DAP/43DAP	1.0042	0.989
52DAP/47DAP	1.14902	0.609
57DAP/52DAP	1.02302	0.905
57DAP/7DAP	1.01188	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.85624	0.129
17DAP/reference	0.79726	0.056
27DAP/reference	0.83442	0.022
39DAP/reference	0.91624	0.264
41DAP/reference	0.93096	0.311
42DAP/reference	0.93532	0.304
43DAP/reference	0.84782	0.076
47DAP/reference	0.91772	0.383
52DAP/reference	0.85566	0.053
57DAP/reference	0.88913	0.086

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95686	0.518
17DAP/reference	0.85148	0.01
27DAP/reference	0.86628	0.144
39DAP/reference	0.95968	0.392
41DAP/reference	0.96578	0.322
42DAP/reference	0.982	0.534
43DAP/reference	0.93595	0.404
47DAP/reference	0.95859	0.434
52DAP/reference	0.92985	0.143
57DAP/reference	0.82147	0.005

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96508	0.455
17DAP/reference	0.9554	0.452
27DAP/reference	0.87611	0.102
39DAP/reference	0.86854	0.063
41DAP/reference	0.89916	0.148
42DAP/reference	0.90215	0.287
43DAP/reference	0.89428	0.143
47DAP/reference	1.0935	0.163
52DAP/reference	1.05135	0.718
57DAP/reference	1.05783	0.924

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.03237	0.966
26DAP/20DAP	0.76541	0.228
34DAP/26DAP	1.19871	1
51DAP/34DAP	0.93777	0.698
52DAP/51DAP	1.38795	0.295
53DAP/52DAP	1.05633	0.895
55DAP/53DAP	0.99294	0.886
57DAP/55DAP	1.17299	0.195
62DAP/57DAP	1.04151	1
68DAP/62DAP	0.99815	0.834
68DAP/14DAP	0.88795	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.89508	0.322

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.8787	0.517
Mature Green Tomato/Ripe Tomato	0.72119	0.411
Immature Eggplant/Mature Eggplant	0.32992
Ripe Pepper/Ripe Tomato	1.76228	1
Mature Eggplant/Ripe Tomato	0.26476	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.10377	1
1-1-2/M82	1.03449	1
12-2/M82	1.09243	1
12-4/M82	0.82305	0.33
1-3/M82	0.88744
2-1-1/M82	0.96653	1
2-1/M82	N/A	N/A
2-6/M82	1.25942	0.452
3-2/M82	0.87281
4-1-1/M82	1.02715	1
4-1/M82	1.19561
4-3-2/M82	1.32977	0.262
4-3/M82	0.53554	0.441
5-3/M82	0.99544	1
6-2/M82	N/A	N/A
6-3/M82	1.0952	1
7-1/M82	0.94242	0.509
7-2/M82	0.5493
9-3-2/M82	1.03847	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.65804
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	1.38294	0.624
IL1-4/WTpooled	0.91968
WT/WTpooled	0.97896	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	0.93394	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.06991	0.921
DC3000/delta hrp 6h	0.95018	0.95
DC3000/delta hrp 12h	1.00898	1
DC3000/delta hrp 24h	1.08671	0.633

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	1.10523	0.748

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.09464	1
Exp 36h	0.82603	0.434
Exp 60h	1.57363	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01367	1
Var 0h	1.30576	0.936
Var 12h I row2-row1	1.04708	0.443
Var 12h NI row2-row1	0.99284	0.906
Var 36h I row2-row1	0.76502	0.283
Var 36h NI row2-row1	0.87989	0.341
Var 60h I row2-row1	1.12502	0.543
Var 60h NI row2-row1	0.96525	1
Time course 0hI-0hNI	1.0872	0.799
Time course 12hI-12hNI	1.01726	0.892
Time course 36hI-36hNI	0.89943	0.284
Time course 60hI-60hNI	1.04844	0.495

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)	1.04794	0.511
transgenic ySAMdc/azygous control (breaker)	1.11028	1
transgenic ySAMdc/azygous control (red)	1.13207	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.96522	0.227

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.96203	0.59

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.89397	1
Manapal/WT (break)	0.98238	1
Manapal/WT (red)	0.9261	0.607