Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.4.3.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.74827	0.232
27DAP/17DAP	1.03205	1
39DAP/27DAP	2.90242	0.028
41DAP/39DAP	1.02005	0.992
42DAP/41DAP	0.47489	0.259
43DAP/42DAP	1.12784	0.937
47DAP/43DAP	0.52833	0.05
52DAP/47DAP	2.9615	0.035
57DAP/52DAP	0.88155	0.86

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.19687	0.105
17DAP/reference	0.58068	0.009
27DAP/reference	0.80761	0.147
39DAP/reference	0.81803	0.188
41DAP/reference	0.68263	0.039
42DAP/reference	1.2782	0.015
43DAP/reference	1.09134	0.646
47DAP/reference	1.15228	0.199
52DAP/reference	1.84271	0.033
57DAP/reference	1.87849	0.008

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.32924	0.03
27DAP/17DAP	1.74685	0.033
39DAP/27DAP	1.13036	0.751
41DAP/39DAP	1.03089	1
42DAP/41DAP	1.36559	0.508
43DAP/42DAP	3.32727	0.013
47DAP/43DAP	0.9668	0.833
52DAP/47DAP	0.46675	0.041
57DAP/52DAP	1.23888	0.204
57DAP/7DAP	0.93602	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.66897	0.029
17DAP/reference	1.21053	0.092
27DAP/reference	1.67121	0.01
39DAP/reference	1.44285	0.01
41DAP/reference	1.45916	0.009
42DAP/reference	1.40371	0.008
43DAP/reference	1.44946	0.029
47DAP/reference	1.42966	0.033
52DAP/reference	1.57693	0.007
57DAP/reference	1.01239	0.831

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.15023	0.463
17DAP/reference	0.74743	0.02
27DAP/reference	1.42685	0.031
39DAP/reference	1.5952	0.063
41DAP/reference	1.65147	0.005
42DAP/reference	1.73368	0.008
43DAP/reference	0.83366	0.114
47DAP/reference	1.14005	0.366
52DAP/reference	0.87925	0.031
57DAP/reference	0.5959	0.014

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.2268	0.602
17DAP/reference	1.28322	0.398
27DAP/reference	1.37687	0.085
39DAP/reference	1.09751	0.211
41DAP/reference	1.22808	0.089
42DAP/reference	1.63375	0.014
43DAP/reference	2.05222	0.038
47DAP/reference	0.87661	0.259
52DAP/reference	1.2007	0.377
57DAP/reference	3.10173	0.019

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.11214	0.966
26DAP/20DAP	0.98965	1
34DAP/26DAP	1.1372	0.819
51DAP/34DAP	0.89307	0.482
52DAP/51DAP	1.24077	0.446
53DAP/52DAP	1.11577	0.688
55DAP/53DAP	1.13107	0.722
57DAP/55DAP	0.70872	0.112
62DAP/57DAP	1.21427	0.515
68DAP/62DAP	2.58075	0.088
68DAP/14DAP	2.73929	0.023

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	5.82386	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	3.25738	0.058
Mature Green Tomato/Ripe Tomato	0.33389	0.031
Immature Eggplant/Mature Eggplant	0.62546	0.063
Ripe Pepper/Ripe Tomato	0.13448	0.224
Mature Eggplant/Ripe Tomato	0.31268	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.70109
1-1-2/M82	0.65882
12-2/M82	N/A	N/A
12-4/M82	0.72659	1
1-3/M82	5.59939	0.248
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	0.89112
3-2/M82	1.6585
4-1-1/M82	1.35386
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	0.57445
5-3/M82	2.51248	1
6-2/M82	5.81149	0.214
6-3/M82	4.28386
7-1/M82	N/A	N/A
7-2/M82	6.90273
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.94088	1
IL2-6/WTpooled	1.6261	0.46
IL7-5/WTpooled	1.34868	1
IL7-3/WTpooled	1.66644	0.362
IL12-4/WTpooled	1.03571	1
IL1-4/WTpooled	1.2674	0.426
WT/WTpooled	0.94378	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	0.93281	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.0451	0.921
DC3000/delta hrp 6h	0.82416	0.95
DC3000/delta hrp 12h	1.0462	1
DC3000/delta hrp 24h	0.46804	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.14301	0.094
DC3000 delta B/DC3000 delta AB	1.29829	0.243

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	0.82813	0.699
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	1.03845	1
Var 0h	0.82349	1
Var 12h I row2-row1	1.02157	0.795
Var 12h NI row2-row1	1.34748	0.649
Var 36h I row2-row1	1.1351	1
Var 36h NI row2-row1	1.27404	1
Var 60h I row2-row1	1.08386
Var 60h NI row2-row1	1.02144	1
Time course 0hI-0hNI	0.94219	0.54
Time course 12hI-12hNI	0.96852	0.782
Time course 36hI-36hNI	0.84502	0.06
Time course 60hI-60hNI	0.95608	0.646

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)	0.94114	0.567
transgenic ySAMdc/azygous control (breaker)	0.41458	0.118
transgenic ySAMdc/azygous control (red)	1.32393	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.7878	0.099

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.97087	0.789

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	2.87863	0.087
Manapal/WT (break)	2.1469	0.381
Manapal/WT (red)	4.83892	0.126