Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.3.20.18

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.87256	0.511
27DAP/17DAP	0.94161	0.911
39DAP/27DAP	0.83587	0.425
41DAP/39DAP	1.18328	0.3
42DAP/41DAP	0.8963	1
43DAP/42DAP	0.88094	0.741
47DAP/43DAP	0.75716	0.228
52DAP/47DAP	1.16786	0.886
57DAP/52DAP	0.90739	0.912

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.83766	0.125
17DAP/reference	0.8476	0.046
27DAP/reference	0.78385	0.018
39DAP/reference	0.92047	0.284
41DAP/reference	0.85409	0.114
42DAP/reference	0.8707	0.005
43DAP/reference	0.97109	0.675
47DAP/reference	0.88865	0.06
52DAP/reference	1.03572	0.991
57DAP/reference	1.03874	0.511

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.03822	0.75
27DAP/17DAP	0.90977	0.097
39DAP/27DAP	0.9824	0.795
41DAP/39DAP	2.39343	0.663
42DAP/41DAP	1.22262	1
43DAP/42DAP	1.16773	1
47DAP/43DAP	0.93737	0.75
52DAP/47DAP	1.79202	0.194
57DAP/52DAP	1.55508	0.382
57DAP/7DAP	1.12527	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.85564	0.183
17DAP/reference	0.87858	0.108
27DAP/reference	0.9477	0.325
39DAP/reference	0.93192	0.307
41DAP/reference	0.97113	0.469
42DAP/reference	0.81032	0.03
43DAP/reference	0.9097	0.23
47DAP/reference	1.06592	0.854
52DAP/reference	0.92696	0.213
57DAP/reference	0.93445	0.215

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96535	0.736
17DAP/reference	0.75547	0.006
27DAP/reference	0.74375	0.039
39DAP/reference	0.96871	0.469
41DAP/reference	0.76262	0.096
42DAP/reference	0.83983	0.135
43DAP/reference	0.86009	0.191
47DAP/reference	0.88149	0.054
52DAP/reference	0.78953	0.008
57DAP/reference	0.88611	0.259

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00983	0.804
17DAP/reference	0.94119	0.452
27DAP/reference	0.98036	0.594
39DAP/reference	1.12196	0.163
41DAP/reference	0.81294	0.043
42DAP/reference	0.91594	0.445
43DAP/reference	0.89041	0.143
47DAP/reference	0.82895	0.057
52DAP/reference	0.87579	0.31
57DAP/reference	0.94673	0.468

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.08814	0.966
26DAP/20DAP	0.90725
34DAP/26DAP	1.65338	0.114
51DAP/34DAP	1.23493	0.402
52DAP/51DAP	1.09759	0.888
53DAP/52DAP	0.98378	0.824
55DAP/53DAP	1.15252	0.908
57DAP/55DAP	1.02052	0.812
62DAP/57DAP	1.08007	1
68DAP/62DAP	1.07597	1
68DAP/14DAP	0.9252	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.23516	0.212

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.57432	0.119
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.52496
Mature Eggplant/Ripe Tomato	1.00902	1

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	1.25315
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	0.92232
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	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.00316	1
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	1.52513	0.75
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	1.0713
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	0.95228

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.12468
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	0.94272	1
DC3000/delta hrp 24h	N/A	N/A

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	N/A	N/A
Exp 36h	N/A	N/A
Exp 60h	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
self-self	N/A	N/A
Var 0h	N/A	N/A
Var 12h I row2-row1	1.33154	0.58
Var 12h NI row2-row1	0.61183	1
Var 36h I row2-row1	1.04775	1
Var 36h NI row2-row1	0.23638
Var 60h I row2-row1	1.10944
Var 60h NI row2-row1	1.30197
Time course 0hI-0hNI	1.028	1
Time course 12hI-12hNI	1.44322	0.335
Time course 36hI-36hNI	1.37032	0.012
Time course 60hI-60hNI	1.29008	0.06

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)	0.99213	0.931
transgenic ySAMdc/azygous control (breaker)	1.04239	1
transgenic ySAMdc/azygous control (red)	1.00559	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.97088	0.353

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.99223	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.25222	0.096
Manapal/WT (break)	0.84882	1
Manapal/WT (red)	0.72574	0.216