Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.3.20.9

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.70978	0.087
27DAP/17DAP	0.99699	0.967
39DAP/27DAP	0.95177	0.67
41DAP/39DAP	1.52523	0.334
42DAP/41DAP	0.67373	0.397
43DAP/42DAP	1.00311	0.937
47DAP/43DAP	0.73831	0.26
52DAP/47DAP	1.18368	0.707
57DAP/52DAP	0.95328	0.938

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91224	0.344
17DAP/reference	0.99696	0.904
27DAP/reference	1.03185	0.623
39DAP/reference	1.21532	0.083
41DAP/reference	1.12612	0.421
42DAP/reference	0.91694	0.062
43DAP/reference	1.00705	0.904
47DAP/reference	0.95512	0.258
52DAP/reference	1.09706	0.912
57DAP/reference	1.01406	0.805

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.04858	0.812
27DAP/17DAP	0.84457	0.446
39DAP/27DAP	0.99455	0.984
41DAP/39DAP	0.97527	0.968
42DAP/41DAP	1.1973	0.773
43DAP/42DAP	1.01101	1
47DAP/43DAP	0.98442	0.911
52DAP/47DAP	1.04358	0.925
57DAP/52DAP	0.90838	0.48
57DAP/7DAP	1.11867	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.85224	0.122
17DAP/reference	0.96164	0.295
27DAP/reference	1.08845	0.551
39DAP/reference	0.71446	0.018
41DAP/reference	0.85439	0.103
42DAP/reference	0.75948	0.016
43DAP/reference	0.93608	0.23
47DAP/reference	0.84708	0.128
52DAP/reference	0.86026	0.046
57DAP/reference	1.05264	0.907

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97475	0.706
17DAP/reference	0.89419	0.139
27DAP/reference	0.94648	0.393
39DAP/reference	0.87988	0.144
41DAP/reference	0.80777	0.028
42DAP/reference	0.89512	0.189
43DAP/reference	1.37709	0.173
47DAP/reference	1.0633	0.133
52DAP/reference	1.0718	0.471
57DAP/reference	1.13978	0.345

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.77094	0.038
17DAP/reference	1.02542	0.932
27DAP/reference	1.15193	0.027
39DAP/reference	1.02255	0.773
41DAP/reference	0.95066	0.512
42DAP/reference	0.91443	0.087
43DAP/reference	0.91999	0.348
47DAP/reference	1.06425	0.355
52DAP/reference	1.18109	0.186
57DAP/reference	1.20958	0.47

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.05053	1
26DAP/20DAP	0.96261	1
34DAP/26DAP	0.99545	0.988
51DAP/34DAP	1.10644	0.883
52DAP/51DAP	0.94185	1
53DAP/52DAP	0.91332	0.712
55DAP/53DAP	1.12655	0.653
57DAP/55DAP	0.81164	0.202
62DAP/57DAP	0.99375	0.994
68DAP/62DAP	1.27346	0.582
68DAP/14DAP	0.9881	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.1364	0.908

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	2.47166	0.034
Immature Eggplant/Mature Eggplant	0.53201
Ripe Pepper/Ripe Tomato	1.4006
Mature Eggplant/Ripe Tomato	2.35531

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.94348	0.907
1-1-2/M82	0.98963	1
12-2/M82	1.08981
12-4/M82	1.14819	1
1-3/M82	0.98192
2-1-1/M82	0.71027
2-1/M82	N/A	N/A
2-6/M82	0.99107
3-2/M82	1.08266	0.967
4-1-1/M82	1.17848
4-1/M82	N/A	N/A
4-3-2/M82	0.66369
4-3/M82	0.77273	0.611
5-3/M82	0.99176	1
6-2/M82	0.78145
6-3/M82	1.08789	1
7-1/M82	1.06409
7-2/M82	0.81037	0.796
9-3-2/M82	0.80272	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.94664	0.247
IL2-6/WTpooled	0.86431	0.473
IL7-5/WTpooled	1.51681	0.495
IL7-3/WTpooled	0.94027	0.418
IL12-4/WTpooled	1.04882	0.839
IL1-4/WTpooled	1.20831	1
WT/WTpooled	0.90552	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	0.97651	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.27292	0.538
DC3000/delta hrp 6h	0.95317
DC3000/delta hrp 12h	1.34726	1
DC3000/delta hrp 24h	1.03674	0.779

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	0.97085	1
Exp 36h	0.94802	0.943
Exp 60h	1.00974	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.005	1
Var 0h	N/A	N/A
Var 12h I row2-row1	1.13292	0.201
Var 12h NI row2-row1	0.89208	0.466
Var 36h I row2-row1	1.00766	1
Var 36h NI row2-row1	1.29597	0.253
Var 60h I row2-row1	1.13342	0.347
Var 60h NI row2-row1	0.96861	1
Time course 0hI-0hNI	0.87625	0.414
Time course 12hI-12hNI	1.1266	0.684
Time course 36hI-36hNI	0.96745	0.476
Time course 60hI-60hNI	0.99583	1

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)	1.0575	0.482
transgenic ySAMdc/azygous control (breaker)	1.1113	1
transgenic ySAMdc/azygous control (red)	1.09285	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.97642	0.383

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.9526	0.284

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.71282	1
Manapal/WT (break)	0.89206	1
Manapal/WT (red)	0.80055	0.199