Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-4.2.19.21

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	2.21598	0.033
27DAP/17DAP	0.62492	0.066
39DAP/27DAP	1.08909	0.922
41DAP/39DAP	1.10396	0.642
42DAP/41DAP	1.54301	0.166
43DAP/42DAP	1.42714	0.541
47DAP/43DAP	1.1489	0.429
52DAP/47DAP	0.53617	0.035
57DAP/52DAP	1.018	0.985

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.58506	0.012
17DAP/reference	0.95089	0.503
27DAP/reference	1.05927	0.58
39DAP/reference	0.89043	0.039
41DAP/reference	0.99985	1
42DAP/reference	1.41028	0.001
43DAP/reference	1.06745	0.569
47DAP/reference	1.59382	0.002
52DAP/reference	1.82338	0.011
57DAP/reference	1.5973	0.009

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.91385	0.299
27DAP/17DAP	1.03722	0.9
39DAP/27DAP	0.98369	0.908
41DAP/39DAP	1.15954	0.214
42DAP/41DAP	1.01355	0.991
43DAP/42DAP	1.0959	0.02
47DAP/43DAP	1.08725	0.581
52DAP/47DAP	1.14662	0.593
57DAP/52DAP	0.80088	0.091
57DAP/7DAP	1.04503	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84696	0.296
17DAP/reference	0.84937	0.108
27DAP/reference	0.81184	0.062
39DAP/reference	0.74757	0.083
41DAP/reference	0.82707	0.166
42DAP/reference	0.72118	0.04
43DAP/reference	0.8729	0.183
47DAP/reference	1.373	0.822
52DAP/reference	0.867	0.15
57DAP/reference	0.85396	0.069

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.18304	0.545
17DAP/reference	1.15923	0.264
27DAP/reference	1.31969	0.126
39DAP/reference	1.37553	0.063
41DAP/reference	1.41137	0.043
42DAP/reference	1.48841	0.008
43DAP/reference	0.95123	0.468
47DAP/reference	1.24884	0.01
52DAP/reference	1.00175	0.713
57DAP/reference	1.08656	0.887

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.86365	0.23
17DAP/reference	1.01497	0.792
27DAP/reference	0.97657	0.594
39DAP/reference	0.90537	0.133
41DAP/reference	0.9724	0.56
42DAP/reference	1.32719	0.701
43DAP/reference	1.25608	0.655
47DAP/reference	1.19753	0.76
52DAP/reference	2.10292	0.549
57DAP/reference	2.27532	0.034

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.93919	1
26DAP/20DAP	0.88484	0.317
34DAP/26DAP	1.0253	1
51DAP/34DAP	1.0642	0.613
52DAP/51DAP	1.10625	0.367
53DAP/52DAP	1.13859	0.25
55DAP/53DAP	1.06724	0.898
57DAP/55DAP	1.29042	0.626
62DAP/57DAP	0.79092	0.088
68DAP/62DAP	0.95799	0.787
68DAP/14DAP	1.6921	0.249

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.8683	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.88916	0.401
Mature Green Tomato/Ripe Tomato	0.25668	0.017
Immature Eggplant/Mature Eggplant	1.59595	0.05
Ripe Pepper/Ripe Tomato	1.5839	0.258
Mature Eggplant/Ripe Tomato	1.48102	N/A

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	N/A	N/A
12-4/M82	N/A	N/A
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
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	N/A	N/A
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	3.10284	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.87335	N/A
IL12-4/WTpooled	1.38269	0.839
IL1-4/WTpooled	0.9329	N/A
WT/WTpooled	0.90717	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	1.34653	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.54766	0.692
DC3000/delta hrp 6h	0.97933	0.95
DC3000/delta hrp 12h	1.26295	1
DC3000/delta hrp 24h	0.84834	0.711

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.05564	0.313
DC3000 delta B/DC3000 delta AB	1.07322	0.423

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.01379	1
Exp 36h	1.16938	0.693
Exp 60h	1.36767	0.227

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

hybridization	ratio	FDR (corrected p value)
self-self	0.94546	1
Var 0h	1.02823	1
Var 12h I row2-row1	0.99664	1
Var 12h NI row2-row1	0.99367	1
Var 36h I row2-row1	1.05503	1
Var 36h NI row2-row1	0.82727	0.549
Var 60h I row2-row1	0.97808	0.952
Var 60h NI row2-row1	1.15812	0.904
Time course 0hI-0hNI	1.0878	0.833
Time course 12hI-12hNI	0.99956	1
Time course 36hI-36hNI	1.11783	0.07
Time course 60hI-60hNI	2.05316	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)	1.04182	0.511
transgenic ySAMdc/azygous control (breaker)	0.96647	1
transgenic ySAMdc/azygous control (red)	1.10849	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.97681	0.651

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.83383	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.93468	1
Manapal/WT (break)	1.34172	0.381
Manapal/WT (red)	N/A	N/A