Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.1.1.4

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.86279	0.339
27DAP/17DAP	0.58693	0.04
39DAP/27DAP	0.73043	0.364
41DAP/39DAP	0.79809	0.279
42DAP/41DAP	1.06285	0.954
43DAP/42DAP	1.03372	1
47DAP/43DAP	0.81813	0.449
52DAP/47DAP	0.71023	0.3
57DAP/52DAP	1.26046	0.96

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.69915	0.006
17DAP/reference	1.00898	1
27DAP/reference	0.83825	0.295
39DAP/reference	0.84869	0.114
41DAP/reference	0.68155	0.018
42DAP/reference	0.97158	0.315
43DAP/reference	0.87872	0.093
47DAP/reference	0.89433	0.065
52DAP/reference	0.84547	0.162
57DAP/reference	0.9564	0.324

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.22856	0.241
27DAP/17DAP	0.85471	0.648
39DAP/27DAP	0.46558	0.029
41DAP/39DAP	1.13808	0.579
42DAP/41DAP	1.00716	1
43DAP/42DAP	0.59726	0.022
47DAP/43DAP	0.87428	0.214
52DAP/47DAP	2.1682	0.048
57DAP/52DAP	2.37917	0.057
57DAP/7DAP	0.49994	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.24159	0.024
17DAP/reference	1.28599	0.01
27DAP/reference	0.9122	0.135
39DAP/reference	1.15881	0.601
41DAP/reference	0.7685	0.032
42DAP/reference	0.80641	0.073
43DAP/reference	0.80703	0.02
47DAP/reference	0.81445	0.079
52DAP/reference	0.83409	0.026
57DAP/reference	1.07585	0.41

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.72829	0.117
17DAP/reference	1.16767	0.471
27DAP/reference	0.82651	0.108
39DAP/reference	0.7438	0.04
41DAP/reference	0.83348	0.04
42DAP/reference	0.82407	0.055
43DAP/reference	0.51572	0.004
47DAP/reference	0.69373	0.013
52DAP/reference	0.60788	0.003
57DAP/reference	0.56544	0.004

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	3.71226	0.016
17DAP/reference	1.87771	0.045
27DAP/reference	1.18737	0.207
39DAP/reference	1.05209	0.858
41DAP/reference	0.95766	0.512
42DAP/reference	1.22041	0.214
43DAP/reference	1.55667	0.008
47DAP/reference	1.75851	0.012
52DAP/reference	1.31016	0.318
57DAP/reference	1.8923	0.011

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.1183	0.966
26DAP/20DAP	0.83048	1
34DAP/26DAP	2.25389	0.819
51DAP/34DAP	1.1857	0.901
52DAP/51DAP	2.97714	0.035
53DAP/52DAP	0.75592	0.083
55DAP/53DAP	1.47409	0.039
57DAP/55DAP	0.52425	0.027
62DAP/57DAP	1.43829	0.003
68DAP/62DAP	1.02874	0.914
68DAP/14DAP	1.18224	0.436

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.35456	0.023

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.83256	0.286
Mature Green Tomato/Ripe Tomato	4.89045	0.015
Immature Eggplant/Mature Eggplant	0.46633	0.058
Ripe Pepper/Ripe Tomato	6.50713	0.256
Mature Eggplant/Ripe Tomato	4.53198	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	1.54918	1
12-2/M82	0.56832	0.955
12-4/M82	0.42587	0.33
1-3/M82	0.80464
2-1-1/M82	0.12838
2-1/M82	0.20731	0.322
2-6/M82	8.67449	0.452
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	0.19843
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	0.59979	1
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	0.39167
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	0.77671	0.247
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.78076
IL12-4/WTpooled	0.78268	0.554
IL1-4/WTpooled	0.96442	1
WT/WTpooled	0.77075	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	1.11078	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.93275	0.642
DC3000/delta hrp 6h	0.98514	0.95
DC3000/delta hrp 12h	0.95397	1
DC3000/delta hrp 24h	1.04651	0.633

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.60432	0.025
DC3000 delta B/DC3000 delta AB	0.53942	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.98619	1
Exp 36h	0.74939	0.449
Exp 60h	0.64866	0.249

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

hybridization	ratio	FDR (corrected p value)
self-self	0.92077	1
Var 0h	0.9181	0.933
Var 12h I row2-row1	0.70021	0.39
Var 12h NI row2-row1	1.03083	1
Var 36h I row2-row1	0.93763	0.805
Var 36h NI row2-row1	1.11645	1
Var 60h I row2-row1	1.28036	0.562
Var 60h NI row2-row1	0.75183	1
Time course 0hI-0hNI	0.92164	0.522
Time course 12hI-12hNI	1.03448	0.777
Time course 36hI-36hNI	0.90571	0.144
Time course 60hI-60hNI	0.13125	0.006

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)	0.92494	0.33
transgenic ySAMdc/azygous control (breaker)	1.27567	1
transgenic ySAMdc/azygous control (red)	4.75952	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.83052	0.227

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	2.21824	0.223

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	4.13138	0.088
Manapal/WT (break)	9.51481	0.14
Manapal/WT (red)	3.37416	0.164