Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.3.13.11

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.91385	0.596
27DAP/17DAP	1.08527	1
39DAP/27DAP	0.91464	0.594
41DAP/39DAP	1.50092	0.321
42DAP/41DAP	0.9572	1
43DAP/42DAP	0.96018	0.898
47DAP/43DAP	1.1166	0.856
52DAP/47DAP	1.34001	0.498
57DAP/52DAP	1.12282	0.952

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02634	0.567
17DAP/reference	1.02503	0.342
27DAP/reference	0.96483	0.406
39DAP/reference	1.00688	0.8
41DAP/reference	1.05156	0.145
42DAP/reference	0.93904	0.023
43DAP/reference	1.00319	1
47DAP/reference	0.93828	0.014
52DAP/reference	0.94808	0.23
57DAP/reference	0.9329	0.047

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.04055	0.593
27DAP/17DAP	0.99297	0.943
39DAP/27DAP	1.09595	0.3
41DAP/39DAP	0.99012	1
42DAP/41DAP	1.00963	1
43DAP/42DAP	0.99684	1
47DAP/43DAP	0.99468	0.985
52DAP/47DAP	1.0165	0.933
57DAP/52DAP	1.02181	0.874
57DAP/7DAP	1.1133	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.12721	0.132
17DAP/reference	1.46437	0.006
27DAP/reference	1.35678	0.008
39DAP/reference	1.18313	0.006
41DAP/reference	1.12939	0.077
42DAP/reference	1.16488	0.012
43DAP/reference	1.31767	0.01
47DAP/reference	1.13142	0.266
52DAP/reference	1.20748	0.031
57DAP/reference	1.09043	0.108

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02524	0.776
17DAP/reference	0.9608	0.399
27DAP/reference	0.93749	0.249
39DAP/reference	0.96587	0.274
41DAP/reference	0.92668	0.199
42DAP/reference	0.92024	0.05
43DAP/reference	0.9908	0.721
47DAP/reference	0.94152	0.016
52DAP/reference	0.94344	0.187
57DAP/reference	0.99472	0.754

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.18328	0.057
17DAP/reference	1.08767	0.657
27DAP/reference	1.58391	0.02
39DAP/reference	1.53605	0.011
41DAP/reference	1.31195	0.022
42DAP/reference	1.34613	0.062
43DAP/reference	1.27989	0.145
47DAP/reference	0.92012	0.224
52DAP/reference	1.43617	0.106
57DAP/reference	1.063	0.888

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.0199	0.966
26DAP/20DAP	0.87003	0.512
34DAP/26DAP	0.928	0.693
51DAP/34DAP	1.03051	0.814
52DAP/51DAP	1.06769	0.431
53DAP/52DAP	1.0336	0.882
55DAP/53DAP	0.99063	0.886
57DAP/55DAP	1.03786	1
62DAP/57DAP	1.0109	1
68DAP/62DAP	0.96444	0.787
68DAP/14DAP	1.25389	0.346

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.03944	0.466

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.84062	0.301
Mature Green Tomato/Ripe Tomato	0.9448	0.774
Immature Eggplant/Mature Eggplant	0.8547	0.144
Ripe Pepper/Ripe Tomato	1.87885	0.256
Mature Eggplant/Ripe Tomato	0.94037	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.08322	0.551
1-1-2/M82	0.91181	1
12-2/M82	1.09255	1
12-4/M82	0.86216	1
1-3/M82	0.95214	0.501
2-1-1/M82	1.08023	1
2-1/M82	N/A	N/A
2-6/M82	0.96997	1
3-2/M82	0.93818	1
4-1-1/M82	0.99737	1
4-1/M82	0.97672	1
4-3-2/M82	0.90759	1
4-3/M82	1.01685	1
5-3/M82	1.01648	1
6-2/M82	0.96936	1
6-3/M82	1.01963	1
7-1/M82	1.17278	0.87
7-2/M82	1.05762	1
9-3-2/M82	0.93248	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.15615	0.659
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.9862	1
IL12-4/WTpooled	0.95284	1
IL1-4/WTpooled	1.07677
WT/WTpooled	1.04739	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	0.96357	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.96026	1
DC3000/delta hrp 6h	0.96371	0.95
DC3000/delta hrp 12h	0.99354	1
DC3000/delta hrp 24h	1.14146	0.243

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.09934	0.06
DC3000 delta B/DC3000 delta AB	1.09198	0.423

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.24615	1
Exp 36h	1.03747	0.943
Exp 60h	1.37179	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99431	1
Var 0h	1.00369	1
Var 12h I row2-row1	1.14746	0.163
Var 12h NI row2-row1	1.02404	1
Var 36h I row2-row1	1.06431	1
Var 36h NI row2-row1	0.93637	0.61
Var 60h I row2-row1	1.10506	0.562
Var 60h NI row2-row1	1.03678	1
Time course 0hI-0hNI	1.07397	0.764
Time course 12hI-12hNI	1.06819	0.65
Time course 36hI-36hNI	1.08917	0.025
Time course 60hI-60hNI	1.35659	0.011

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)	0.91482	0.299
transgenic ySAMdc/azygous control (breaker)	0.86498	0.173
transgenic ySAMdc/azygous control (red)	0.95529	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.02407	0.301

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.9635	0.241

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)	0.91533	1
Manapal/WT (red)	0.81486	0.181