Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.3.16.9

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.09447	0.681
27DAP/17DAP	1.02953	0.92
39DAP/27DAP	0.94475	0.583
41DAP/39DAP	1.038	0.58
42DAP/41DAP	1.06361	1
43DAP/42DAP	0.94898	0.877
47DAP/43DAP	0.97131	0.879
52DAP/47DAP	1.29482	0.371
57DAP/52DAP	1.06959	0.977

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91059	0.231
17DAP/reference	0.83266	0.074
27DAP/reference	0.80925	0.065
39DAP/reference	0.80758	0.072
41DAP/reference	0.75506	0.016
42DAP/reference	1.05601	0.565
43DAP/reference	0.92568	0.211
47DAP/reference	1.0476	0.391
52DAP/reference	1.08545	0.878
57DAP/reference	1.07484	0.548

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.00337	1
27DAP/17DAP	1.00552	0.988
39DAP/27DAP	1.00006	1
41DAP/39DAP	1.00687	0.896
42DAP/41DAP	0.99752	0.902
43DAP/42DAP	1.04352	0.23
47DAP/43DAP	0.98852	0.928
52DAP/47DAP	1.00646	0.986
57DAP/52DAP	1.02856	0.851
57DAP/7DAP	0.99277	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.85556	0.168
17DAP/reference	0.81773	0.02
27DAP/reference	0.97093	0.494
39DAP/reference	1.0104	0.745
41DAP/reference	0.88153	0.111
42DAP/reference	0.76818	0.117
43DAP/reference	0.84327	0.076
47DAP/reference	1.06569	0.685
52DAP/reference	1.05551	0.781
57DAP/reference	0.97273	0.223

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84168	0.018
17DAP/reference	0.92676	0.297
27DAP/reference	1.00642	0.765
39DAP/reference	0.72179	0.089
41DAP/reference	0.89407	0.199
42DAP/reference	1.10944	0.543
43DAP/reference	1.07383	0.997
47DAP/reference	1.04355	0.572
52DAP/reference	0.41849	0.004
57DAP/reference	0.47784	0.005

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91619	0.29
17DAP/reference	1.03812	0.924
27DAP/reference	0.96574	0.49
39DAP/reference	0.99106	0.693
41DAP/reference	1.31352	0.056
42DAP/reference	1.28415	0.279
43DAP/reference	1.57782	0.019
47DAP/reference	1.03903	0.847
52DAP/reference	1.36629	0.1
57DAP/reference	1.91083	0.011

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.62294	0.945
26DAP/20DAP	1.02681	0.941
34DAP/26DAP	1.01569	1
51DAP/34DAP	0.98686	0.844
52DAP/51DAP	0.95724	1
53DAP/52DAP	1.04966	0.83
55DAP/53DAP	0.99764	0.925
57DAP/55DAP	1.08747	0.764
62DAP/57DAP	0.93103	0.871
68DAP/62DAP	0.92161	0.7
68DAP/14DAP	1.05569	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.90251	0.129

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.01362	1
Mature Green Tomato/Ripe Tomato	0.99093	0.774
Immature Eggplant/Mature Eggplant	0.96317	0.651
Ripe Pepper/Ripe Tomato	0.74208	0.224
Mature Eggplant/Ripe Tomato	0.96896	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.95611
1-1-2/M82	0.92854	1
12-2/M82	0.82562
12-4/M82	0.96038	1
1-3/M82	1.17627	0.248
2-1-1/M82	1.08989
2-1/M82	N/A	N/A
2-6/M82	1.17989
3-2/M82	1.00711
4-1-1/M82	1.11803	1
4-1/M82	0.98497	1
4-3-2/M82	0.92203	1
4-3/M82	1.02403	1
5-3/M82	1.08646	1
6-2/M82	1.38154
6-3/M82	0.7367
7-1/M82	1.08209
7-2/M82	0.87896	0.796
9-3-2/M82	0.97259	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	0.77886
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	4.38269	1
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	1.13452	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.99205	1
DC3000/delta hrp 6h	0.99512	0.95
DC3000/delta hrp 12h	1.1612	1
DC3000/delta hrp 24h	1.00039	1

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.04348	0.441
DC3000 delta B/DC3000 delta AB	1.03031	0.614

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.02057	1
Exp 36h	1.23918	1
Exp 60h	1.13063	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	1.0171	1
Var 0h	1.14142	0.936
Var 12h I row2-row1	1.15267	0.324
Var 12h NI row2-row1	1.00231	1
Var 36h I row2-row1	0.96644	1
Var 36h NI row2-row1	0.98604	0.852
Var 60h I row2-row1	1.07283	0.562
Var 60h NI row2-row1	1.08236	0.904
Time course 0hI-0hNI	1.04894	0.833
Time course 12hI-12hNI	1.0791	0.554
Time course 36hI-36hNI	1.08885	0.01
Time course 60hI-60hNI	1.49426	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)	0.98492	0.614
transgenic ySAMdc/azygous control (breaker)	0.98063	0.49
transgenic ySAMdc/azygous control (red)	1.02493	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.74429	0.115

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.15267	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.92667	1
Manapal/WT (break)	1.0359	1
Manapal/WT (red)	1.21565	0.222