Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.3.7.5

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.78142	0.219
27DAP/17DAP	0.81264	0.473
39DAP/27DAP	1.17082	0.782
41DAP/39DAP	0.71217	0.087
42DAP/41DAP	1.3199	0.931
43DAP/42DAP	1.03191	1
47DAP/43DAP	0.81652	0.444
52DAP/47DAP	0.93369	0.742
57DAP/52DAP	1.106	0.902

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91258	0.284
17DAP/reference	0.94082	0.567
27DAP/reference	1.57494	0.093
39DAP/reference	1.02439	0.842
41DAP/reference	0.85928	0.154
42DAP/reference	0.91856	0.169
43DAP/reference	0.86044	0.211
47DAP/reference	1.17759	0.009
52DAP/reference	1.66716	0.007
57DAP/reference	1.20677	0.021

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	2.20358	0.036
27DAP/17DAP	1.16427	0.859
39DAP/27DAP	0.98248	0.844
41DAP/39DAP	0.81499	0.372
42DAP/41DAP	1.07818	0.991
43DAP/42DAP	0.64611	0.027
47DAP/43DAP	0.98838	0.93
52DAP/47DAP	1.25956	0.455
57DAP/52DAP	1.2932	0.293
57DAP/7DAP	0.83417	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92221	0.224
17DAP/reference	1.32713	0.022
27DAP/reference	1.48868	0.014
39DAP/reference	1.39823	0.024
41DAP/reference	1.3478	0.013
42DAP/reference	1.26127	0.076
43DAP/reference	1.39081	0.008
47DAP/reference	1.3752	0.142
52DAP/reference	1.60265	0.008
57DAP/reference	1.72718	0.022

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.61377	0.027
17DAP/reference	0.89838	0.269
27DAP/reference	1.60696	0.073
39DAP/reference	2.1651	0.011
41DAP/reference	1.91321	0.018
42DAP/reference	1.15467	0.157
43DAP/reference	1.12078	1
47DAP/reference	1.00133	0.714
52DAP/reference	1.46837	0.085
57DAP/reference	0.86321	0.194

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.24858	0.081
17DAP/reference	1.10547	0.496
27DAP/reference	1.34667	0.025
39DAP/reference	1.28461	0.019
41DAP/reference	1.19388	0.031
42DAP/reference	1.38371	0.032
43DAP/reference	1.82753	0.011
47DAP/reference	1.50992	0.155
52DAP/reference	1.63764	0.033
57DAP/reference	3.09544	0.006

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.55972
26DAP/20DAP	1.96372	0.173
34DAP/26DAP	0.97965	0.988
51DAP/34DAP	1.52846	0.352
52DAP/51DAP	1.3111	0.053
53DAP/52DAP	1.07273	0.697
55DAP/53DAP	0.83839	0.544
57DAP/55DAP	0.61084	0.088
62DAP/57DAP	0.69763	0.28
68DAP/62DAP	4.45811	0.013
68DAP/14DAP	2.91211

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.21882	0.415

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	6.11456	0.058
Mature Green Tomato/Ripe Tomato	1.91749	0.209
Immature Eggplant/Mature Eggplant	0.49342	0.057
Ripe Pepper/Ripe Tomato	0.65847	0.293
Mature Eggplant/Ripe Tomato	1.07398	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	1.42803
12-2/M82	N/A	N/A
12-4/M82	1.13859	1
1-3/M82	3.07611
2-1-1/M82	0.70403
2-1/M82	N/A	N/A
2-6/M82	1.03473	1
3-2/M82	N/A	N/A
4-1-1/M82	0.84723
4-1/M82	2.2923	0.444
4-3-2/M82	1.14938	1
4-3/M82	0.76029	1
5-3/M82	1.52023	0.572
6-2/M82	1.18529
6-3/M82	1.18089	1
7-1/M82	0.80602
7-2/M82	1.75654	0.385
9-3-2/M82	1.27417	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	N/A	N/A
IL12-4/WTpooled	0.77234
IL1-4/WTpooled	0.64364
WT/WTpooled	N/A	N/A

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	1.15473	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.9869	1
DC3000/delta hrp 6h	0.99866	0.95
DC3000/delta hrp 12h	1.01634	1
DC3000/delta hrp 24h	0.4204	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.58394	0.023
DC3000 delta B/DC3000 delta AB	0.63595	0.024

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	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	0.99074	1
Var 0h	0.96009	0.933
Var 12h I row2-row1	0.8573	0.353
Var 12h NI row2-row1	0.91915	0.627
Var 36h I row2-row1	1.17256	0.908
Var 36h NI row2-row1	1.29796	1
Var 60h I row2-row1	0.94259	0.832
Var 60h NI row2-row1	1.0556	1
Time course 0hI-0hNI	0.90313	0.272
Time course 12hI-12hNI	1.02253	1
Time course 36hI-36hNI	0.9174	0.269
Time course 60hI-60hNI	0.16805	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)	1.04797	0.748
transgenic ySAMdc/azygous control (breaker)	0.70084	0.173
transgenic ySAMdc/azygous control (red)	1.17593	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.62651	0.448

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.4593	0.239

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	2.24952	0.083
Manapal/WT (break)	3.4603	0.13
Manapal/WT (red)	0.87488	0.607