Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.2.3.6

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	2.28426	0.033
27DAP/17DAP	2.41465	0.112
39DAP/27DAP	1.55294	0.217
41DAP/39DAP	0.71795	0.131
42DAP/41DAP	0.73727	0.774
43DAP/42DAP	1.25451	0.823
47DAP/43DAP	0.63942	0.11
52DAP/47DAP	0.90411	0.711
57DAP/52DAP	1.01831	0.993

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.21537	0.685
17DAP/reference	0.65536	0.097
27DAP/reference	0.79497	0.054
39DAP/reference	0.505	0.007
41DAP/reference	0.42926	0.009
42DAP/reference	1.85249	0.001
43DAP/reference	1.0193	0.82
47DAP/reference	1.34736	0.593
52DAP/reference	0.81564	0.158
57DAP/reference	1.0046

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.71741	0.036
27DAP/17DAP	1.93315	0.044
39DAP/27DAP	0.87888	0.616
41DAP/39DAP	0.99205	0.91
42DAP/41DAP	0.8891	0.451
43DAP/42DAP	1.26396	0.192
47DAP/43DAP	0.77122	0.115
52DAP/47DAP	1.20669	0.639
57DAP/52DAP	0.90512	0.545
57DAP/7DAP	1.8794	0.249

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.20797	0.213
17DAP/reference	1.30504	0.042
27DAP/reference	1.3913	0.013
39DAP/reference	2.02485	0.007
41DAP/reference	1.87705	0.057
42DAP/reference	1.77613	0.009
43DAP/reference	1.13622	0.83
47DAP/reference	1.72173	0.104
52DAP/reference	0.71351	0.021
57DAP/reference	0.76537	0.037

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.29746	0.289
17DAP/reference	1.06869	0.873
27DAP/reference	2.40826	0.037
39DAP/reference	1.30957	0.436
41DAP/reference	1.63849	0.023
42DAP/reference	1.56762	0.031
43DAP/reference	1.03788	0.581
47DAP/reference	0.73722	0.026
52DAP/reference	0.53253	0.003
57DAP/reference	0.49122	0.006

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01381	1
17DAP/reference	0.97246	0.624
27DAP/reference	1.49688	0.056
39DAP/reference	1.59908	0.006
41DAP/reference	1.51141	0.015
42DAP/reference	1.82789	0.036
43DAP/reference	2.35206	0.029
47DAP/reference	0.77743	0.103
52DAP/reference	1.03569	0.77
57DAP/reference	1.15118	0.41

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.36931	0.966
26DAP/20DAP	1.04716	0.875
34DAP/26DAP	0.97857	0.991
51DAP/34DAP	N/A	N/A
52DAP/51DAP	1.12999	0.651
53DAP/52DAP	1.06383	0.961
55DAP/53DAP	0.99857	0.908
57DAP/55DAP	1.02677	0.969
62DAP/57DAP	N/A	N/A
68DAP/62DAP	1.02832	0.977
68DAP/14DAP	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	3.16911	0.017

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.68791	0.187
Mature Green Tomato/Ripe Tomato	2.94339	0.02
Immature Eggplant/Mature Eggplant	1.5827	0.05
Ripe Pepper/Ripe Tomato	0.34724	0.224
Mature Eggplant/Ripe Tomato	0.65348	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	2.56407
12-2/M82	N/A	N/A
12-4/M82	1.33649	1
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	0.77454
2-6/M82	N/A	N/A
3-2/M82	1.27107
4-1-1/M82	N/A	N/A
4-1/M82	3.44091	0.512
4-3-2/M82	1.41627	0.284
4-3/M82	0.96945
5-3/M82	1.0678	1
6-2/M82	0.99539
6-3/M82	N/A	N/A
7-1/M82	0.27839
7-2/M82	N/A	N/A
9-3-2/M82	1.50047	0.196

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.96434	1
IL2-6/WTpooled	3.99469
IL7-5/WTpooled	0.9339	1
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	1.45838
IL1-4/WTpooled	1.18257	1
WT/WTpooled	1.74669

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	0.9957	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.04312	0.921
DC3000/delta hrp 6h	0.73645	0.81
DC3000/delta hrp 12h	1.15543	1
DC3000/delta hrp 24h	0.78317	0.094

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.91194	0.66
DC3000 delta B/DC3000 delta AB	0.93836	0.511

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.03022	1
Exp 36h	1.10948	0.693
Exp 60h	0.9755	0.855

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

hybridization	ratio	FDR (corrected p value)
self-self	0.97391	1
Var 0h	N/A	N/A
Var 12h I row2-row1	0.86458
Var 12h NI row2-row1	0.94478
Var 36h I row2-row1	0.95072	0.805
Var 36h NI row2-row1	N/A	N/A
Var 60h I row2-row1	N/A	N/A
Var 60h NI row2-row1	N/A	N/A
Time course 0hI-0hNI	0.95598	0.725
Time course 12hI-12hNI	1.00551	1
Time course 36hI-36hNI	0.85513	0.041
Time course 60hI-60hNI	0.4834	0.005

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)	1.22734	0.455
transgenic ySAMdc/azygous control (breaker)	0.80104	0.251
transgenic ySAMdc/azygous control (red)	1.01438	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.17577	0.083

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.93373	0.431

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.15355	1
Manapal/WT (break)	1.57378	0.123
Manapal/WT (red)	1.31279	0.222