Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.2.12.5

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.85264	0.405
27DAP/17DAP	0.8113	0.456
39DAP/27DAP	1.07261	0.946
41DAP/39DAP	1.04057	1
42DAP/41DAP	1.05241	0.971
43DAP/42DAP	0.95798	0.765
47DAP/43DAP	1.13	0.321
52DAP/47DAP	0.87399	0.646
57DAP/52DAP	1.20274	0.853

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.34304	0.008
17DAP/reference	1.20515	0.02
27DAP/reference	1.19629	0.024
39DAP/reference	1.17813	0.023
41DAP/reference	1.47214	0.019
42DAP/reference	1.31931	0.001
43DAP/reference	1.14106	0.287
47DAP/reference	1.18503	0.007
52DAP/reference	1.31739	0.017
57DAP/reference	1.04688	0.762

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.06154	0.749
27DAP/17DAP	0.9989	0.969
39DAP/27DAP	0.95696	0.703
41DAP/39DAP	1.07825	0.883
42DAP/41DAP	0.97777	0.774
43DAP/42DAP	0.96856	0.751
47DAP/43DAP	0.98994	0.947
52DAP/47DAP	1.16125	0.549
57DAP/52DAP	1.15941	0.173
57DAP/7DAP	1.14291	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.50063	0.069
17DAP/reference	0.45255	0.011
27DAP/reference	0.90658	0.248
39DAP/reference	0.49147	0.011
41DAP/reference	1.02692	0.778
42DAP/reference	1.91184	0.1
43DAP/reference	1.9718	0.012
47DAP/reference	1.14717	0.279
52DAP/reference	0.54039	0.012
57DAP/reference	0.42789	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.21218	0.65
17DAP/reference	1.43227	0.011
27DAP/reference	1.24165	0.367
39DAP/reference	1.35219	0.164
41DAP/reference	1.34538	0.262
42DAP/reference	1.33701	0.062
43DAP/reference	1.37531	0.457
47DAP/reference	1.32143	0.012
52DAP/reference	1.5081	0.006
57DAP/reference	1.6791	0.007

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.46178	0.032
17DAP/reference	0.91469	0.328
27DAP/reference	0.45934	0.031
39DAP/reference	0.54791	0.02
41DAP/reference	0.46913	0.019
42DAP/reference	1.56267	0.03
43DAP/reference	2.04868	0.007
47DAP/reference	1.25653	0.055
52DAP/reference	1.08569	0.683
57DAP/reference	1.20952	0.549

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.16646	0.966
26DAP/20DAP	1.22586	0.338
34DAP/26DAP	1.26866	0.819
51DAP/34DAP	1.02745	0.946
52DAP/51DAP	1.34994	0.146
53DAP/52DAP	0.78483	0.05
55DAP/53DAP	1.07783	0.876
57DAP/55DAP	0.7855	0.178
62DAP/57DAP	1.05825	1
68DAP/62DAP	1.04851	0.769
68DAP/14DAP	0.57519	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.72408	0.036

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.06694	0.523
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.99069	1
Mature Eggplant/Ripe Tomato	1.10728

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.08071	1
1-1-2/M82	0.82713	1
12-2/M82	N/A	N/A
12-4/M82	1.37685	0.455
1-3/M82	N/A	N/A
2-1-1/M82	0.93096
2-1/M82	N/A	N/A
2-6/M82	0.81435	1
3-2/M82	0.89234	0.752
4-1-1/M82	0.71403
4-1/M82	2.09071
4-3-2/M82	1.08119	1
4-3/M82	0.86623	1
5-3/M82	0.96487	1
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	0.93231	1
9-3-2/M82	1.02044	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.48829	0.383
IL7-5/WTpooled	0.47863
IL7-3/WTpooled	0.80723	0.418
IL12-4/WTpooled	0.74574	0.71
IL1-4/WTpooled	1.06595
WT/WTpooled	1.26677	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	1.07394	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.12673	0.921
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	1.10246	1
DC3000/delta hrp 24h	1.00132	1

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.97637	0.691
DC3000 delta B/DC3000 delta AB	0.87666	0.261

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	1.04977	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.97927	1
Var 0h	0.78567	1
Var 12h I row2-row1	0.82676	0.338
Var 12h NI row2-row1	0.93227	0.546
Var 36h I row2-row1	0.96634	1
Var 36h NI row2-row1	1.04435	1
Var 60h I row2-row1	0.98339	0.952
Var 60h NI row2-row1	0.99275	1
Time course 0hI-0hNI	0.99826	1
Time course 12hI-12hNI	1.03386	0.724
Time course 36hI-36hNI	1.10722	0.056
Time course 60hI-60hNI	0.5344	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)	1.27144	0.286
transgenic ySAMdc/azygous control (breaker)	1.1154	1
transgenic ySAMdc/azygous control (red)	0.98357	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.91061	0.122

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.8677	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.03523	1
Manapal/WT (break)	1.26564	0.381
Manapal/WT (red)	1.20778	0.413