Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.4.13.18

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.64108	0.09
27DAP/17DAP	1.18968	0.808
39DAP/27DAP	1.06074	0.903
41DAP/39DAP	1.02818	0.904
42DAP/41DAP	1.27483	0.929
43DAP/42DAP	1.36889	0.58
47DAP/43DAP	0.6347	0.107
52DAP/47DAP	1.42715	0.268
57DAP/52DAP	1.17892	0.977

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95038	0.402
17DAP/reference	0.79681	0.008
27DAP/reference	0.91975	0.327
39DAP/reference	0.85704	0.072
41DAP/reference	0.71466	0.012
42DAP/reference	0.82804	0.008
43DAP/reference	1.06518	0.36
47DAP/reference	0.83389	0.004
52DAP/reference	0.91551	0.139
57DAP/reference	1.00606	1

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.15874	0.749
27DAP/17DAP	1.36024	0.128
39DAP/27DAP	1.17899	0.548
41DAP/39DAP	0.87564	0.31
42DAP/41DAP	1.03814	0.781
43DAP/42DAP	3.46202	0.013
47DAP/43DAP	0.998	0.99
52DAP/47DAP	0.93059	0.666
57DAP/52DAP	1.07684	0.957
57DAP/7DAP	1.77665	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.50562	0.049
17DAP/reference	1.30827	0.009
27DAP/reference	1.26531	0.012
39DAP/reference	1.50818	0.017
41DAP/reference	1.43166	0.043
42DAP/reference	1.44436	0.007
43DAP/reference	1.47753	0.007
47DAP/reference	1.11894	0.224
52DAP/reference	1.18286	0.008
57DAP/reference	1.16252	0.268

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00486	0.831
17DAP/reference	0.81762	0.039
27DAP/reference	0.84268	0.097
39DAP/reference	0.8905	0.06
41DAP/reference	0.86244	0.118
42DAP/reference	0.87874	0.089
43DAP/reference	0.90167	0.243
47DAP/reference	0.92265	0.221
52DAP/reference	0.91753	0.156
57DAP/reference	0.82901	0.092

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.37268	0.037
17DAP/reference	0.9611	0.56
27DAP/reference	1.3367	0.028
39DAP/reference	1.1912	0.043
41DAP/reference	1.16052	0.319
42DAP/reference	1.25882	0.117
43DAP/reference	1.23533	0.116
47DAP/reference	1.01279	1
52DAP/reference	1.44959	0.1
57DAP/reference	0.98342	0.583

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.95832	1
26DAP/20DAP	1.48983	0.415
34DAP/26DAP	1.28235	0.542
51DAP/34DAP	0.92356	0.698
52DAP/51DAP	1.53349	0.253
53DAP/52DAP	1.06243	1
55DAP/53DAP	1.21459	0.634
57DAP/55DAP	1.10274	0.969
62DAP/57DAP	1.15426	0.678
68DAP/62DAP	1.11372	0.8
68DAP/14DAP	0.87619	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.60669	0.061

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.35385
Immature Eggplant/Mature Eggplant	2.57483	0.066
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	3.18639

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.7114
12-2/M82	N/A	N/A
12-4/M82	1.46075
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	1.07475
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	2.36098
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	0.79132
IL2-6/WTpooled	0.72426
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.85349	0.31
IL12-4/WTpooled	0.97357	1
IL1-4/WTpooled	0.93114
WT/WTpooled	1.13034	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	0.97174	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.07874	0.894
DC3000/delta hrp 6h	0.84222	0.95
DC3000/delta hrp 12h	1.19543	1
DC3000/delta hrp 24h	1.99832	0.043

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.16505	0.313
DC3000 delta B/DC3000 delta AB	0.76625	0.125

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.07905	1
Exp 36h	1.35832	0.326
Exp 60h	1.42468	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99568	1
Var 0h	0.4774	1
Var 12h I row2-row1	1.04915	0.654
Var 12h NI row2-row1	1.11753	0.235
Var 36h I row2-row1	0.87384	0.805
Var 36h NI row2-row1	0.87728	0.61
Var 60h I row2-row1	0.77335	0.293
Var 60h NI row2-row1	1.04188	0.904
Time course 0hI-0hNI	0.94747	0.56
Time course 12hI-12hNI	0.95275	0.546
Time course 36hI-36hNI	0.96721	0.441
Time course 60hI-60hNI	2.14835	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)	1.27845	0.397
transgenic ySAMdc/azygous control (breaker)	1.2147	1
transgenic ySAMdc/azygous control (red)	1.3463	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.057	0.148

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.84498	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	3.60377	0.088
Manapal/WT (break)	0.97757	1
Manapal/WT (red)	0.78291	0.216