Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.3.5.7

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.78574	0.2
27DAP/17DAP	0.629	0.066
39DAP/27DAP	0.68163	0.255
41DAP/39DAP	0.81606	0.288
42DAP/41DAP	0.89115	1
43DAP/42DAP	1.42922	0.293
47DAP/43DAP	0.71824	0.25
52DAP/47DAP	0.87988	0.602
57DAP/52DAP	0.90267	0.919

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.21311	0.29
17DAP/reference	1.33948	0.33
27DAP/reference	1.02791	1
39DAP/reference	1.47479	0.083
41DAP/reference	2.00636	0.029
42DAP/reference	1.26432	0.022
43DAP/reference	1.02799	0.866
47DAP/reference	1.01243	0.602
52DAP/reference	0.92804	0.31
57DAP/reference	0.93322	0.358

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.99408	0.801
27DAP/17DAP	0.8984	0.58
39DAP/27DAP	0.55984	0.033
41DAP/39DAP	0.79979	0.256
42DAP/41DAP	0.92144	0.484
43DAP/42DAP	0.57581	0.022
47DAP/43DAP	0.8073	0.068
52DAP/47DAP	0.96578	0.902
57DAP/52DAP	1.59571	0.476
57DAP/7DAP	0.27247	0.108

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.74731	0.074
17DAP/reference	1.22237	0.054
27DAP/reference	0.91914	0.185
39DAP/reference	1.01126	1
41DAP/reference	1.05956	0.977
42DAP/reference	0.96512	0.458
43DAP/reference	0.87834	0.105
47DAP/reference	1.17318	0.7
52DAP/reference	0.87417	0.179
57DAP/reference	0.97479	0.458

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01912	1
17DAP/reference	0.96924	0.548
27DAP/reference	1.29537	0.239
39DAP/reference	0.9125	0.024
41DAP/reference	0.90006	0.268
42DAP/reference	0.9514	0.392
43DAP/reference	1.47314	0.064
47DAP/reference	1.31966	0.12
52DAP/reference	1.22602	0.026
57DAP/reference	0.7334	0.073

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.81998	0.135
17DAP/reference	0.91512	0.519
27DAP/reference	1.15689	0.596
39DAP/reference	0.81607	0.008
41DAP/reference	1.02012	0.818
42DAP/reference	0.92856	0.445
43DAP/reference	0.90971	0.348
47DAP/reference	1.27591	0.424
52DAP/reference	0.98116	0.747
57DAP/reference	0.57791	0.016

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.75338	0.008
26DAP/20DAP	1.15913	0.608
34DAP/26DAP	0.96585	0.936
51DAP/34DAP	0.93268	0.532
52DAP/51DAP	0.91457	1
53DAP/52DAP	0.90487	0.409
55DAP/53DAP	0.53349	0.016
57DAP/55DAP	1.37503	0.906
62DAP/57DAP	1.20989	0.868
68DAP/62DAP	0.75326
68DAP/14DAP	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.27737	0.023

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	7.14755	0.015
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.28024
Mature Eggplant/Ripe Tomato	N/A	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.01374	1
1-1-2/M82	0.89492	1
12-2/M82	1.00186
12-4/M82	1.02618
1-3/M82	0.81034	0.501
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	1.03424	0.695
3-2/M82	0.93371
4-1-1/M82	0.73087
4-1/M82	1.04683
4-3-2/M82	N/A	N/A
4-3/M82	1.09041	1
5-3/M82	0.96552	1
6-2/M82	0.91787	1
6-3/M82	1.06636	1
7-1/M82	N/A	N/A
7-2/M82	0.95838	0.881
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.33054
IL2-6/WTpooled	1.00563	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.99174	1
IL12-4/WTpooled	0.77142	0.566
IL1-4/WTpooled	0.89399
WT/WTpooled	1.09779	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	0.86553	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.06365	0.774
DC3000/delta hrp 6h	0.35389
DC3000/delta hrp 12h	0.99704
DC3000/delta hrp 24h	0.94776	0.607

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.57406	0.024
DC3000 delta B/DC3000 delta AB	0.59333	0.02

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	1.05845	1
Var 0h	N/A	N/A
Var 12h I row2-row1	0.82322	0.318
Var 12h NI row2-row1	0.90041	0.443
Var 36h I row2-row1	1.1691	1
Var 36h NI row2-row1	1.17889	0.482
Var 60h I row2-row1	0.96779	0.952
Var 60h NI row2-row1	1.06573	0.904
Time course 0hI-0hNI	0.99947	1
Time course 12hI-12hNI	1.05262	0.709
Time course 36hI-36hNI	0.96697	0.468
Time course 60hI-60hNI	0.12228	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)	N/A	N/A
transgenic ySAMdc/azygous control (breaker)	1.63711	1
transgenic ySAMdc/azygous control (red)	N/A	N/A

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.13241	0.148

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.1195	1

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)	1.26355	0.183
Manapal/WT (red)	0.76006	0.181