Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.2.13.17

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.08512	0.812
27DAP/17DAP	1.11462	1
39DAP/27DAP	0.79916	0.449
41DAP/39DAP	1.44492	0.416
42DAP/41DAP	1.10759	1
43DAP/42DAP	0.95859	0.906
47DAP/43DAP	0.97458	0.825
52DAP/47DAP	1.19958	0.646
57DAP/52DAP	1.02638	0.992

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9886	0.63
17DAP/reference	0.99817	1
27DAP/reference	0.94257	0.157
39DAP/reference	0.98983	0.841
41DAP/reference	0.97756	0.542
42DAP/reference	0.90818	0.009
43DAP/reference	0.95003	0.259
47DAP/reference	0.88378	0.005
52DAP/reference	0.87585	0.023
57DAP/reference	0.88413	0.015

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.0948	0.348
27DAP/17DAP	0.96935	0.782
39DAP/27DAP	1.05131	0.565
41DAP/39DAP	0.97873	0.997
42DAP/41DAP	0.97894	0.776
43DAP/42DAP	1.01789	0.746
47DAP/43DAP	1.04655	0.708
52DAP/47DAP	1.03154	0.868
57DAP/52DAP	1.02608	0.851
57DAP/7DAP	1.14491	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93843
17DAP/reference	0.86854	0.013
27DAP/reference	0.92655	0.125
39DAP/reference	0.96961	0.083
41DAP/reference	0.93116	0.086
42DAP/reference	0.99491	0.641
43DAP/reference	0.94823	0.121
47DAP/reference	0.90963	0.168
52DAP/reference	0.96495	0.196
57DAP/reference	0.95997	0.199

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.05289	0.531
17DAP/reference	1.00053	0.873
27DAP/reference	0.89368	0.144
39DAP/reference	0.87742	0.074
41DAP/reference	0.94514	0.331
42DAP/reference	0.88979	0.042
43DAP/reference	1.07413	0.59
47DAP/reference	0.86883	0.011
52DAP/reference	0.92331	0.086
57DAP/reference	1.04908	0.771

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98215	0.391
17DAP/reference	0.92207	0.3
27DAP/reference	0.99719	0.805
39DAP/reference	0.89795	0.083
41DAP/reference	0.93232	0.237
42DAP/reference	0.83693	0.108
43DAP/reference	0.87222	0.158
47DAP/reference	0.9192	0.161
52DAP/reference	0.91872	0.36
57DAP/reference	0.69307	0.016

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.9392	0.915
26DAP/20DAP	0.98425	1
34DAP/26DAP	0.99846	1
51DAP/34DAP	1.00982	0.988
52DAP/51DAP	1.07832	0.588
53DAP/52DAP	1.06207	0.738
55DAP/53DAP	0.98022	0.807
57DAP/55DAP	1.00525	0.902
62DAP/57DAP	1.11304	0.8
68DAP/62DAP	0.87795	0.505
68DAP/14DAP	0.96895	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.06777	0.627

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.50261	0.075
Mature Green Tomato/Ripe Tomato	0.89833	0.347
Immature Eggplant/Mature Eggplant	1.05037	0.462
Ripe Pepper/Ripe Tomato	0.89533	1
Mature Eggplant/Ripe Tomato	0.82737	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.02022	1
1-1-2/M82	0.92646	1
12-2/M82	1.01958	1
12-4/M82	0.98247	1
1-3/M82	0.95961	0.501
2-1-1/M82	1.15149	0.689
2-1/M82	1.50319	1
2-6/M82	1.03483	0.695
3-2/M82	N/A	N/A
4-1-1/M82	1.05418	1
4-1/M82	0.99296	1
4-3-2/M82	0.90367	1
4-3/M82	1.062	1
5-3/M82	0.9716	1
6-2/M82	1.01554	1
6-3/M82	1.01458	1
7-1/M82	0.92698
7-2/M82	1.07401	1
9-3-2/M82	0.9256	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.06622	0.584
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.87899	1
IL12-4/WTpooled	0.96603	1
IL1-4/WTpooled	1.0604
WT/WTpooled	0.99584	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	0.98693	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.06219	0.914
DC3000/delta hrp 6h	0.92169
DC3000/delta hrp 12h	1.22517	1
DC3000/delta hrp 24h	1.07012	0.383

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.19336	0.134
DC3000 delta B/DC3000 delta AB	1.12474	0.308

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.19496	1
Exp 36h	1.10217	1
Exp 60h	1.20534	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	0.97763	1
Var 0h	1.04992	1
Var 12h I row2-row1	1.18235	0.194
Var 12h NI row2-row1	1.17084	1
Var 36h I row2-row1	1.00305	1
Var 36h NI row2-row1	0.84042	0.584
Var 60h I row2-row1	1.04944	1
Var 60h NI row2-row1	1.17281	0.904
Time course 0hI-0hNI	1.12028	0.799
Time course 12hI-12hNI	1.03275	0.803
Time course 36hI-36hNI	1.19321	0.012
Time course 60hI-60hNI	1.60743	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)	1.03169	0.798
transgenic ySAMdc/azygous control (breaker)	1.13834	0.172
transgenic ySAMdc/azygous control (red)	1.10541	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.99821	0.806

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.97041	0.35

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	N/A	N/A
Manapal/WT (break)	0.84386	1
Manapal/WT (red)	N/A	N/A