Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.4.5.7

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.08911	0.964
27DAP/17DAP	1.22269	0.809
39DAP/27DAP	1.30565	0.489
41DAP/39DAP	1.34717	0.288
42DAP/41DAP	1.08381	0.92
43DAP/42DAP	0.94689	0.887
47DAP/43DAP	0.87142	0.625
52DAP/47DAP	0.81548	0.539
57DAP/52DAP	0.8565	0.85

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.78104	0.111
17DAP/reference	1.35942	0.122
27DAP/reference	0.92822	0.514
39DAP/reference	1.06716	0.828
41DAP/reference	1.81435	0.014
42DAP/reference	1.28364	0.219
43DAP/reference	1.0718	0.325
47DAP/reference	1.13317	0.215
52DAP/reference	0.83962	0.158
57DAP/reference	0.7966	0.042

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.13022	0.196
27DAP/17DAP	0.99907	0.969
39DAP/27DAP	1.18451	0.343
41DAP/39DAP	0.79879	0.209
42DAP/41DAP	1.22915	0.065
43DAP/42DAP	0.97966	0.831
47DAP/43DAP	0.87883	0.1
52DAP/47DAP	0.96121	0.837
57DAP/52DAP	0.94482	0.601
57DAP/7DAP	0.9559	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84623	0.296
17DAP/reference	0.81211	0.011
27DAP/reference	0.77887	0.01
39DAP/reference	0.88754	0.015
41DAP/reference	0.81346	0.02
42DAP/reference	0.78256	0.01
43DAP/reference	0.692	0.011
47DAP/reference	0.83558	0.101
52DAP/reference	0.84552	0.027
57DAP/reference	0.74928	0.017

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.2086	0.111
17DAP/reference	1.22194	0.223
27DAP/reference	1.15508	0.345
39DAP/reference	1.1357	0.155
41DAP/reference	1.16716	0.277
42DAP/reference	1.09095	0.351
43DAP/reference	1.08609	0.89
47DAP/reference	1.23386	0.212
52DAP/reference	1.13939	0.559
57DAP/reference	1.17705	0.593

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.05801	1
17DAP/reference	0.99443	0.839
27DAP/reference	0.86245	0.067
39DAP/reference	0.92486	0.299
41DAP/reference	0.95503	0.459
42DAP/reference	0.74084	0.023
43DAP/reference	0.97157	0.523
47DAP/reference	1.09403	0.501
52DAP/reference	0.67236	0.072
57DAP/reference	0.88009	0.174

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.21377	0.966
26DAP/20DAP	0.95971	1
34DAP/26DAP	0.81398	0.479
51DAP/34DAP	1.28524	0.2
52DAP/51DAP	0.81115	1
53DAP/52DAP	1.14588	0.753
55DAP/53DAP	1.04098	0.964
57DAP/55DAP	1.23422	0.666
62DAP/57DAP	1.2468	0.902
68DAP/62DAP	0.68012	0.579
68DAP/14DAP	0.42088	0.09

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	2.07128	0.021

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.6105	0.209
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	4.45922

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.8701	0.605
1-1-2/M82	0.93045	1
12-2/M82	1.02989	1
12-4/M82	1.16819	0.438
1-3/M82	0.70341
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	1.05254	1
3-2/M82	1.27155
4-1-1/M82	1.56683	1
4-1/M82	1.18497	0.287
4-3-2/M82	1.38916
4-3/M82	N/A	N/A
5-3/M82	1.08214	1
6-2/M82	1.12599	0.253
6-3/M82	1.06176	1
7-1/M82	N/A	N/A
7-2/M82	0.96138
9-3-2/M82	1.84231

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.01165	1
IL2-6/WTpooled	1.04346	1
IL7-5/WTpooled	1.24047	0.792
IL7-3/WTpooled	0.89559	1
IL12-4/WTpooled	0.81571	0.566
IL1-4/WTpooled	0.82343	0.476
WT/WTpooled	1.0812	0.999

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	1.55031	0.309

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.9594	1
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	1.425	1
DC3000/delta hrp 24h	1.11585	0.296

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.74664
DC3000 delta B/DC3000 delta AB	1.39297	0.137

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.80401	1
Exp 36h	1.39246	0.489
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	1.01165
Var 0h	1.09523	0.98
Var 12h I row2-row1	1.00945	0.795
Var 12h NI row2-row1	1.08264	1
Var 36h I row2-row1	1.29674	0.339
Var 36h NI row2-row1	0.88196	0.61
Var 60h I row2-row1	0.79972	0.306
Var 60h NI row2-row1	0.94039	1
Time course 0hI-0hNI	0.9609	0.656
Time course 12hI-12hNI	1.06059	0.445
Time course 36hI-36hNI	1.28737	0.005
Time course 60hI-60hNI	2.02904	0.008

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)	N/A	N/A
transgenic ySAMdc/azygous control (breaker)	0.98806	1
transgenic ySAMdc/azygous control (red)	1.0638	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.85267	0.146

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.24512	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	N/A	N/A
Manapal/WT (break)	1.1024	1
Manapal/WT (red)	0.61376	0.181