Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.3.13.18

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.87477	0.324
27DAP/17DAP	1.0174	0.967
39DAP/27DAP	0.87342	0.507
41DAP/39DAP	1.24151	0.423
42DAP/41DAP	0.99736	1
43DAP/42DAP	0.94139	0.705
47DAP/43DAP	1.22565	0.469
52DAP/47DAP	1.08835	0.804
57DAP/52DAP	0.99809	0.983

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.86346	0.136
17DAP/reference	0.90841	0.046
27DAP/reference	0.98711	0.711
39DAP/reference	1.00282	0.871
41DAP/reference	0.85917	0.201
42DAP/reference	0.86206	0.006
43DAP/reference	1.03062	0.617
47DAP/reference	0.88398	0.011
52DAP/reference	0.91517	0.121
57DAP/reference	0.94424	0.324

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.00827	1
27DAP/17DAP	0.97002	0.878
39DAP/27DAP	1.07528	0.57
41DAP/39DAP	0.93476	0.849
42DAP/41DAP	1.00071	0.876
43DAP/42DAP	1.08702	0.413
47DAP/43DAP	1.0247	0.969
52DAP/47DAP	0.99971	0.951
57DAP/52DAP	0.99605	0.852
57DAP/7DAP	1.11943	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97918	0.495
17DAP/reference	0.94078	0.064
27DAP/reference	0.91623	0.048
39DAP/reference	0.95076	0.109
41DAP/reference	0.95564	0.194
42DAP/reference	0.96662	0.275
43DAP/reference	0.91178	0.015
47DAP/reference	0.98905	0.671
52DAP/reference	1.05066	0.459
57DAP/reference	1.02103	1

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.86434	0.096
17DAP/reference	0.80138	0.029
27DAP/reference	0.92148	0.16
39DAP/reference	0.81953	0.021
41DAP/reference	1.03285	1
42DAP/reference	0.85175	0.028
43DAP/reference	0.86043	0.048
47DAP/reference	0.87791	0.01
52DAP/reference	0.89876	0.072
57DAP/reference	0.83479	0.043

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99239	0.699
17DAP/reference	0.95702	0.342
27DAP/reference	0.89354	0.048
39DAP/reference	0.92352	0.05
41DAP/reference	0.95954	0.293
42DAP/reference	0.90049	0.087
43DAP/reference	0.84956	0.073
47DAP/reference	0.97329	0.465
52DAP/reference	0.77425	0.073
57DAP/reference	1.04754	0.73

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.04079	0.966
26DAP/20DAP	1.00959	1
34DAP/26DAP	1.01947	1
51DAP/34DAP	1.25411	0.079
52DAP/51DAP	1.12183	0.522
53DAP/52DAP	0.91571	0.649
55DAP/53DAP	1.11294	0.722
57DAP/55DAP	0.92648	0.647
62DAP/57DAP	1.07325	0.833
68DAP/62DAP	1.0779	0.991
68DAP/14DAP	1.24836	0.179

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.88999	0.304

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.74702
Mature Green Tomato/Ripe Tomato	1.21562	0.948
Immature Eggplant/Mature Eggplant	0.53279
Ripe Pepper/Ripe Tomato	1.49116	1
Mature Eggplant/Ripe Tomato	2.16538

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.95861	0.944
1-1-2/M82	1.00851	1
12-2/M82	1.11797	1
12-4/M82	1.12443	1
1-3/M82	0.85233	0.441
2-1-1/M82	1.00786	1
2-1/M82	N/A	N/A
2-6/M82	1.02958	0.594
3-2/M82	0.96971
4-1-1/M82	1.09684	1
4-1/M82	1.13306
4-3-2/M82	1.01164
4-3/M82	0.77999	0.72
5-3/M82	1.06318	1
6-2/M82	0.95634	1
6-3/M82	1.0373	1
7-1/M82	N/A	N/A
7-2/M82	1.10411	1
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.6383	0.337
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.89192	0.418
IL12-4/WTpooled	1.13472	0.737
IL1-4/WTpooled	1.12848
WT/WTpooled	1.03072	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	0.92187	0.256

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.97302	1
DC3000/delta hrp 6h	0.92922	0.95
DC3000/delta hrp 12h	0.62572
DC3000/delta hrp 24h	1.04102	0.821

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.47098	0.042
DC3000 delta B/DC3000 delta AB	1.02735	0.636

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.09366	1
Exp 36h	1.16317	0.693
Exp 60h	1.22556	0.283

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

hybridization	ratio	FDR (corrected p value)
self-self	0.95566	1
Var 0h	0.96471	1
Var 12h I row2-row1	1.11951	0.196
Var 12h NI row2-row1	0.88843	0.466
Var 36h I row2-row1	1.03965	1
Var 36h NI row2-row1	0.98909	0.852
Var 60h I row2-row1	1.48772	0.562
Var 60h NI row2-row1	1.24964	0.904
Time course 0hI-0hNI	1.10906	0.63
Time course 12hI-12hNI	0.94354	0.546
Time course 36hI-36hNI	0.96069	0.389
Time course 60hI-60hNI	1.17872	0.06

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)	0.95232	0.428
transgenic ySAMdc/azygous control (breaker)	1.02078	1
transgenic ySAMdc/azygous control (red)	0.95463	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.98631	0.353

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.00203	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.91406	1
Manapal/WT (break)	0.84919	1
Manapal/WT (red)	0.7381	0.181