Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.4.19.21

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.30232	0.602
27DAP/17DAP	1.3284	0.877
39DAP/27DAP	1.14877	0.944
41DAP/39DAP	0.90732	0.678
42DAP/41DAP	1.04911	1
43DAP/42DAP	0.97377	0.912
47DAP/43DAP	1.35829	0.746
52DAP/47DAP	1.21882	0.95
57DAP/52DAP	1.04437	0.993

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.44057	0.013
17DAP/reference	0.90515	0.224
27DAP/reference	0.94326	0.385
39DAP/reference	1.0278	1
41DAP/reference	0.85457	0.114
42DAP/reference	1.36977	0.001
43DAP/reference	1.09584	0.152
47DAP/reference	1.62467	0.001
52DAP/reference	1.70925	0.016
57DAP/reference	1.86922	0.008

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.918	0.323
27DAP/17DAP	1.04806	0.863
39DAP/27DAP	1.0768	0.526
41DAP/39DAP	1.1569	0.276
42DAP/41DAP	0.97608	0.768
43DAP/42DAP	1.03252	0.699
47DAP/43DAP	1.01674	0.926
52DAP/47DAP	1.01604	1
57DAP/52DAP	1.09228	0.783
57DAP/7DAP	1.34922	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.06352	1
17DAP/reference	0.96096	0.447
27DAP/reference	1.0048	0.656
39DAP/reference	1.22076	0.044
41DAP/reference	1.01889	0.848
42DAP/reference	1.06672	0.889
43DAP/reference	1.05391	0.923
47DAP/reference	1.2003	0.43
52DAP/reference	1.02786	1
57DAP/reference	0.9012	0.162

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.21215	0.164
17DAP/reference	1.1982	0.098
27DAP/reference	1.2081	0.225
39DAP/reference	1.12241	0.233
41DAP/reference	0.96824	0.348
42DAP/reference	1.18415	0.089
43DAP/reference	0.84243	0.135
47DAP/reference	1.24246	0.059
52DAP/reference	0.71568	0.003
57DAP/reference	0.93625	0.338

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.86673	0.098
17DAP/reference	1.07524	0.87
27DAP/reference	0.7919	0.133
39DAP/reference	1.02649	0.935
41DAP/reference	0.84656	0.107
42DAP/reference	1.06607	0.789
43DAP/reference	1.01522	0.66
47DAP/reference	0.88246	0.12
52DAP/reference	1.1403	0.614
57DAP/reference	2.25837	0.016

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.12533	0.966
26DAP/20DAP	0.82208	0.317
34DAP/26DAP	0.9497	0.874
51DAP/34DAP	1.00008	0.967
52DAP/51DAP	1.09667	0.626
53DAP/52DAP	0.99409	0.902
55DAP/53DAP	1.17224	0.434
57DAP/55DAP	1.01932	0.986
62DAP/57DAP	0.78445	0.088
68DAP/62DAP	0.80435	0.263
68DAP/14DAP	1.16663	0.826

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.36973	0.015

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.88089	0.384
Mature Green Tomato/Ripe Tomato	N/A	N/A
Immature Eggplant/Mature Eggplant	1.43997	0.05
Ripe Pepper/Ripe Tomato	1.5846	1
Mature Eggplant/Ripe Tomato	1.68033

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	N/A	N/A
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	N/A	N/A
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.12501	1
IL2-6/WTpooled	0.98605	1
IL7-5/WTpooled	0.63397	1
IL7-3/WTpooled	1.21527	1
IL12-4/WTpooled	0.92029	0.71
IL1-4/WTpooled	1.10641	1
WT/WTpooled	0.87085	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	0.98735	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	N/A	N/A
DC3000/delta hrp 6h	0.90876	0.95
DC3000/delta hrp 12h	0.90986	1
DC3000/delta hrp 24h	2.79426

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.44208	0.16
DC3000 delta B/DC3000 delta AB	1.12011	0.381

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.92939	1
Exp 36h	1.00208	1
Exp 60h	1.18645	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00063	1
Var 0h	1.12009	0.594
Var 12h I row2-row1	1.0682	0.379
Var 12h NI row2-row1	0.85718	0.546
Var 36h I row2-row1	0.9997	1
Var 36h NI row2-row1	0.93405	0.743
Var 60h I row2-row1	0.83832	0.293
Var 60h NI row2-row1	1.18965	0.904
Time course 0hI-0hNI	1.01185	1
Time course 12hI-12hNI	0.96674	0.761
Time course 36hI-36hNI	1.09777	0.07
Time course 60hI-60hNI	1.97738	0.01

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)	1.0452	0.286
transgenic ySAMdc/azygous control (breaker)	0.94055	1
transgenic ySAMdc/azygous control (red)	1.07925	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.14893	0.155

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.87329	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.90855	1
Manapal/WT (break)	1.16666	0.183
Manapal/WT (red)	N/A	N/A