Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.3.5.1

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.76959	0.419
27DAP/17DAP	0.8829	0.807
39DAP/27DAP	0.86469	0.564
41DAP/39DAP	0.95128	0.811
42DAP/41DAP	1.17283	0.941
43DAP/42DAP	1.05414	1
47DAP/43DAP	1.14117	1
52DAP/47DAP	0.97612	0.803
57DAP/52DAP	1.30413	0.944

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.37718	0.012
17DAP/reference	1.42135	0.011
27DAP/reference	1.03331	1
39DAP/reference	1.26997	0.041
41DAP/reference	1.45483	0.022
42DAP/reference	1.01775	0.755
43DAP/reference	1.04319	0.73
47DAP/reference	1.06549	0.558
52DAP/reference	0.88082	0.172
57DAP/reference	0.81568	0.031

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.73826	0.131
27DAP/17DAP	1.30343	0.488
39DAP/27DAP	1.52458	0.499
41DAP/39DAP	1.55501	0.565
42DAP/41DAP	1.27578	0.111
43DAP/42DAP	1.07547	0.297
47DAP/43DAP	0.81433	0.781
52DAP/47DAP	0.95914	0.902
57DAP/52DAP	0.58281	0.29
57DAP/7DAP	0.25016

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.14996	0.705
17DAP/reference	1.06424	1
27DAP/reference	1.13847	0.131
39DAP/reference	0.84108	0.146
41DAP/reference	0.80985	0.032
42DAP/reference	0.70135	0.033
43DAP/reference	0.73395	0.023
47DAP/reference	0.92555	0.066
52DAP/reference	0.99988	0.74
57DAP/reference	0.94141	0.183

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.0396	0.712
17DAP/reference	1.15096	0.271
27DAP/reference	1.19597	0.102
39DAP/reference	1.32785	0.213
41DAP/reference	1.0543	0.846
42DAP/reference	1.07993	0.649
43DAP/reference	1.03599	0.863
47DAP/reference	1.22248	0.095
52DAP/reference	1.1798	0.343
57DAP/reference	1.08203	0.688

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.88248	0.311
17DAP/reference	0.90725	0.624
27DAP/reference	0.91594	0.49
39DAP/reference	0.95517	0.504
41DAP/reference	0.93099	0.237
42DAP/reference	0.93494	0.445
43DAP/reference	1.23337	0.081
47DAP/reference	0.82118	0.145
52DAP/reference	1.95903	0.363
57DAP/reference	1.18427	0.218

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.86562	0.966
26DAP/20DAP	1.15627	1
34DAP/26DAP	0.66376	0.771
51DAP/34DAP	0.97414
52DAP/51DAP	0.86009	1
53DAP/52DAP	1.43709	0.594
55DAP/53DAP	0.95412	0.864
57DAP/55DAP	1.30904	0.881
62DAP/57DAP	0.97089	0.994
68DAP/62DAP	0.79357
68DAP/14DAP	0.66657	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.42034

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	N/A	N/A
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	31.33
Mature Eggplant/Ripe Tomato	N/A	N/A

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	1.19694
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.12251	1
IL12-4/WTpooled	0.77572	0.71
IL1-4/WTpooled	0.97933	1
WT/WTpooled	1.09715	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	1.07608

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	0.76551	0.95
DC3000/delta hrp 12h	0.91933
DC3000/delta hrp 24h	0.11026

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	N/A
DC3000 delta B/DC3000 delta AB	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.97013	1
Exp 36h	N/A	N/A
Exp 60h	0.69095	0.32

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

hybridization	ratio	FDR (corrected p value)
self-self	N/A	N/A
Var 0h	0.48028
Var 12h I row2-row1	N/A	N/A
Var 12h NI row2-row1	N/A	N/A
Var 36h I row2-row1	N/A	N/A
Var 36h NI row2-row1	N/A	N/A
Var 60h I row2-row1	N/A	N/A
Var 60h NI row2-row1	N/A	N/A
Time course 0hI-0hNI	N/A	N/A
Time course 12hI-12hNI	N/A	N/A
Time course 36hI-36hNI	N/A	N/A
Time course 60hI-60hNI	N/A	N/A

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)	1.27189	0.347
transgenic ySAMdc/azygous control (breaker)	1.20407	1
transgenic ySAMdc/azygous control (red)	1.08975	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.98126	0.263

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.82386	0.255

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.78651	1
Manapal/WT (break)	0.9427	1
Manapal/WT (red)	N/A	N/A