Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.4.8.4

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.14767	0.904
27DAP/17DAP	1.03693	1
39DAP/27DAP	1.04399	1
41DAP/39DAP	0.93331	0.72
42DAP/41DAP	0.99748	1
43DAP/42DAP	0.94985	0.851
47DAP/43DAP	0.62006	0.103
52DAP/47DAP	1.15983	0.769
57DAP/52DAP	1.0039	0.983

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87224	0.145
17DAP/reference	1.05447	0.492
27DAP/reference	0.97275	0.683
39DAP/reference	1.07966	0.368
41DAP/reference	1.06149	0.759
42DAP/reference	0.881	0.078
43DAP/reference	1.01992	1
47DAP/reference	0.94727	0.3
52DAP/reference	0.84193	0.024
57DAP/reference	1.08526	0.379

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.06403	0.749
27DAP/17DAP	0.98374	0.943
39DAP/27DAP	1.33807	0.236
41DAP/39DAP	1.07459	0.705
42DAP/41DAP	1.02857	0.939
43DAP/42DAP	0.84424	0.143
47DAP/43DAP	0.93421	0.764
52DAP/47DAP	1.08072	0.81
57DAP/52DAP	1.18094	0.688
57DAP/7DAP	2.27993	0.23

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.77215	0.076
17DAP/reference	1.02487	0.971
27DAP/reference	1.06959	0.246
39DAP/reference	0.92477	0.146
41DAP/reference	0.80282	0.058
42DAP/reference	0.71147	0.021
43DAP/reference	0.81282	0.054
47DAP/reference	0.83979	0.222
52DAP/reference	0.63708	0.012
57DAP/reference	0.70393	0.013

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00451	0.884
17DAP/reference	0.87507	0.019
27DAP/reference	1.0053	0.686
39DAP/reference	1.14644	0.412
41DAP/reference	1.15057	0.406
42DAP/reference	1.07163	0.915
43DAP/reference	1.60208	0.055
47DAP/reference	1.10272	0.056
52DAP/reference	1.02327	1
57DAP/reference	1.12044	0.398

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.82482	0.041
17DAP/reference	1.12342	0.627
27DAP/reference	0.84763	0.102
39DAP/reference	0.89796	0.246
41DAP/reference	1.05774	0.692
42DAP/reference	0.97152	0.671
43DAP/reference	0.8674	0.131
47DAP/reference	1.21065	0.11
52DAP/reference	1.29156	0.448
57DAP/reference	1.10932	0.394

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.02672	0.966
26DAP/20DAP	0.89852	1
34DAP/26DAP	0.8652	0.777
51DAP/34DAP	1.24666	0.524
52DAP/51DAP	1.24585	0.377
53DAP/52DAP	1.13841	0.921
55DAP/53DAP	1.38967	0.842
57DAP/55DAP	1.21591	0.915
62DAP/57DAP	1.22615	0.723
68DAP/62DAP	0.78861	0.263
68DAP/14DAP	0.92493	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.63246	0.077

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.43812	0.053
Immature Eggplant/Mature Eggplant	0.27895
Ripe Pepper/Ripe Tomato	1.2481	1
Mature Eggplant/Ripe Tomato	1.28933	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.92155	0.883
1-1-2/M82	1.13629
12-2/M82	1.11834	1
12-4/M82	0.94182	1
1-3/M82	0.9607	1
2-1-1/M82	0.79277
2-1/M82	0.79765
2-6/M82	1.01983	1
3-2/M82	1.00164
4-1-1/M82	1.12535	0.968
4-1/M82	N/A	N/A
4-3-2/M82	0.99195
4-3/M82	1.36374	0.268
5-3/M82	1.0268	1
6-2/M82	1.00217	1
6-3/M82	1.02032	1
7-1/M82	1.15584
7-2/M82	0.9766	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	4.30885
IL2-6/WTpooled	0.3003	0.348
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.52265	0.362
IL12-4/WTpooled	1.34027	0.595
IL1-4/WTpooled	1.39661	1
WT/WTpooled	0.94563	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	0.91315	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.03133	0.921
DC3000/delta hrp 6h	1.09513	1
DC3000/delta hrp 12h	1.02845	1
DC3000/delta hrp 24h	1.11833	0.322

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.25397	0.598
DC3000 delta B/DC3000 delta AB	1.22648	0.336

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	1.08048	1
Exp 60h	1.05618	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98415	1
Var 0h	0.66995	1
Var 12h I row2-row1	1.02052	0.736
Var 12h NI row2-row1	0.92762	0.713
Var 36h I row2-row1	1.03024	1
Var 36h NI row2-row1	0.97584	0.852
Var 60h I row2-row1	1.4869	1
Var 60h NI row2-row1	0.9887	1
Time course 0hI-0hNI	0.98637	0.973
Time course 12hI-12hNI	1.07789	0.381
Time course 36hI-36hNI	1.26218	0.015
Time course 60hI-60hNI	1.18779	0.008

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)	1.02754	0.654
transgenic ySAMdc/azygous control (breaker)	1.29695	0.248
transgenic ySAMdc/azygous control (red)	0.87708	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.9525	0.046

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.94156	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.85056	1
Manapal/WT (break)	0.87362	1
Manapal/WT (red)	0.75989	0.181