Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.4.2.13

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.21503	0.545
27DAP/17DAP	0.50795	0.032
39DAP/27DAP	0.6146	0.247
41DAP/39DAP	0.52933	0.041
42DAP/41DAP	0.62086	0.774
43DAP/42DAP	1.3995	0.501
47DAP/43DAP	0.50448	0.049
52DAP/47DAP	1.08686	0.873
57DAP/52DAP	1.10066	1

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.24017	0.139
17DAP/reference	0.97491	0.597
27DAP/reference	0.88559	0.359
39DAP/reference	0.67651	0.044
41DAP/reference	0.46075	0.01
42DAP/reference	0.56527	0.001
43DAP/reference	0.29166	0.012
47DAP/reference	0.28528	0.001
52DAP/reference	0.30315	0.012
57DAP/reference	0.39813	0.008

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.80313	0.036
27DAP/17DAP	0.79723	0.363
39DAP/27DAP	0.28912	0.028
41DAP/39DAP	1.54761	0.355
42DAP/41DAP	0.82451	0.119
43DAP/42DAP	0.40344	0.022
47DAP/43DAP	0.62176	0.008
52DAP/47DAP	0.80695	0.22
57DAP/52DAP	0.82105	0.339
57DAP/7DAP	0.21216	0.219

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.04082	0.024
17DAP/reference	1.32631	0.008
27DAP/reference	0.86349	0.146
39DAP/reference	0.86594	0.198
41DAP/reference	0.53344	0.012
42DAP/reference	0.40688	0.015
43DAP/reference	0.42886	0.011
47DAP/reference	0.34619	0.026
52DAP/reference	0.74044	0.043
57DAP/reference	0.7602	0.042

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02126	0.884
17DAP/reference	0.99132	0.536
27DAP/reference	1.24043	0.316
39DAP/reference	0.67529	0.042
41DAP/reference	0.75054	0.04
42DAP/reference	0.56304	0.013
43DAP/reference	0.32098	0.003
47DAP/reference	0.37802	0.01
52DAP/reference	0.4191	0.003
57DAP/reference	0.20506	0.002

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	4.37746	0.015
17DAP/reference	3.19486	0.111
27DAP/reference	2.95743	0.014
39DAP/reference	2.20785	0.005
41DAP/reference	1.48079	0.023
42DAP/reference	0.97094	0.671
43DAP/reference	1.12117	0.634
47DAP/reference	0.55746	0.005
52DAP/reference	0.50749	0.068
57DAP/reference	2.852	0.014

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.31094	0.966
26DAP/20DAP	0.92581	1
34DAP/26DAP	0.79416	0.18
51DAP/34DAP	0.71379	0.104
52DAP/51DAP	0.93587	1
53DAP/52DAP	0.9288	0.868
55DAP/53DAP	1.02092	0.964
57DAP/55DAP	0.81335	0.202
62DAP/57DAP	1.20522	0.303
68DAP/62DAP	1.76542	0.206
68DAP/14DAP	0.7396	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.65363	0.055

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	3.30863	0.058
Mature Green Tomato/Ripe Tomato	11.3035	0.015
Immature Eggplant/Mature Eggplant	0.46246	0.062
Ripe Pepper/Ripe Tomato	10.8604	0.256
Mature Eggplant/Ripe Tomato	41.3849	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.94945	1
12-2/M82	0.17784
12-4/M82	0.86401	1
1-3/M82	N/A	N/A
2-1-1/M82	0.44112
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	1.6752	0.395
4-1-1/M82	1.06075
4-1/M82	2.15108
4-3-2/M82	2.97442	0.241
4-3/M82	N/A	N/A
5-3/M82	3.49011	0.572
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	1.13485	0.741
7-2/M82	N/A	N/A
9-3-2/M82	1.66333	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.65466	0.358
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.24438	1
IL12-4/WTpooled	1.09028	0.646
IL1-4/WTpooled	0.90162
WT/WTpooled	0.9959	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	1.06393	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.97572	1
DC3000/delta hrp 6h	0.77509	0.915
DC3000/delta hrp 12h	1.03319	1
DC3000/delta hrp 24h	0.99311	1

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.78366	0.025
DC3000 delta B/DC3000 delta AB	0.53988	0.041

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.95408	1
Exp 36h	0.96322	0.879
Exp 60h	1.03121	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.94124	1
Var 0h	1.03866	1
Var 12h I row2-row1	0.93896	0.77
Var 12h NI row2-row1	1.04605	1
Var 36h I row2-row1	1.11413	0.908
Var 36h NI row2-row1	0.97059	0.791
Var 60h I row2-row1	1.39738	0.562
Var 60h NI row2-row1	1.05127	1
Time course 0hI-0hNI	0.93153	0.545
Time course 12hI-12hNI	0.98643	0.95
Time course 36hI-36hNI	1.06121	0.58
Time course 60hI-60hNI	0.52699	0.026

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)	1.1389	0.748
transgenic ySAMdc/azygous control (breaker)	5.42954	0.162
transgenic ySAMdc/azygous control (red)	2.02971	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.60191	0.11

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.78672	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	4.77951	0.096
Manapal/WT (break)	8.93053	0.183
Manapal/WT (red)	11.4831	0.137