Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.2.7.7

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.68611	0.067
27DAP/17DAP	0.70951	0.285
39DAP/27DAP	0.91461	0.608
41DAP/39DAP	0.81251	0.37
42DAP/41DAP	1.0111	0.997
43DAP/42DAP	0.90179	0.787
47DAP/43DAP	1.17869	0.463
52DAP/47DAP	1.01623	0.973
57DAP/52DAP	1.11755	0.946

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91755	0.293
17DAP/reference	0.6857	0.028
27DAP/reference	0.85875	0.275
39DAP/reference	0.62467	0.037
41DAP/reference	0.52878	0.016
42DAP/reference	0.92235	0.163
43DAP/reference	0.73933	0.135
47DAP/reference	0.78676	0.009
52DAP/reference	0.73619	0.131
57DAP/reference	1.02516	0.802

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.84099	0.148
27DAP/17DAP	1.33918	0.367
39DAP/27DAP	0.55222	0.032
41DAP/39DAP	0.7424	0.193
42DAP/41DAP	1.17829	0.708
43DAP/42DAP	1.13018	0.324
47DAP/43DAP	0.96363	0.846
52DAP/47DAP	0.9423	0.79
57DAP/52DAP	0.75931	0.466
57DAP/7DAP	0.47484	0.149

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.66734	0.024
17DAP/reference	1.27558	0.011
27DAP/reference	1.16831	0.16
39DAP/reference	0.82557	0.083
41DAP/reference	0.93448	0.122
42DAP/reference	1.1248	0.534
43DAP/reference	0.95248	0.385
47DAP/reference	0.85371	0.128
52DAP/reference	1.02643	1
57DAP/reference	0.96004	0.426

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.26708	0.449
17DAP/reference	1.22967	0.426
27DAP/reference	1.16984	0.497
39DAP/reference	0.75435	0.072
41DAP/reference	0.86488	0.064
42DAP/reference	0.94867	0.237
43DAP/reference	0.69656	0.021
47DAP/reference	0.62344	0.011
52DAP/reference	0.70989	0.047
57DAP/reference	0.5156	0.004

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.60609	0.025
17DAP/reference	1.49461	0.074
27DAP/reference	1.50787	0.023
39DAP/reference	1.07411	0.578
41DAP/reference	1.15424	0.502
42DAP/reference	1.06116	0.743
43DAP/reference	1.19788	0.069
47DAP/reference	0.79485	0.017
52DAP/reference	1.06451	0.888
57DAP/reference	1.24467	0.132

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.55586
26DAP/20DAP	1.29942	0.534
34DAP/26DAP	1.07717	1
51DAP/34DAP	1.53049	0.04
52DAP/51DAP	0.90567	1
53DAP/52DAP	0.90106	0.595
55DAP/53DAP	0.66205	0.025
57DAP/55DAP	0.49489	0.01
62DAP/57DAP	1.46718	0.133
68DAP/62DAP	0.86558	0.464
68DAP/14DAP	0.95518

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.37495	0.028

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.6077	0.058
Mature Green Tomato/Ripe Tomato	4.56559	0.015
Immature Eggplant/Mature Eggplant	0.2489	0.062
Ripe Pepper/Ripe Tomato	34.8419	0.233
Mature Eggplant/Ripe Tomato	26.7338	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.51404
12-2/M82	0.92277
12-4/M82	1.04116	1
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	0.82394	1
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	3.00196
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.91641	0.321
IL2-6/WTpooled	1.10023	0.46
IL7-5/WTpooled	1.23616	0.792
IL7-3/WTpooled	0.87874	0.298
IL12-4/WTpooled	1.16536	0.557
IL1-4/WTpooled	0.97973	0.834
WT/WTpooled	1.04745	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	0.88051	0.341

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.11094	0.921
DC3000/delta hrp 6h	0.83242	0.95
DC3000/delta hrp 12h	1.63595	1
DC3000/delta hrp 24h	0.34752	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.5124	0.024
DC3000 delta B/DC3000 delta AB	0.50689	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.94152	1
Exp 36h	0.66928	0.471
Exp 60h	0.50979	0.251

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00186	1
Var 0h	0.78912	0.98
Var 12h I row2-row1	0.72121	0.338
Var 12h NI row2-row1	0.91137	0.488
Var 36h I row2-row1	1.04601	1
Var 36h NI row2-row1	1.38625	0.482
Var 60h I row2-row1	0.95218	0.285
Var 60h NI row2-row1	1.09889	1
Time course 0hI-0hNI	0.96002	0.799
Time course 12hI-12hNI	0.94712	0.668
Time course 36hI-36hNI	0.74495	0.023
Time course 60hI-60hNI	0.11737	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)	0.99261	0.862
transgenic ySAMdc/azygous control (breaker)	0.67355	0.139
transgenic ySAMdc/azygous control (red)	1.69137	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.5222	0.083

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	2.73588	0.233

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	2.07785	0.09
Manapal/WT (break)	4.33263	0.183
Manapal/WT (red)	1.02922	1