Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.3.18.16

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.12931	0.893
27DAP/17DAP	1.26557	0.761
39DAP/27DAP	0.78158	0.495
41DAP/39DAP	0.90555	0.574
42DAP/41DAP	1.52522	0.1
43DAP/42DAP	1.02042	1
47DAP/43DAP	1.40527	0.618
52DAP/47DAP	0.92633	0.63
57DAP/52DAP	1.12479	0.98

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.78387	0.043
17DAP/reference	0.83873	0.01
27DAP/reference	1.00269	1
39DAP/reference	0.84666	0.072
41DAP/reference	0.81234	0.01
42DAP/reference	0.91602	0.02
43DAP/reference	0.89387	0.031
47DAP/reference	1.03756	0.989
52DAP/reference	1.05118	0.453
57DAP/reference	1.34612	0.009

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.87549	0.34
27DAP/17DAP	1.05988	1
39DAP/27DAP	0.81472	0.502
41DAP/39DAP	1.19135	0.921
42DAP/41DAP	1.1823	0.773
43DAP/42DAP	1.16536	0.699
47DAP/43DAP	1.12841	0.88
52DAP/47DAP	1.01505	0.979
57DAP/52DAP	0.75285	0.239
57DAP/7DAP	1.23426	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.30091	0.132
17DAP/reference	1.39512	0.026
27DAP/reference	1.35753	0.014
39DAP/reference	1.49649	0.012
41DAP/reference	1.55369	0.017
42DAP/reference	1.73427	0.006
43DAP/reference	1.29143	0.2
47DAP/reference	1.37445	0.145
52DAP/reference	1.44543	0.008
57DAP/reference	1.46967	0.007

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.89349	0.257
17DAP/reference	0.80344	0.045
27DAP/reference	0.88012	0.15
39DAP/reference	0.9456	0.235
41DAP/reference	0.96047	0.284
42DAP/reference	0.86946	0.089
43DAP/reference	0.878	0.196
47DAP/reference	0.80386	0.013
52DAP/reference	0.89279	0.013
57DAP/reference	0.78414	0.01

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.2533	0.058
17DAP/reference	1.16997	0.456
27DAP/reference	1.56724	0.022
39DAP/reference	1.37852	0.038
41DAP/reference	1.36869	0.016
42DAP/reference	1.30408	0.065
43DAP/reference	1.12702	0.828
47DAP/reference	0.969	0.409
52DAP/reference	1.30521	0.335
57DAP/reference	1.13034	0.086

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.9873	1
26DAP/20DAP	0.99047	1
34DAP/26DAP	0.9035	0.861
51DAP/34DAP	0.84871	0.737
52DAP/51DAP	1.19248	0.446
53DAP/52DAP	1.01293	0.776
55DAP/53DAP	1.08143	0.908
57DAP/55DAP	0.66059	0.081
62DAP/57DAP	1.30245	0.217
68DAP/62DAP	1.96424	0.019
68DAP/14DAP	1.43434	0.419

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.56582	0.03

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.19078
Mature Green Tomato/Ripe Tomato	0.66376	0.072
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	1.66193	0.258
Mature Eggplant/Ripe Tomato	0.99152

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	1.28774
12-2/M82	N/A	N/A
12-4/M82	1.13986	1
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	1.22762	0.967
4-1-1/M82	N/A	N/A
4-1/M82	1.00564
4-3-2/M82	0.77882	0.698
4-3/M82	0.93057
5-3/M82	1.06195
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	0.88253
7-2/M82	N/A	N/A
9-3-2/M82	1.06065	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.86155	1
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	0.8419	0.422
WT/WTpooled	0.71865

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	0.82532	0.341

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.17723	0.921
DC3000/delta hrp 6h	0.94465	0.95
DC3000/delta hrp 12h	1.05065	1
DC3000/delta hrp 24h	0.69789	0.05

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	0.88922	1
Exp 36h	1.13648	0.879
Exp 60h	0.68877	0.343

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

hybridization	ratio	FDR (corrected p value)
self-self	0.96029	1
Var 0h	1.01083	0.98
Var 12h I row2-row1	1.06695	0.692
Var 12h NI row2-row1	1.04549	1
Var 36h I row2-row1	1.32827	1
Var 36h NI row2-row1	0.93506	0.791
Var 60h I row2-row1	0.92677	0.952
Var 60h NI row2-row1	1.29179	1
Time course 0hI-0hNI	0.9879	0.911
Time course 12hI-12hNI	0.99467	0.964
Time course 36hI-36hNI	0.97519	0.484
Time course 60hI-60hNI	0.44893	0.047

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)	1.19121	0.325
transgenic ySAMdc/azygous control (breaker)	1.03723	1
transgenic ySAMdc/azygous control (red)	0.96211	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.99909	0.886

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.85637	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.11405	1
Manapal/WT (break)	1.20034	1
Manapal/WT (red)	0.6556	0.184