Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.2.9.2

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.66435	0.291
27DAP/17DAP	1.16735	0.836
39DAP/27DAP	1.5943	0.249
41DAP/39DAP	0.76263	0.218
42DAP/41DAP	1.15814	0.994
43DAP/42DAP	1.28457	0.84
47DAP/43DAP	1.1531	0.647
52DAP/47DAP	1.06594	0.957
57DAP/52DAP	1.91449	0.886

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.79074	0.101
17DAP/reference	1.2372	0.33
27DAP/reference	1.88952	0.023
39DAP/reference	1.47412	0.067
41DAP/reference	1.34118	0.058
42DAP/reference	1.67498	0.001
43DAP/reference	1.92129	0.007
47DAP/reference	3.25575	0.001
52DAP/reference	3.48686	0.007
57DAP/reference	3.61565	0.008

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.26745	0.038
27DAP/17DAP	1.12411	0.65
39DAP/27DAP	1.14063	0.441
41DAP/39DAP	1.46116	1
42DAP/41DAP	1.26022	0.143
43DAP/42DAP	1.02839	0.788
47DAP/43DAP	1.01618	0.963
52DAP/47DAP	0.99266	0.93
57DAP/52DAP	1.14426	0.411
57DAP/7DAP	1.58644	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.18044	0.201
17DAP/reference	1.15874	0.092
27DAP/reference	1.29093	0.026
39DAP/reference	1.6571	0.005
41DAP/reference	1.08677	0.745
42DAP/reference	1.12038	0.174
43DAP/reference	1.35358	0.019
47DAP/reference	2.14555	0.014
52DAP/reference	1.40853	0.081
57DAP/reference	1.78544	0.008

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.60327	0.006
17DAP/reference	1.00751	0.83
27DAP/reference	1.28214	0.056
39DAP/reference	1.30439	0.019
41DAP/reference	1.14524	0.177
42DAP/reference	1.31286	0.012
43DAP/reference	1.04004	0.748
47DAP/reference	1.6968	0.008
52DAP/reference	1.03164	0.838
57DAP/reference	1.03126	0.789

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.76749	0.034
17DAP/reference	0.75084	0.136
27DAP/reference	1.21919	0.028
39DAP/reference	1.21135	0.045
41DAP/reference	1.13183	0.039
42DAP/reference	1.53998	0.011
43DAP/reference	1.64448	0.007
47DAP/reference	1.78497	0.023
52DAP/reference	2.21385	0.027
57DAP/reference	5.11367	0.006

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.95807	1
26DAP/20DAP	2.24318	0.097
34DAP/26DAP	0.90307	0.642
51DAP/34DAP	0.80113	0.112
52DAP/51DAP	0.66602	0.151
53DAP/52DAP	1.22269	0.089
55DAP/53DAP	0.68478	0.031
57DAP/55DAP	1.08976	0.997
62DAP/57DAP	1.13627	0.902
68DAP/62DAP	1.1651	0.912
68DAP/14DAP	1.12157	0.889

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	2.11964	0.02

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.05494	0.666
Mature Green Tomato/Ripe Tomato	0.9234	0.715
Immature Eggplant/Mature Eggplant	1.60123	0.05
Ripe Pepper/Ripe Tomato	0.4576	0.224
Mature Eggplant/Ripe Tomato	0.41158	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.96998	0.961
1-1-2/M82	1.23272	0.977
12-2/M82	0.94926
12-4/M82	1.0964	1
1-3/M82	1.85141	0.248
2-1-1/M82	1.09354	1
2-1/M82	0.80055	0.325
2-6/M82	0.84364	1
3-2/M82	1.16406	0.967
4-1-1/M82	1.0296	1
4-1/M82	1.42282	1
4-3-2/M82	1.00597	1
4-3/M82	0.94902	1
5-3/M82	1.08578	1
6-2/M82	1.10065	1
6-3/M82	1.02262	1
7-1/M82	1.08048	1
7-2/M82	1.22465	0.385
9-3-2/M82	1.05136	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.9195
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	N/A	N/A
WT/WTpooled	1.14738	0.874

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	1.16262	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.0317	0.921
DC3000/delta hrp 6h	0.91859	0.95
DC3000/delta hrp 12h	0.92653	1
DC3000/delta hrp 24h	0.94531	0.654

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.2563	0.043
DC3000 delta B/DC3000 delta AB	1.37213	0.085

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.28024	0.254
Exp 36h	1.29705	1
Exp 60h	1.46031	0.227

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00654	1
Var 0h	0.53602	1
Var 12h I row2-row1	0.89953	0.418
Var 12h NI row2-row1	1.10498	1
Var 36h I row2-row1	1.1817	0.908
Var 36h NI row2-row1	0.91028	0.61
Var 60h I row2-row1	0.79349	0.306
Var 60h NI row2-row1	0.89438	0.932
Time course 0hI-0hNI	1.1508	0.574
Time course 12hI-12hNI	0.98125	0.889
Time course 36hI-36hNI	1.4	0.008
Time course 60hI-60hNI	2.35821	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)	1.07843	0.571
transgenic ySAMdc/azygous control (breaker)	1.08255	0.178
transgenic ySAMdc/azygous control (red)	0.90491	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.56785	0.069

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.72178	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.95309	1
Manapal/WT (break)	0.93613	1
Manapal/WT (red)	0.95252	0.607