Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.2.5.3

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.08971	0.77
27DAP/17DAP	0.93796	0.922
39DAP/27DAP	0.83557	0.425
41DAP/39DAP	1.77407	0.349
42DAP/41DAP	0.9265	1
43DAP/42DAP	1.07943	1
47DAP/43DAP	0.93264	0.744
52DAP/47DAP	1.08981	0.918
57DAP/52DAP	1.1927	0.892

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.0078	1
17DAP/reference	1.00678	0.813
27DAP/reference	1.02382	0.58
39DAP/reference	1.03506	0.628
41DAP/reference	1.01841	0.587
42DAP/reference	0.952	0.078
43DAP/reference	0.96925	0.538
47DAP/reference	0.97438	0.3
52DAP/reference	0.96638	0.427
57DAP/reference	0.87562	0.014

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.8923	0.185
27DAP/17DAP	0.9847	0.887
39DAP/27DAP	1.09539	0.296
41DAP/39DAP	1.00485	1
42DAP/41DAP	0.97759	0.762
43DAP/42DAP	1.06473	0.25
47DAP/43DAP	0.98035	0.855
52DAP/47DAP	0.96879	0.797
57DAP/52DAP	0.97429	0.68
57DAP/7DAP	1.04481	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.05667	0.664
17DAP/reference	1.04696	0.437
27DAP/reference	0.99562	0.698
39DAP/reference	1.03692	0.436
41DAP/reference	0.95817	0.311
42DAP/reference	0.96316	0.393
43DAP/reference	0.93853	0.202
47DAP/reference	0.82446	0.057
52DAP/reference	1.08563	0.016
57DAP/reference	1.03727	0.746

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.1381	0.077
17DAP/reference	1.06792	0.113
27DAP/reference	1.01785	0.974
39DAP/reference	1.00668	1
41DAP/reference	0.88726	0.038
42DAP/reference	0.94279	0.089
43DAP/reference	1.01506	0.899
47DAP/reference	0.96335	0.24
52DAP/reference	1.07272	0.034
57DAP/reference	1.03224	0.705

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.07271	0.303
17DAP/reference	1.00226	0.918
27DAP/reference	1.04318	0.34
39DAP/reference	1.01716	0.578
41DAP/reference	0.93782	0.331
42DAP/reference	0.85506	0.134
43DAP/reference	0.95005	0.416
47DAP/reference	0.98151	0.538
52DAP/reference	0.99075	0.821
57DAP/reference	0.63702	0.016

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.06882	0.966
26DAP/20DAP	0.9855	1
34DAP/26DAP	1.00388	1
51DAP/34DAP	1.04567	0.692
52DAP/51DAP	0.96414	1
53DAP/52DAP	0.9861	0.924
55DAP/53DAP	1.02391	0.904
57DAP/55DAP	1.06509	0.935
62DAP/57DAP	1.12819	0.445
68DAP/62DAP	1.0752	0.897
68DAP/14DAP	0.83521	0.121

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.90344	0.079

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.62773	0.072
Immature Eggplant/Mature Eggplant	N/A	N/A
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	0.92682	0.673
1-1-2/M82	1.0987	1
12-2/M82	0.90391
12-4/M82	1.01492	1
1-3/M82	0.78468
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	1.14501	0.505
3-2/M82	0.95124	1
4-1-1/M82	N/A	N/A
4-1/M82	1.11807	1
4-3-2/M82	0.81991	0.698
4-3/M82	0.8036
5-3/M82	1.01732	1
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	1.02107
7-2/M82	0.97911	1
9-3-2/M82	0.92316	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.96952	1
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	1.54892
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	1.09198
IL1-4/WTpooled	0.99557	1
WT/WTpooled	1.47469

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	0.99325	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.97013	1
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	1.01938	1
DC3000/delta hrp 24h	1.04879	0.633

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.99297	1
DC3000 delta B/DC3000 delta AB	1.0258	0.593

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	0.93356	0.994

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00889	1
Var 0h	0.59535	0.933
Var 12h I row2-row1	1.05766	0.443
Var 12h NI row2-row1	0.90979	0.494
Var 36h I row2-row1	0.95255	1
Var 36h NI row2-row1	1.01398	1
Var 60h I row2-row1	1.31088	0.562
Var 60h NI row2-row1	1.08861	0.904
Time course 0hI-0hNI	1.08529	0.719
Time course 12hI-12hNI	1.03383	0.746
Time course 36hI-36hNI	1.01509	0.799
Time course 60hI-60hNI	0.96555	0.319

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)	N/A	N/A
transgenic ySAMdc/azygous control (breaker)	1.8939	0.172
transgenic ySAMdc/azygous control (red)	1.22608	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.97692	0.362

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.01747	1

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)	0.9435	1
Manapal/WT (red)	N/A	N/A