Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.1.3.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.89436	0.475
27DAP/17DAP	0.87987	0.704
39DAP/27DAP	1.48921	0.181
41DAP/39DAP	1.05333	1
42DAP/41DAP	1.15781	0.945
43DAP/42DAP	1.12571	0.94
47DAP/43DAP	0.92216	0.724
52DAP/47DAP	0.75579	0.425
57DAP/52DAP	1.13353	0.912

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92554	0.344
17DAP/reference	0.99066	0.701
27DAP/reference	1.56864	0.02
39DAP/reference	1.12745	0.615
41DAP/reference	1.0112	0.814
42DAP/reference	1.16494	0.05
43DAP/reference	1.26809	0.009
47DAP/reference	1.43258	0.001
52DAP/reference	0.99983	0.73
57DAP/reference	1.14704	0.019

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.11449	0.699
27DAP/17DAP	0.83553	0.446
39DAP/27DAP	1.08973	0.672
41DAP/39DAP	0.88819	0.333
42DAP/41DAP	1.023	0.884
43DAP/42DAP	0.87885	0.336
47DAP/43DAP	1.06574	0.892
52DAP/47DAP	1.19957	0.463
57DAP/52DAP	0.86047	0.428
57DAP/7DAP	0.73973	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.19741	0.147
17DAP/reference	0.94623	0.295
27DAP/reference	0.89038	0.171
39DAP/reference	1.19905	0.252
41DAP/reference	1.10449	0.836
42DAP/reference	1.09258	0.405
43DAP/reference	0.99107	0.58
47DAP/reference	1.36443	0.06
52DAP/reference	1.15111	0.081
57DAP/reference	1.26298	0.049

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.83077	0.157
17DAP/reference	1.05443	0.999
27DAP/reference	1.13977	0.292
39DAP/reference	1.36103	0.034
41DAP/reference	1.22118	0.03
42DAP/reference	1.3371	0.01
43DAP/reference	0.9812	0.494
47DAP/reference	1.56598	0.008
52DAP/reference	1.15051	0.181
57DAP/reference	1.0504	0.874

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.13204	0.109
17DAP/reference	1.21641	0.62
27DAP/reference	1.09473	0.227
39DAP/reference	1.12705	0.422
41DAP/reference	1.21697	0.115
42DAP/reference	1.31995	0.097
43DAP/reference	1.51423	0.059
47DAP/reference	1.21623	0.133
52DAP/reference	1.16892	0.631
57DAP/reference	1.79835	0.013

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.09726	0.966
26DAP/20DAP	0.72712	0.317
34DAP/26DAP	0.93761	0.945
51DAP/34DAP	0.95565	0.747
52DAP/51DAP	0.8925	1
53DAP/52DAP	1.14726	0.723
55DAP/53DAP	1.42563	0.722
57DAP/55DAP	0.98592	0.754
62DAP/57DAP	3.62546	0.678
68DAP/62DAP	1.12692	0.977
68DAP/14DAP	1.01833	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.14365	0.7

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.80625	0.261
Mature Green Tomato/Ripe Tomato	1.47738	0.119
Immature Eggplant/Mature Eggplant	0.94113	0.545
Ripe Pepper/Ripe Tomato	0.79661	1
Mature Eggplant/Ripe Tomato	1.40484	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.91664	0.708
1-1-2/M82	1.19325	1
12-2/M82	0.84116	0.955
12-4/M82	0.95481	1
1-3/M82	1.90461	0.248
2-1-1/M82	1.04212	1
2-1/M82	0.7038	0.345
2-6/M82	0.98202	1
3-2/M82	1.39505
4-1-1/M82	1.21656	1
4-1/M82	1.46862	1
4-3-2/M82	1.46532	0.284
4-3/M82	1.55353	0.268
5-3/M82	1.21745	1
6-2/M82	1.06904	1
6-3/M82	0.92003	1
7-1/M82	1.06995	1
7-2/M82	1.85473	0.282
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.30823
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	N/A	N/A
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	0.61567	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.94219	1
DC3000/delta hrp 6h	0.90073	0.95
DC3000/delta hrp 12h	1.03983	1
DC3000/delta hrp 24h	0.52937	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.3491	0.025
DC3000 delta B/DC3000 delta AB	0.31267	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.89558	0.328
Exp 36h	1.00188	1
Exp 60h	0.93565	0.754

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

hybridization	ratio	FDR (corrected p value)
self-self	0.93599	1
Var 0h	1.06148	0.936
Var 12h I row2-row1	0.93139	0.856
Var 12h NI row2-row1	0.59019	0.33
Var 36h I row2-row1	0.75808	0.374
Var 36h NI row2-row1	1.75478	0.482
Var 60h I row2-row1	N/A	N/A
Var 60h NI row2-row1	1.69749	0.904
Time course 0hI-0hNI	0.72468	0.044
Time course 12hI-12hNI	0.9835	0.906
Time course 36hI-36hNI	0.7207	0.024
Time course 60hI-60hNI	0.05825	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)	1.03025	0.798
transgenic ySAMdc/azygous control (breaker)	1.05761	1
transgenic ySAMdc/azygous control (red)	1.1833	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.11315	0.317

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.2662	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.84172	1
Manapal/WT (break)	1.23339	0.381
Manapal/WT (red)	1.38368	0.413