Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.3.19.7

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.02746	0.77
27DAP/17DAP	1.12364	1
39DAP/27DAP	1.11832	0.873
41DAP/39DAP	1.41505	0.447
42DAP/41DAP	1.31259	0.556
43DAP/42DAP	1.18618	0.906
47DAP/43DAP	1.11154	0.569
52DAP/47DAP	0.95786	0.81
57DAP/52DAP	1.14447	1

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.8743	0.402
17DAP/reference	1.04557	0.907
27DAP/reference	1.40084	0.035
39DAP/reference	1.64575	0.162
41DAP/reference	1.02186	0.667
42DAP/reference	0.93029	0.25
43DAP/reference	0.91349	0.675
47DAP/reference	0.86896	0.148
52DAP/reference	1.40775	0.008
57DAP/reference	0.65468	0.34

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.30607	0.326
27DAP/17DAP	1.22034	0.724
39DAP/27DAP	1.61799	0.103
41DAP/39DAP	1.15402	0.612
42DAP/41DAP	0.9197	0.481
43DAP/42DAP	1.16291	0.382
47DAP/43DAP	0.98242	0.877
52DAP/47DAP	1.41562	0.21
57DAP/52DAP	0.90907	0.375
57DAP/7DAP	1.48882	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.69879	0.069
17DAP/reference	0.95228	0.338
27DAP/reference	1.09991	0.453
39DAP/reference	1.2407	0.044
41DAP/reference	1.0654	0.701
42DAP/reference	1.48633	0.009
43DAP/reference	1.60134	0.008
47DAP/reference	1.79106	0.155
52DAP/reference	1.77461	0.013
57DAP/reference	1.22075	0.005

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84101	0.248
17DAP/reference	0.92327	0.461
27DAP/reference	1.09581	0.507
39DAP/reference	1.07476	0.956
41DAP/reference	1.15501	0.221
42DAP/reference	1.20622	0.094
43DAP/reference	0.85941	0.224
47DAP/reference	0.98215	0.543
52DAP/reference	1.19231	0.279
57DAP/reference	0.80629	0.046

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87352	0.135
17DAP/reference	0.97246	0.601
27DAP/reference	1.21776	0.531
39DAP/reference	0.99269	0.693
41DAP/reference	1.48671	0.12
42DAP/reference	1.54796	0.012
43DAP/reference	1.46331	0.021
47DAP/reference	1.2302	0.339
52DAP/reference	1.21795	0.534
57DAP/reference	1.57957	0.031

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.65964	0.071
26DAP/20DAP	1.29816	0.315
34DAP/26DAP	0.85769	0.735
51DAP/34DAP	1.008	0.927
52DAP/51DAP	1.06146	0.915
53DAP/52DAP	1.20263	0.343
55DAP/53DAP	0.93949	0.698
57DAP/55DAP	1.30463	0.898
62DAP/57DAP	1.11037	0.902
68DAP/62DAP	1.20976	0.885
68DAP/14DAP	1.77729	0.043

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.89526	0.151

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.04436	0.948
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.33101	0.224
Mature Eggplant/Ripe Tomato	0.41645	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.26918	0.551
1-1-2/M82	1.01816	1
12-2/M82	1.24603	1
12-4/M82	1.23619
1-3/M82	2.46247	0.479
2-1-1/M82	0.92667	0.784
2-1/M82	N/A	N/A
2-6/M82	0.85178	1
3-2/M82	1.36819	0.388
4-1-1/M82	1.09925	1
4-1/M82	1.0584	1
4-3-2/M82	1.24127	1
4-3/M82	0.96222	1
5-3/M82	1.00437	1
6-2/M82	1.12935	1
6-3/M82	1.24882	1
7-1/M82	N/A	N/A
7-2/M82	0.89531	0.553
9-3-2/M82	1.08681	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.8545
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.80745	0.298
IL12-4/WTpooled	1.08017	0.695
IL1-4/WTpooled	0.67178	0.402
WT/WTpooled	1.07616	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	1.21767	0.193

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.96914	1
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	0.78373	1
DC3000/delta hrp 24h	0.93631	0.554

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.62828	0.045
DC3000 delta B/DC3000 delta AB	2.2128	0.071

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	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	0.99251	1
Var 0h	0.46398	1
Var 12h I row2-row1	0.70854	0.467
Var 12h NI row2-row1	1.78621	0.281
Var 36h I row2-row1	1.07148	1
Var 36h NI row2-row1	0.49731	0.478
Var 60h I row2-row1	0.75365	0.582
Var 60h NI row2-row1	0.74284	0.292
Time course 0hI-0hNI	0.98026	0.934
Time course 12hI-12hNI	1.05332	0.824
Time course 36hI-36hNI	2.59148	0.005
Time course 60hI-60hNI	6.66863	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)	0.89272	0.567
transgenic ySAMdc/azygous control (breaker)	1.29995	1
transgenic ySAMdc/azygous control (red)	0.93204	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.87837	0.029

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.81004	0.255

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	N/A	N/A
Manapal/WT (break)	1.23868	0.183
Manapal/WT (red)	0.96943	0.863