Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.1.19.5

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.08874	0.798
27DAP/17DAP	0.85377	0.604
39DAP/27DAP	1.22913	0.755
41DAP/39DAP	0.77637	0.238
42DAP/41DAP	0.96763	1
43DAP/42DAP	1.07469	0.985
47DAP/43DAP	1.0643	0.733
52DAP/47DAP	0.85415	0.637
57DAP/52DAP	1.02245	0.983

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.4121	0.009
17DAP/reference	1.3714	0.028
27DAP/reference	1.2081	0.2
39DAP/reference	1.20096	0.062
41DAP/reference	1.86368	0.016
42DAP/reference	1.24539	0.003
43DAP/reference	1.31851	0.078
47DAP/reference	1.29438	0.002
52DAP/reference	1.25045	0.025
57DAP/reference	0.96378	0.456

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.3789	0.067
27DAP/17DAP	0.87843	0.537
39DAP/27DAP	0.8306	0.269
41DAP/39DAP	1.09517	0.997
42DAP/41DAP	1.43836	0.021
43DAP/42DAP	0.84551	0.149
47DAP/43DAP	0.83597	0.243
52DAP/47DAP	2.05572	0.048
57DAP/52DAP	2.08535	0.05
57DAP/7DAP	1.41974	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.43672	0.026
17DAP/reference	1.7029	0.015
27DAP/reference	1.62677	0.012
39DAP/reference	1.68706	0.007
41DAP/reference	1.63724	0.011
42DAP/reference	1.50162	0.132
43DAP/reference	1.37616	0.015
47DAP/reference	1.12479	0.421
52DAP/reference	1.61979	0.014
57DAP/reference	1.47587	0.022

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.36177	0.055
17DAP/reference	1.58327	0.009
27DAP/reference	1.34665	0.029
39DAP/reference	1.3428	0.033
41DAP/reference	1.30601	0.012
42DAP/reference	1.4472	0.01
43DAP/reference	1.50905	0.064
47DAP/reference	1.2126	0.009
52DAP/reference	1.61679	0.006
57DAP/reference	1.48596	0.052

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.36909	0.074
17DAP/reference	1.30004	0.209
27DAP/reference	1.15213	0.164
39DAP/reference	1.2329	0.015
41DAP/reference	1.40841	0.014
42DAP/reference	1.56379	0.226
43DAP/reference	1.19056	0.439
47DAP/reference	1.41546	0.115
52DAP/reference	1.55297	0.048
57DAP/reference	1.07737	0.593

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.2474	0.966
26DAP/20DAP	2.19354	0.855
34DAP/26DAP	4.35675	1
51DAP/34DAP	2.40115	0.829
52DAP/51DAP	5.07217	0.033
53DAP/52DAP	0.68646	0.051
55DAP/53DAP	1.59142	0.046
57DAP/55DAP	0.596	0.066
62DAP/57DAP	1.59555	0.024
68DAP/62DAP	1.63747	0.869
68DAP/14DAP	0.61591	0.121

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.1695	0.019

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.40333
Mature Green Tomato/Ripe Tomato	1.83975	0.064
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.04615
Mature Eggplant/Ripe Tomato	0.2994	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.8177	0.708
1-1-2/M82	1.19606	1
12-2/M82	0.88631	0.727
12-4/M82	0.84217	0.619
1-3/M82	1.20264	1
2-1-1/M82	1.01987	1
2-1/M82	0.91452	0.318
2-6/M82	1.18528	0.339
3-2/M82	0.82541
4-1-1/M82	1.51033	0.876
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	1.1565	1
5-3/M82	1.05241	1
6-2/M82	0.74107
6-3/M82	0.98552	1
7-1/M82	1.11776	0.539
7-2/M82	1.11359	1
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.79264	0.243
IL2-6/WTpooled	1.1709	0.531
IL7-5/WTpooled	0.95616	1
IL7-3/WTpooled	0.95343	1
IL12-4/WTpooled	1.00221	1
IL1-4/WTpooled	0.95229	1
WT/WTpooled	1.0022	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	0.86535	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.9829	1
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	1.17488	1
DC3000/delta hrp 24h	1.72431	0.051

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.9263	0.538
DC3000 delta B/DC3000 delta AB	0.77225	0.044

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	N/A	N/A
Exp 60h	0.80559	0.32

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

hybridization	ratio	FDR (corrected p value)
self-self	1.0103	1
Var 0h	1.11164	1
Var 12h I row2-row1	0.72363	0.418
Var 12h NI row2-row1	1.06314	1
Var 36h I row2-row1	1.13618	1
Var 36h NI row2-row1	1.45864	0.253
Var 60h I row2-row1	0.87081	0.582
Var 60h NI row2-row1	0.9967	1
Time course 0hI-0hNI	0.82784	0.202
Time course 12hI-12hNI	1.09959	0.867
Time course 36hI-36hNI	0.89961	0.28
Time course 60hI-60hNI	0.58824	0.006

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)	1.13781	0.798
transgenic ySAMdc/azygous control (breaker)	0.80626	0.49
transgenic ySAMdc/azygous control (red)	0.91007	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.91325	0.046

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.21206	0.231

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)	N/A	N/A
Manapal/WT (red)	1.29189	0.137