Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.4.19.14

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.05987	0.891
27DAP/17DAP	0.87214	0.683
39DAP/27DAP	1.23072	0.75
41DAP/39DAP	1.18811	0.591
42DAP/41DAP	0.9536	1
43DAP/42DAP	0.92263	0.834
47DAP/43DAP	0.83372	0.487
52DAP/47DAP	0.78158	0.486
57DAP/52DAP	0.98556	0.98

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93678	0.465
17DAP/reference	0.94077	0.474
27DAP/reference	1.06132	0.782
39DAP/reference	0.79053	0.159
41DAP/reference	0.86301	0.154
42DAP/reference	0.97699	0.398
43DAP/reference	1.03856	0.928
47DAP/reference	1.12092	0.728
52DAP/reference	1.27448	0.407
57DAP/reference	1.30307	0.052

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.05254	0.785
27DAP/17DAP	1.02882	0.945
39DAP/27DAP	1.09865	0.388
41DAP/39DAP	1.01642	1
42DAP/41DAP	1.02189	0.961
43DAP/42DAP	1.09608	0.324
47DAP/43DAP	1.01103	0.951
52DAP/47DAP	0.99518	0.951
57DAP/52DAP	1.00867	1
57DAP/7DAP	0.99954	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.08114	0.705
17DAP/reference	1.2023	0.134
27DAP/reference	1.25213	0.023
39DAP/reference	1.38656	0.012
41DAP/reference	1.23384	0.314
42DAP/reference	1.38247	0.076
43DAP/reference	1.27999	0.105
47DAP/reference	1.20079	0.582
52DAP/reference	1.15024	0.459
57DAP/reference	1.16985	0.698

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.78988	0.268
17DAP/reference	0.59599	0.023
27DAP/reference	1.01615	1
39DAP/reference	0.96798	0.469
41DAP/reference	1.29408	0.162
42DAP/reference	0.97217	0.482
43DAP/reference	0.87657	0.212
47DAP/reference	0.89901	0.277
52DAP/reference	0.60196	0.006
57DAP/reference	0.6948	0.007

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.13035	0.408
17DAP/reference	1.10917	0.384
27DAP/reference	1.09668	0.596
39DAP/reference	0.97459	0.464
41DAP/reference	0.94262	0.331
42DAP/reference	1.07395	0.55
43DAP/reference	1.01118	0.767
47DAP/reference	0.96136	0.525
52DAP/reference	1.07094	0.888
57DAP/reference	1.16898	0.291

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.90546	1
26DAP/20DAP	0.99336	1
34DAP/26DAP	1.08679	0.819
51DAP/34DAP	0.93894	0.571
52DAP/51DAP	0.8703	0.151
53DAP/52DAP	1.10772	0.444
55DAP/53DAP	1.00643	0.964
57DAP/55DAP	1.32874	0.178
62DAP/57DAP	1.02784	1
68DAP/62DAP	0.93079	0.345
68DAP/14DAP	1.39697

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.94581	0.422

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.46443	0.166
Immature Eggplant/Mature Eggplant	1.71915	0.157
Ripe Pepper/Ripe Tomato	0.78992	1
Mature Eggplant/Ripe Tomato	1.62387	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	N/A	N/A
12-2/M82	0.85405
12-4/M82	0.93868
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	1.00645
2-6/M82	N/A	N/A
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	N/A	N/A
6-2/M82	1.29189
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	0.94576

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.51452	0.277
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.36728	1
IL12-4/WTpooled	1.29402
IL1-4/WTpooled	0.91989	0.834
WT/WTpooled	2.17751	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	0.94189	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.00019	1
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	N/A	N/A
DC3000/delta hrp 24h	0.41804	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.07439
DC3000 delta B/DC3000 delta AB	1.04996	0.528

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	N/A	N/A
Exp 60h	1.2242	0.221

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01885	1
Var 0h	1.13952	1
Var 12h I row2-row1	0.98815	0.856
Var 12h NI row2-row1	0.88114	0.713
Var 36h I row2-row1	1.02513	1
Var 36h NI row2-row1	0.79018	0.469
Var 60h I row2-row1	0.88787	0.582
Var 60h NI row2-row1	1.09156	0.904
Time course 0hI-0hNI	1.02303	0.833
Time course 12hI-12hNI	1.03055	0.724
Time course 36hI-36hNI	1.15852	0.009
Time course 60hI-60hNI	1.56264	0.008

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)	0.97475	0.789
transgenic ySAMdc/azygous control (breaker)	0.97588	1
transgenic ySAMdc/azygous control (red)	0.89351	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.38121	0.135

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.95609	0.35

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.98242	1
Manapal/WT (break)	0.96278	1
Manapal/WT (red)	0.82734	0.274