Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.3.9.8

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.91448	0.543
27DAP/17DAP	0.62415	0.115
39DAP/27DAP	0.5885	0.221
41DAP/39DAP	0.71524	0.103
42DAP/41DAP	0.92163	1
43DAP/42DAP	1.43992	0.625
47DAP/43DAP	0.6498	0.089
52DAP/47DAP	0.8637	0.618
57DAP/52DAP	1.07718	1

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.31078	0.032
17DAP/reference	1.18616	0.059
27DAP/reference	1.45149	0.009
39DAP/reference	1.10509	0.453
41DAP/reference	1.05726	0.393
42DAP/reference	0.98411	0.44
43DAP/reference	1.02121	0.838
47DAP/reference	0.77154	0.001
52DAP/reference	0.75335	0.029
57DAP/reference	0.95429	0.435

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.51819	0.058
27DAP/17DAP	1.163	0.863
39DAP/27DAP	0.50229	0.035
41DAP/39DAP	0.97044	0.986
42DAP/41DAP	0.77724	0.147
43DAP/42DAP	0.73524	0.029
47DAP/43DAP	0.93095	0.701
52DAP/47DAP	0.87702	0.35
57DAP/52DAP	0.95447	0.75
57DAP/7DAP	0.63943	0.219

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.21146	0.085
17DAP/reference	0.91878	0.108
27DAP/reference	0.76314	0.011
39DAP/reference	0.58373	0.011
41DAP/reference	0.59198	0.027
42DAP/reference	0.57468	0.01
43DAP/reference	0.55469	0.011
47DAP/reference	0.69194	0.066
52DAP/reference	0.46857	0.011
57DAP/reference	0.49564	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.25992	0.094
17DAP/reference	1.27745	0.024
27DAP/reference	1.0749	0.735
39DAP/reference	0.82671	0.065
41DAP/reference	0.94219	0.331
42DAP/reference	0.97193	0.482
43DAP/reference	1.00353	0.581
47DAP/reference	0.80231	0.012
52DAP/reference	0.74632	0.025
57DAP/reference	0.85843	0.073

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.36976	0.015
17DAP/reference	2.21483	0.026
27DAP/reference	2.08783	0.02
39DAP/reference	1.26783	0.021
41DAP/reference	0.85071	0.064
42DAP/reference	0.81475	0.087
43DAP/reference	0.84313	0.088
47DAP/reference	0.82831	0.08
52DAP/reference	0.95896	0.464
57DAP/reference	1.18938	0.233

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.27331
26DAP/20DAP	1.09056	0.793
34DAP/26DAP	1.03563	1
51DAP/34DAP	1.57687	0.032
52DAP/51DAP	1.01639	0.925
53DAP/52DAP	0.73241	0.06
55DAP/53DAP	0.83798	0.169
57DAP/55DAP	1.5798	0.188
62DAP/57DAP	1.05132	0.935
68DAP/62DAP	1.01958	0.787
68DAP/14DAP	0.98509	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.28731	0.02

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.8475	0.309
Mature Green Tomato/Ripe Tomato	10.3427	0.015
Immature Eggplant/Mature Eggplant	0.37912
Ripe Pepper/Ripe Tomato	26.0739	0.256
Mature Eggplant/Ripe Tomato	6.70809	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.96278	0.944
1-1-2/M82	0.7277
12-2/M82	1.21842
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	1.26886
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	1.03609
6-2/M82	N/A	N/A
6-3/M82	0.98524	1
7-1/M82	1.0658
7-2/M82	1.08532	1
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.43928	0.277
IL2-6/WTpooled	1.28811	0.46
IL7-5/WTpooled	1.4474	0.792
IL7-3/WTpooled	1.07737	1
IL12-4/WTpooled	1.38593	0.516
IL1-4/WTpooled	1.02967	1
WT/WTpooled	0.94134	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	0.88351	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.049	0.921
DC3000/delta hrp 6h	1.01205	1
DC3000/delta hrp 12h	1.07966	1
DC3000/delta hrp 24h	0.46084	0.038

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.45961	0.025
DC3000 delta B/DC3000 delta AB	0.441	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.00003	1
Exp 36h	0.80492	0.539
Exp 60h	0.75398	0.522

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

hybridization	ratio	FDR (corrected p value)
self-self	1.02064	1
Var 0h	1.04049	0.936
Var 12h I row2-row1	0.96854	0.948
Var 12h NI row2-row1	1.05224	1
Var 36h I row2-row1	1.25137	0.908
Var 36h NI row2-row1	1.2501	1
Var 60h I row2-row1	1.19366	0.562
Var 60h NI row2-row1	1.11119	0.904
Time course 0hI-0hNI	0.93398	0.37
Time course 12hI-12hNI	1.00926	0.849
Time course 36hI-36hNI	1.05561	0.401
Time course 60hI-60hNI	0.16678	0.006

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)	1.12807	0.612
transgenic ySAMdc/azygous control (breaker)	1.56246	0.172
transgenic ySAMdc/azygous control (red)	1.60904	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.90215	0.038

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	3.09528	0.233

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	2.942	0.09
Manapal/WT (break)	4.22193	0.13
Manapal/WT (red)	1.21048	0.133