Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.1.11.6

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.89085	0.31
27DAP/17DAP	0.95833	0.939
39DAP/27DAP	1.0184	1
41DAP/39DAP	1.35954	0.328
42DAP/41DAP	1.04306	0.994
43DAP/42DAP	0.99897	0.937
47DAP/43DAP	0.88392	0.618
52DAP/47DAP	1.34016	0.456
57DAP/52DAP	0.99657	0.983

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98898	0.679
17DAP/reference	N/A	N/A
27DAP/reference	0.9593	0.406
39DAP/reference	1.04613	0.581
41DAP/reference	1.05705	0.079
42DAP/reference	0.95213	0.196
43DAP/reference	0.9761
47DAP/reference	0.96105	0.279
52DAP/reference	0.94369	0.546
57DAP/reference	0.90393	0.056

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.01084	1
27DAP/17DAP	1.07718	0.69
39DAP/27DAP	0.99054	1
41DAP/39DAP	1.03465	0.876
42DAP/41DAP	1.01691	0.984
43DAP/42DAP	1.0238	0.627
47DAP/43DAP	1.02763	0.901
52DAP/47DAP	1.00922	0.979
57DAP/52DAP	1.04599	0.74
57DAP/7DAP	1.2067	0.249

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97719	0.326
17DAP/reference	0.94537	0.015
27DAP/reference	0.95425	0.03
39DAP/reference	1.00428	0.96
41DAP/reference	0.98124	0.298
42DAP/reference	1.03182	0.308
43DAP/reference	0.97636	0.252
47DAP/reference	0.87754	0.101
52DAP/reference	0.91228	0.033
57DAP/reference	0.94991	0.018

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02834	0.516
17DAP/reference	1.00497	1
27DAP/reference	1.07106	0.769
39DAP/reference	1.05913	0.477
41DAP/reference	1.28563	0.146
42DAP/reference	0.92408	0.089
43DAP/reference	1.04134	0.598
47DAP/reference	1.0049	1
52DAP/reference	0.94904	0.078
57DAP/reference	0.98317	0.649

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94551	0.183
17DAP/reference	1.01396	0.924
27DAP/reference	0.93906	0.067
39DAP/reference	0.94289	0.05
41DAP/reference	0.92767	0.032
42DAP/reference	0.90014	0.049
43DAP/reference	0.94072	0.061
47DAP/reference	0.95964	0.249
52DAP/reference	0.95346	0.493
57DAP/reference	0.86497	0.1

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.99896	1
26DAP/20DAP	0.96129	1
34DAP/26DAP	0.94337	0.509
51DAP/34DAP	0.84103	0.136
52DAP/51DAP	0.97617	1
53DAP/52DAP	1.0149	0.901
55DAP/53DAP	0.9627	0.746
57DAP/55DAP	0.91984	0.664
62DAP/57DAP	1.00203	1
68DAP/62DAP	1.11379	1
68DAP/14DAP	0.92699	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.94813	0.253

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.91012	0.551
Mature Green Tomato/Ripe Tomato	0.93806	0.569
Immature Eggplant/Mature Eggplant	0.87262	0.366
Ripe Pepper/Ripe Tomato	1.67363	1
Mature Eggplant/Ripe Tomato	0.86731	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.10405	0.877
1-1-2/M82	0.97393	1
12-2/M82	1.0926	1
12-4/M82	0.99955	1
1-3/M82	1.00455	1
2-1-1/M82	1.09767	0.764
2-1/M82	N/A	N/A
2-6/M82	1.0552	0.425
3-2/M82	1.00034	1
4-1-1/M82	1.00834	1
4-1/M82	0.96373	1
4-3-2/M82	0.9684	1
4-3/M82	0.8408	0.72
5-3/M82	1.00942	1
6-2/M82	1.01565	1
6-3/M82	0.93852	1
7-1/M82	0.99546
7-2/M82	1.01257	1
9-3-2/M82	0.89012	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.00508	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.94168	0.293
IL12-4/WTpooled	1.08565	0.595
IL1-4/WTpooled	1.17607
WT/WTpooled	1.00362	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	1.10751	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.0685	0.823
DC3000/delta hrp 6h	0.93261	0.95
DC3000/delta hrp 12h	1.02856	1
DC3000/delta hrp 24h	1.03455	0.71

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.97863	0.92
DC3000 delta B/DC3000 delta AB	1.00184	1

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.04577	1
Exp 36h	1.03423	1
Exp 60h	1.33943	0.237

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

hybridization	ratio	FDR (corrected p value)
self-self	0.95236	1
Var 0h	0.49241	1
Var 12h I row2-row1	1.07688	0.296
Var 12h NI row2-row1	0.94431	0.82
Var 36h I row2-row1	1.03222	1
Var 36h NI row2-row1	0.89848	0.645
Var 60h I row2-row1	1.30346	0.562
Var 60h NI row2-row1	1.00707	1
Time course 0hI-0hNI	1.04358	0.852
Time course 12hI-12hNI	1.05682	0.654
Time course 36hI-36hNI	0.95839	0.317
Time course 60hI-60hNI	0.96519	0.646

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)	1.01102	0.863
transgenic ySAMdc/azygous control (breaker)	1.08573	1
transgenic ySAMdc/azygous control (red)	0.87905	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.01521	0.334

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.58964	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.97245	1
Manapal/WT (break)	0.94764	1
Manapal/WT (red)	1.05082	1