Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.2.8.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.86181	0.389
27DAP/17DAP	1.07278	0.864
39DAP/27DAP	0.78452	0.421
41DAP/39DAP	1.42634	0.295
42DAP/41DAP	1.12047	0.941
43DAP/42DAP	1.06189	1
47DAP/43DAP	1.00752	0.913
52DAP/47DAP	1.14595	0.949
57DAP/52DAP	1.08446	0.969

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94018	0.352
17DAP/reference	1.00005	1
27DAP/reference	0.93718	0.359
39DAP/reference	1.09957	0.453
41DAP/reference	1.04067	0.451
42DAP/reference	0.87786	0.019
43DAP/reference	1.04473	0.899
47DAP/reference	0.81812	0.003
52DAP/reference	0.7226	0.018
57DAP/reference	0.75419	0.025

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.90333	0.35
27DAP/17DAP	0.99694	0.969
39DAP/27DAP	1.25824	0.137
41DAP/39DAP	0.94397	0.839
42DAP/41DAP	0.90149	0.436
43DAP/42DAP	1.02574	0.664
47DAP/43DAP	1.03384	0.892
52DAP/47DAP	1.09947	0.718
57DAP/52DAP	0.99306	0.841
57DAP/7DAP	1.13592	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94452	0.445
17DAP/reference	0.87655	0.108
27DAP/reference	0.93219	0.071
39DAP/reference	0.84964	0.064
41DAP/reference	0.77877	0.073
42DAP/reference	0.86971	0.151
43DAP/reference	0.95791	0.403
47DAP/reference	0.87971	0.168
52DAP/reference	0.80582	0.097
57DAP/reference	0.79052	0.014

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.09824	0.397
17DAP/reference	1.0474	0.773
27DAP/reference	0.91347	0.249
39DAP/reference	0.80911	0.038
41DAP/reference	0.83403	0.037
42DAP/reference	0.80994	0.013
43DAP/reference	1.20137	0.089
47DAP/reference	0.88857	0.04
52DAP/reference	1.01021	1
57DAP/reference	1.08841	0.789

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.05048	0.644
17DAP/reference	1.01075	0.886
27DAP/reference	0.92413	0.27
39DAP/reference	0.94124	0.179
41DAP/reference	0.97751	0.618
42DAP/reference	0.75405	0.108
43DAP/reference	0.71083	0.037
47DAP/reference	0.90419	0.296
52DAP/reference	1.12131	0.928
57DAP/reference	0.50322	0.016

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.06598	0.966
26DAP/20DAP	0.85142	0.228
34DAP/26DAP	1.06641	1
51DAP/34DAP	1.31011	0.281
52DAP/51DAP	1.01791	1
53DAP/52DAP	0.97182	0.854
55DAP/53DAP	1.22527	0.399
57DAP/55DAP	1.01318	1
62DAP/57DAP	1.22516	0.8
68DAP/62DAP	1.01586	0.885
68DAP/14DAP	1.07538	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.1162	0.246

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.73992	0.132
Immature Eggplant/Mature Eggplant	0.61952	0.064
Ripe Pepper/Ripe Tomato	1.1871
Mature Eggplant/Ripe Tomato	1.00118	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.00393	1
1-1-2/M82	1.03033	1
12-2/M82	1.2971	1
12-4/M82	0.89121	1
1-3/M82	2.1867	0.248
2-1-1/M82	0.88886	0.92
2-1/M82	0.6093	0.322
2-6/M82	1.31312	0.364
3-2/M82	1.9576
4-1-1/M82	0.85062	1
4-1/M82	0.6452	0.737
4-3-2/M82	1.01726	1
4-3/M82	1.38567	1
5-3/M82	0.84776	0.447
6-2/M82	0.95473
6-3/M82	1.09836	1
7-1/M82	0.95325	1
7-2/M82	1.69887	0.385
9-3-2/M82	0.87729

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.96631	1
IL2-6/WTpooled	1.05747	0.788
IL7-5/WTpooled	0.79235	1
IL7-3/WTpooled	1.19069	0.362
IL12-4/WTpooled	0.69891	0.554
IL1-4/WTpooled	1.01444	1
WT/WTpooled	0.80968	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	0.73823	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.13404	0.921
DC3000/delta hrp 6h	1.2049	1
DC3000/delta hrp 12h	1.1077	1
DC3000/delta hrp 24h	1.45311	0.067

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.81881	0.081
DC3000 delta B/DC3000 delta AB	1.11749	0.539

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.81287	0.328
Exp 36h	0.87666	0.661
Exp 60h	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99942	1
Var 0h	0.48637	0.933
Var 12h I row2-row1	0.938	0.357
Var 12h NI row2-row1	0.69515	0.906
Var 36h I row2-row1	0.95543	1
Var 36h NI row2-row1	0.98832	0.852
Var 60h I row2-row1	1.01055	0.562
Var 60h NI row2-row1	1.01384	0.904
Time course 0hI-0hNI	0.98293	0.95
Time course 12hI-12hNI	0.90377	0.215
Time course 36hI-36hNI	0.86084	0.052
Time course 60hI-60hNI	0.79885	0.007

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)	0.9249	0.229
transgenic ySAMdc/azygous control (breaker)	0.94821	0.251
transgenic ySAMdc/azygous control (red)	1.08629	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.98933	0.471

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.01305	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.0419	1
Manapal/WT (break)	1.06632	1
Manapal/WT (red)	0.91335	0.216