Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.4.18.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.98135	0.77
27DAP/17DAP	0.92122	0.913
39DAP/27DAP	1.1198	0.825
41DAP/39DAP	0.97027	0.905
42DAP/41DAP	0.90852	1
43DAP/42DAP	1.10491	0.956
47DAP/43DAP	1.09578	0.909
52DAP/47DAP	1.24096	0.688
57DAP/52DAP	0.99474	0.971

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.86881	0.149
17DAP/reference	1.06841	0.185
27DAP/reference	1.00923	1
39DAP/reference	1.1703	0.318
41DAP/reference	1.13266	0.451
42DAP/reference	0.94769	0.134
43DAP/reference	0.91953	0.2
47DAP/reference	0.97656	0.445
52DAP/reference	1.05516	0.663
57DAP/reference	1.09421	0.31

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.15709	0.319
27DAP/17DAP	0.95898	0.821
39DAP/27DAP	1.11688	0.565
41DAP/39DAP	1.08566	1
42DAP/41DAP	1.01084	0.87
43DAP/42DAP	0.73938	0.033
47DAP/43DAP	0.84866	0.265
52DAP/47DAP	0.95203	0.837
57DAP/52DAP	0.89504	0.488
57DAP/7DAP	1.17269	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.8045	0.129
17DAP/reference	0.88745	0.082
27DAP/reference	1.10178	0.246
39DAP/reference	1.08707	0.538
41DAP/reference	1.05536	0.745
42DAP/reference	1.11185	0.046
43DAP/reference	0.90699	0.183
47DAP/reference	1.00871	1
52DAP/reference	1.04182	0.732
57DAP/reference	1.0792	0.268

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.19199	0.384
17DAP/reference	1.13887	0.311
27DAP/reference	1.11719	0.67
39DAP/reference	0.98209	0.539
41DAP/reference	0.98046	0.481
42DAP/reference	1.23003	0.105
43DAP/reference	1.44237	0.242
47DAP/reference	1.26442	0.036
52DAP/reference	1.16687	0.098
57DAP/reference	1.10129	0.208

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.74403	0.032
17DAP/reference	1.00474	0.839
27DAP/reference	1.06453	0.596
39DAP/reference	1.05494	0.935
41DAP/reference	1.1366	0.188
42DAP/reference	0.95168	0.552
43DAP/reference	0.83605	0.165
47DAP/reference	1.07638	0.104
52DAP/reference	0.79179	0.141
57DAP/reference	1.10159	0.549

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.58174	0.966
26DAP/20DAP	0.92463	0.512
34DAP/26DAP	0.87949	0.619
51DAP/34DAP	0.8174	0.458
52DAP/51DAP	1.05039	0.939
53DAP/52DAP	0.96311	0.811
55DAP/53DAP	1.01063	0.939
57DAP/55DAP	1.00448	0.911
62DAP/57DAP	0.88624	0.466
68DAP/62DAP	1.0984	0.984
68DAP/14DAP	1.13734	0.85

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.81836	0.198

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	4.3325	0.058
Mature Green Tomato/Ripe Tomato	4.39065	0.015
Immature Eggplant/Mature Eggplant	3.80715
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	N/A	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.05038	1
1-1-2/M82	0.7106
12-2/M82	N/A	N/A
12-4/M82	1.03413
1-3/M82	0.46578
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	0.95373	1
3-2/M82	N/A	N/A
4-1-1/M82	0.65986
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	1.01925	1
6-2/M82	0.48362
6-3/M82	1.22493	1
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.98593	1
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	0.87542	1
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	1.0255
WT/WTpooled	N/A	N/A

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	1.00241	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.04739	0.921
DC3000/delta hrp 6h	0.9425	0.95
DC3000/delta hrp 12h	1.10489	1
DC3000/delta hrp 24h	0.96026	0.782

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	0.77223	1
Exp 36h	0.78828	0.456
Exp 60h	0.83045	0.586

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

hybridization	ratio	FDR (corrected p value)
self-self	1.02359	1
Var 0h	1.01183	1
Var 12h I row2-row1	1.28827	0.296
Var 12h NI row2-row1	1.12018	1
Var 36h I row2-row1	0.9133	0.805
Var 36h NI row2-row1	0.87219	1
Var 60h I row2-row1	1.14893	1
Var 60h NI row2-row1	1.24788	0.904
Time course 0hI-0hNI	1.75468	0.799
Time course 12hI-12hNI	0.97476	0.847
Time course 36hI-36hNI	0.66844	0.023
Time course 60hI-60hNI	0.60079	0.015

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)	0.88282	0.485
transgenic ySAMdc/azygous control (breaker)	0.87099	0.49
transgenic ySAMdc/azygous control (red)	1.16543	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.09073	0.057

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.96296	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	2.73303	0.083
Manapal/WT (break)	1.12694	1
Manapal/WT (red)	1.54811	0.126