Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.4.13.21

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.42798	0.67
27DAP/17DAP	0.81101	0.536
39DAP/27DAP	1.20153	0.713
41DAP/39DAP	1.10176	0.575
42DAP/41DAP	0.96748	1
43DAP/42DAP	0.99978	0.925
47DAP/43DAP	1.9965	0.316
52DAP/47DAP	1.30172	0.453
57DAP/52DAP	0.77349	0.727

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99909	0.771
17DAP/reference	1.21038	0.143
27DAP/reference	0.99311	0.797
39DAP/reference	1.01914	0.903
41DAP/reference	1.10717	0.093
42DAP/reference	0.81843	0.001
43DAP/reference	1.00953	0.957
47DAP/reference	1.12738	0.243
52DAP/reference	1.45489	0.031
57DAP/reference	1.0217	0.901

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.8769	0.178
27DAP/17DAP	1.09479	0.677
39DAP/27DAP	0.98308	0.898
41DAP/39DAP	1.03846	0.887
42DAP/41DAP	0.85942	0.284
43DAP/42DAP	1.05033	0.446
47DAP/43DAP	0.93834	0.559
52DAP/47DAP	1.07923	0.8
57DAP/52DAP	0.92371	0.587
57DAP/7DAP	1.34945	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.87748	0.034
17DAP/reference	3.4349	0.006
27DAP/reference	3.12428	0.006
39DAP/reference	4.29626	0.005
41DAP/reference	4.18236	0.01
42DAP/reference	4.40453	0.006
43DAP/reference	5.22063	0.006
47DAP/reference	2.15927	0.229
52DAP/reference	3.44245	0.007
57DAP/reference	3.37103	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.13964	0.234
17DAP/reference	0.91298	0.214
27DAP/reference	0.96763	0.452
39DAP/reference	1.11484	0.263
41DAP/reference	0.86229	0.121
42DAP/reference	0.88283	0.121
43DAP/reference	1.08981	0.607
47DAP/reference	0.93789	0.159
52DAP/reference	0.8515	0.031
57DAP/reference	0.8512	0.008

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.45017	0.043
17DAP/reference	1.57169	0.467
27DAP/reference	3.41299	0.016
39DAP/reference	2.7802	0.012
41DAP/reference	2.71847	0.009
42DAP/reference	2.82607	0.015
43DAP/reference	2.53026	0.096
47DAP/reference	0.84499	0.033
52DAP/reference	3.95318	0.097
57DAP/reference	1.9019	0.279

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.16554	0.966
26DAP/20DAP	0.82749	1
34DAP/26DAP	1.07743	1
51DAP/34DAP	1.07221	0.883
52DAP/51DAP	1.1815	0.253
53DAP/52DAP	1.09115	0.723
55DAP/53DAP	1.11001	0.703
57DAP/55DAP	1.06508	0.955
62DAP/57DAP	1.15299	0.678
68DAP/62DAP	0.81828	0.429
68DAP/14DAP	0.83412	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.91032	0.239

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.43327	0.017
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.12455	0.224
Mature Eggplant/Ripe Tomato	0.04278	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.16895	0.877
1-1-2/M82	0.94663	0.804
12-2/M82	1.0351	1
12-4/M82	0.72393	0.358
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	0.90808
2-6/M82	0.98299	0.501
3-2/M82	0.71492	0.455
4-1-1/M82	1.64549	0.949
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	0.64716
5-3/M82	0.6528	0.395
6-2/M82	0.38948
6-3/M82	1.02167	1
7-1/M82	1.04911
7-2/M82	N/A	N/A
9-3-2/M82	1.44894

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.47325	0.277
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	0.62735
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	0.65303
IL1-4/WTpooled	0.9954	1
WT/WTpooled	0.91613	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	0.87391	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.12817	0.823
DC3000/delta hrp 6h	0.95102	0.95
DC3000/delta hrp 12h	0.89361	1
DC3000/delta hrp 24h	1.06461	0.728

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	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	1.11926	1
Var 0h	1.90826
Var 12h I row2-row1	0.71431	0.692
Var 12h NI row2-row1	0.92956	0.713
Var 36h I row2-row1	1.0166	1
Var 36h NI row2-row1	0.98634	1
Var 60h I row2-row1	7.7085	1
Var 60h NI row2-row1	1.0152	1
Time course 0hI-0hNI	1.00842	1
Time course 12hI-12hNI	0.87866	0.216
Time course 36hI-36hNI	0.72436	0.024
Time course 60hI-60hNI	2.6379	0.673

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)	1.41469	0.212
transgenic ySAMdc/azygous control (breaker)	1.16256	1
transgenic ySAMdc/azygous control (red)	1.06135	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.99707	0.858

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.09588	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.1563	0.307
Manapal/WT (break)	2.79095	0.14
Manapal/WT (red)	4.8468	0.126