Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.1.13.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.78414	0.169
27DAP/17DAP	1.08448	0.92
39DAP/27DAP	1.0526	0.876
41DAP/39DAP	1.51479	0.494
42DAP/41DAP	0.73982	0.774
43DAP/42DAP	1.19051	0.906
47DAP/43DAP	1.0011	0.851
52DAP/47DAP	1.96845	0.264
57DAP/52DAP	0.90366	0.895

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.0457	0.611
17DAP/reference	1.04008	0.457
27DAP/reference	1.05342	0.509
39DAP/reference	0.99842	0.587
41DAP/reference	1.29621	0.038
42DAP/reference	0.83953	0.003
43DAP/reference	1.08718	0.325
47DAP/reference	0.86018	0.083
52DAP/reference	0.9333	0.319
57DAP/reference	0.87898	0.035

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.91188	0.376
27DAP/17DAP	1.36476	0.194
39DAP/27DAP	1.00801	1
41DAP/39DAP	1.21384	0.876
42DAP/41DAP	1.15749	0.601
43DAP/42DAP	1.40648	0.013
47DAP/43DAP	0.9121	0.606
52DAP/47DAP	1.14209	0.58
57DAP/52DAP	1.08781	0.745
57DAP/7DAP	0.78854	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98443	0.613
17DAP/reference	1.09291	0.199
27DAP/reference	1.07256	0.371
39DAP/reference	0.96455	0.411
41DAP/reference	0.87983	0.146
42DAP/reference	1.00444	0.675
43DAP/reference	0.97139	0.44
47DAP/reference	0.93395	0.383
52DAP/reference	0.78459	0.022
57DAP/reference	0.91054	0.25

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.07476	0.577
17DAP/reference	1.01418	1
27DAP/reference	0.84096	0.071
39DAP/reference	0.78823	0.054
41DAP/reference	0.78649	0.027
42DAP/reference	0.90922	0.121
43DAP/reference	1.19883	0.137
47DAP/reference	0.93041	0.178
52DAP/reference	1.05633	0.789
57DAP/reference	1.07848	0.737

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95572	0.268
17DAP/reference	1.00105	0.839
27DAP/reference	0.9975	0.763
39DAP/reference	1.02173	1
41DAP/reference	1.0374	0.984
42DAP/reference	0.88992	0.134
43DAP/reference	0.77535	0.051
47DAP/reference	1.0578	0.562
52DAP/reference	0.91439	0.36
57DAP/reference	0.68209	0.016

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.94231	1
26DAP/20DAP	1.03861
34DAP/26DAP	0.97246	0.991
51DAP/34DAP	0.76065	0.376
52DAP/51DAP	0.96875	1
53DAP/52DAP	0.84364	0.612
55DAP/53DAP	1.37557	0.733
57DAP/55DAP	1.11153	0.51
62DAP/57DAP	1.01007	1
68DAP/62DAP	0.92973	0.747
68DAP/14DAP	0.6129	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.86491

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.31044
Immature Eggplant/Mature Eggplant	42.158
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	0.42228

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.13564	1
1-1-2/M82	0.79365	0.958
12-2/M82	N/A	N/A
12-4/M82	0.83296	0.619
1-3/M82	0.76664	0.378
2-1-1/M82	0.80422	0.784
2-1/M82	1.0876
2-6/M82	1.05175	0.695
3-2/M82	0.80981
4-1-1/M82	1.22821
4-1/M82	1.04793
4-3-2/M82	N/A	N/A
4-3/M82	1.10861	1
5-3/M82	0.95768	0.642
6-2/M82	1.08796
6-3/M82	1.10855	1
7-1/M82	0.75075
7-2/M82	0.63899	0.57
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.03461	1
IL2-6/WTpooled	1.00787	1
IL7-5/WTpooled	0.94815	1
IL7-3/WTpooled	1.24861	1
IL12-4/WTpooled	1.09605	0.737
IL1-4/WTpooled	1.12677	1
WT/WTpooled	1.01559	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	0.75964	0.497

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.95511	1
DC3000/delta hrp 6h	0.99719	0.95
DC3000/delta hrp 12h	1.08361	1
DC3000/delta hrp 24h	0.8821	0.269

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	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.78743	0.242
Exp 36h	N/A	N/A
Exp 60h	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
self-self	0.97265	1
Var 0h	0.89931	0.258
Var 12h I row2-row1	1.13139	0.189
Var 12h NI row2-row1	0.90742	0.82
Var 36h I row2-row1	0.59093	0.203
Var 36h NI row2-row1	1.15274	0.482
Var 60h I row2-row1	1.03785
Var 60h NI row2-row1	1.11589	0.691
Time course 0hI-0hNI	0.951	0.754
Time course 12hI-12hNI	0.98004	0.874
Time course 36hI-36hNI	0.82363	0.036
Time course 60hI-60hNI	0.39886	0.007

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)	0.95456	0.485
transgenic ySAMdc/azygous control (breaker)	1.49568	0.172
transgenic ySAMdc/azygous control (red)	1.24657	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.95447	0.153

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.32584	0.227

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.44319	0.105
Manapal/WT (break)	1.29177	0.14
Manapal/WT (red)	1.30755	0.222