Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.4.7.17

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.09953	0.863
27DAP/17DAP	1.27242	0.766
39DAP/27DAP	0.87235	0.564
41DAP/39DAP	1.17249	0.522
42DAP/41DAP	1.20486	0.722
43DAP/42DAP	1.1077	1
47DAP/43DAP	1.02489	0.999
52DAP/47DAP	1.10687	0.828
57DAP/52DAP	0.99662	0.983

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.3791	0.207
17DAP/reference	1.36238	1
27DAP/reference	0.87766	0.304
39DAP/reference	1.68064	0.474
41DAP/reference	1.28962	0.365
42DAP/reference	5.34172	0.001
43DAP/reference	3.15773	0.006
47DAP/reference	2.36823	0.001
52DAP/reference	1.37911	0.272
57DAP/reference	2.306	0.008

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.19713	0.719
27DAP/17DAP	1.2941	0.527
39DAP/27DAP	0.82213	0.1
41DAP/39DAP	0.95856	0.893
42DAP/41DAP	1.0444	1
43DAP/42DAP	1.13468	0.112
47DAP/43DAP	0.94165	0.701
52DAP/47DAP	1.19586	0.549
57DAP/52DAP	1.57213	0.238
57DAP/7DAP	1.58554	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98248	0.613
17DAP/reference	0.91944	0.253
27DAP/reference	0.99944	0.614
39DAP/reference	0.84245	0.039
41DAP/reference	0.99846	0.646
42DAP/reference	0.88668	0.13
43DAP/reference	0.82283	0.064
47DAP/reference	3.3909	0.024
52DAP/reference	0.97957	0.523
57DAP/reference	1.01278	0.831

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91767	0.412
17DAP/reference	1.8328	0.01
27DAP/reference	2.25532	0.013
39DAP/reference	1.522	0.038
41DAP/reference	1.66598	0.005
42DAP/reference	2.92555	0.007
43DAP/reference	1.2622	0.801
47DAP/reference	2.47019	0.008
52DAP/reference	1.06201	0.596
57DAP/reference	1.28455	1

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.16146	0.347
17DAP/reference	1.27125	0.306
27DAP/reference	0.82763	0.126
39DAP/reference	1.1188	0.711
41DAP/reference	1.24525	0.333
42DAP/reference	2.41972	0.063
43DAP/reference	3.57413	0.037
47DAP/reference	1.61568	0.085
52DAP/reference	1.11029	0.851
57DAP/reference	4.12187	0.01

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.98292	1
26DAP/20DAP	1.05625	0.806
34DAP/26DAP	0.84456	0.741
51DAP/34DAP	1.35416	0.73
52DAP/51DAP	0.71395	0.151
53DAP/52DAP	1.08424	0.738
55DAP/53DAP	0.85541	0.404
57DAP/55DAP	1.23943	0.898
62DAP/57DAP	1.21045	0.767
68DAP/62DAP	1.15209	0.448
68DAP/14DAP	0.70605	0.121

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.41377	0.172

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.68222	0.058
Mature Green Tomato/Ripe Tomato	0.86066	0.079
Immature Eggplant/Mature Eggplant	0.80146	0.159
Ripe Pepper/Ripe Tomato	0.42652	0.293
Mature Eggplant/Ripe Tomato	0.51011	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.88717	0.673
1-1-2/M82	1.01029	1
12-2/M82	N/A	N/A
12-4/M82	0.96419	1
1-3/M82	1.91091
2-1-1/M82	0.90431	0.92
2-1/M82	N/A	N/A
2-6/M82	0.93062	1
3-2/M82	0.98357
4-1-1/M82	2.05601
4-1/M82	0.79024
4-3-2/M82	1.26538	1
4-3/M82	2.7381	0.268
5-3/M82	1.01304	1
6-2/M82	2.72835
6-3/M82	1.39837
7-1/M82	1.03959	1
7-2/M82	1.29789	0.324
9-3-2/M82	1.00425	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.99201	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.15455	1
IL12-4/WTpooled	1.2351	0.624
IL1-4/WTpooled	0.98493
WT/WTpooled	0.99528	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	0.84083	0.256

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.99451	1
DC3000/delta hrp 6h	0.86268	0.95
DC3000/delta hrp 12h	1.70235	1
DC3000/delta hrp 24h	0.84231	0.145

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	0.84215	1
Exp 36h	2.27394	1
Exp 60h	1.07123	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.03056	1
Var 0h	1.09465	0.936
Var 12h I row2-row1	1.07024	0.544
Var 12h NI row2-row1	1.14183	0.649
Var 36h I row2-row1	1.18505	1
Var 36h NI row2-row1	1.01712	1
Var 60h I row2-row1	0.84559	0.439
Var 60h NI row2-row1	0.9865	1
Time course 0hI-0hNI	1.05559	0.799
Time course 12hI-12hNI	0.82575	0.05
Time course 36hI-36hNI	0.886	0.144
Time course 60hI-60hNI	0.8904	0.081

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)	1.08998	0.748
transgenic ySAMdc/azygous control (breaker)	0.72062	0.142
transgenic ySAMdc/azygous control (red)	0.84406	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.20509	0.071

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.46272	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.00929	1
Manapal/WT (break)	0.99165	1
Manapal/WT (red)	0.89972	0.315