| | 1 | = Example data sets = |
| | 2 | Below a list of publicly available datasets in XGAP format. [[BR]] Please email [mailto:m.a.swertz@rug.nl] to publish your data to this list. |
| | 3 | |
| | 4 | [[TOC()]] |
| | 5 | |
| | 6 | === Unpublished epigenetic data example === |
| | 7 | |
| | 8 | Example of an epigenetic experiment using ChIP-on-chip for methylation detection. |
| | 9 | |
| | 10 | * [http://gbic.target.rug.nl/xgap/targz/Methylationdataexample.tar.gz Download in Archiver format (tar.gz)] |
| | 11 | * [http://gbic.target.rug.nl/xgap/zip/Methylationdataexample.zip Download in zipped plain format (zip)] |
| | 12 | |
| | 13 | === Unpublished alternative splicing data example === |
| | 14 | |
| | 15 | Example of isoform data that uses tiling arrays for detection of alternative splicing |
| | 16 | |
| | 17 | * [http://gbic.target.rug.nl/xgap/zip/tilingexample.zip Download in zipped plain format] |
| | 18 | |
| | 19 | === Baile et al. === |
| | 20 | Identification of QTL for locomotor activation and anxiety using related inbred strains B6 and C58/J |
| | 21 | |
| | 22 | * [http://gbic.target.rug.nl/xgap/targz/Bailey.tar.gz Download in Archiver format (tar.gz)] |
| | 23 | * [http://gbic.target.rug.nl/xgap/zip/Bailey.zip Download in zipped plain format (zip)] |
| | 24 | * Source: [http://www.ncbi.nlm.nih.gov/pubmed/19130624 Baile JS, Grabowski-Boas L, Steff BM, Wiltshire T, Churchil GA, Tarantino LM. (2008) Identification of quantitative trait loci for locomotor activation and anxiety using closely related inbred strains.] |
| | 25 | |
| | 26 | === Beamer et al. === |
| | 27 | Bone mineral density in F2 progeny from a C57BL/6J x CAST/EiJ intercross |
| | 28 | |
| | 29 | * [http://gbic.target.rug.nl/xgap/targz/Beamer.tar.gz Download in Archiver format (tar.gz)] |
| | 30 | * [http://gbic.target.rug.nl/xgap/zip/Beamer.zip Download in zipped plain format (zip)] |
| | 31 | * Source: [http://www.ncbi.nlm.nih.gov/pubmed/10556421 Beamer WG, Shultz KL, Churchill GA, Frankel WN, Baylink DJ, Rosen CJ, Donahue LR. (1999) Quantitative trait loci for bone density in C57BL/6J and CAST/EiJ inbred mice.] |
| | 32 | |
| | 33 | === Lyons et al. === |
| | 34 | QTL analysis: Plasma lipids and susceptibility to gallstones in F2 progeny of DBA/2J x CAST/EiJ on a high-fat diet'''''' |
| | 35 | |
| | 36 | * [http://gbic.target.rug.nl/xgap/targz/Lyons.tar.gz Download in Archiver format (tar.gz)] |
| | 37 | * [http://gbic.target.rug.nl/xgap/zip/Lyons.zip Download in zipped plain format (zip)] |
| | 38 | * Source: [http://www.ncbi.nlm.nih.gov/pubmed/12588951 Lyons MA, Wittenburg H, Li R, Walsh KA, Churchill GA, Carey MC, Paigen B. (2003) Quantitative trait loci that determine lipoprotein cholesterol levels in DBA/2J and CAST/Ei inbred mice.] |
| | 39 | * Source: [http://www.ncbi.nlm.nih.gov/pubmed/12810825 Lyons MA, Wittenburg H, Li R, Walsh KA, Leonard MR, Korstanje R, Churchill GA, Carey MC, Paigen B. (2003) Lith6: a new QTL for cholesterol gallstones from an intercross of CAST/Ei and DBA/2J inbred mouse strains.] |
| | 40 | |
| | 41 | === Fu et al. === |
| | 42 | MetaNetwork example dataset |
| | 43 | |
| | 44 | * [http://gbic.target.rug.nl/xgap/targz/Fu.tar.gz Download in Archiver format (tar.gz)] |
| | 45 | * [http://gbic.target.rug.nl/xgap/zip/Fu.zip Download in zipped plain format (zip)] |
| | 46 | * Source: [http://www.ncbi.nlm.nih.gov/pubmed/17406631 View pubmed:17406631] - !MetaNetwork: a computational protocol for the genetic study of metabolic networks. Fu J, Swertz MA, Keurentjes JJ, Jansen RC. Nat Protoc. 2007;2(3):685-94. |
| | 47 | |
| | 48 | === Myers et al. === |
| | 49 | This set includes Genotypes, SNP locations, and Expression data. |
| | 50 | |
| | 51 | * [http://gbic.target.rug.nl/xgap/targz/Myers.tar.gz Download in Archiver format (tar.gz)] |
| | 52 | * [http://gbic.target.rug.nl/xgap/zip/Myers.zip Download in zipped plain format (zip)] |
| | 53 | |
| | 54 | === Stranger/Human === |
| | 55 | Whole-genome gene expression variation in 210 unrelated !HapMap individuals. This set includes genotype and expression data and panel, gene and clone annotations. |
| | 56 | |
| | 57 | * [http://gbic.target.rug.nl/xgap/targz/Stranger.tar.gz Download in Archiver format (tar.gz)] |
| | 58 | * [http://gbic.target.rug.nl/xgap/zip/Stranger.zip Download in zipped plain format (zip)] |
| | 59 | * [http://gbicserver1.biol.rug.nl:8080/xgap4exampledatasets/molgenis.do?__target=molgenis_main_Investigations&__action=filter_set&__filter_attribute=id&__filter_operator=EQUALS&__filter_value=645186 View data on xgap server] |
| | 60 | * [http://www.ncbi.nlm.nih.gov/pubmed/17289997 View pubmed:17289997] - Stranger BE, Forrest MS, Dunning M, Ingle CE et al. Relative impact of nucleotide and copy number variation on gene expression phenotypes. Science 2007 Feb 9;315(5813):848-53. |
| | 61 | |
| | 62 | === Keurentjes/Arabidopsis === |
| | 63 | Genetic analysis of natural variation in the metabolite composition in Arabidopsis thaliana using empirical untargeted metabolomics using liquid chromatography-time of flight mass spectrometry (LC-QTOF MS). This set includes gene expression, genotype, and lcms data sets and qtls and gene, invidiual, marker, masspeak, and sample annotations. |
| | 64 | |
| | 65 | * [http://gbic.biol.rug.nl/xgap/data/keurentjes.zip Download data in xgap format (zip)] |
| | 66 | * [http://gbicserver1.biol.rug.nl:8080/xgap4exampledatasets/molgenis.do?__target=molgenis_main_Investigations&__action=filter_set&__filter_attribute=id&__filter_operator=EQUALS&__filter_value=546020 View data on xgap server] |
| | 67 | * [http://www.ncbi.nlm.nih.gov/pubmed/16751770 View pubmed:16751770] - The genetics of plant metabolism. Keurentjes JJ, Fu J, de Vos CH, Lommen A, Hall RD, Bino RJ, van der Plas LH, Jansen RC, Vreugdenhil D, Koornneef M. Nat Genet. 2006 Jul;38(7):842-9. Epub 2006 Jun 4. |
| | 68 | |
| | 69 | === Bystrykh/Mouse === |
| | 70 | mRNA gene expression in hematopoietic stem cells from adult female BXD mice using Affymetrix U74Av2 chips. This set includes genotype, probe level gene expression and probset level gene expression data and individual, marker, probe, probeset and strain annotations. |
| | 71 | |
| | 72 | * [http://gbic.biol.rug.nl/xgap/data/bystrykh.zip Download data in xgap format (zip)] |
| | 73 | * [http://gbicserver1.biol.rug.nl:8080/xgap4exampledatasets/molgenis.do?__target=molgenis_main_Investigations&__action=filter_set&__filter_attribute=id&__filter_operator=EQUALS&__filter_value=332963 View data on xgap server] |
| | 74 | * [http://www.ncbi.nlm.nih.gov/pubmed/15711547 View pubmed:15711547] - Uncovering regulatory pathways that affect hematopoietic stem cell function using 'genetical genomics'. Bystrykh L, Weersing E, Dontje B, Sutton S, Pletcher MT, Wiltshire T, Su AI, Vellenga E, Wang J, Manly KF, Lu L, Chesler EJ, Alberts R, Jansen RC, Williams RW, Cooke MP, de Haan G. Nat Genet. 2005 Mar;37(3):225-32. Epub 2005 Feb 13. |
| | 75 | |
| | 76 | === Heap/Human === |
| | 77 | Primary human leucocyte RNA expression of unrelated celiac disease cases and unrelated healthy controls. This set includes genotype and gene expression data sets and probe, marker, and sample annotations. |
| | 78 | |
| | 79 | * [http://gbic.biol.rug.nl/xgap/data/heap.zip Download data in xgap format (zip)] |
| | 80 | * [http://gbicserver1.biol.rug.nl:8080/xgap4exampledatasets/molgenis.do?__target=molgenis_main_Investigations&__action=filter_set&__filter_attribute=id&__filter_operator=EQUALS&__filter_value=3 View data on xgap server] |
| | 81 | * [http://www.ncbi.nlm.nih.gov/pubmed/19128478 View pubmed:19128478] - Complex nature of SNP genotype effects on gene expression in primary human leucocytes. Heap GA, Trynka G, Jansen RC, Bruinenberg M, Swertz MA, Dinesen LC, Hunt KA, Wijmenga C, Vanheel DA, Franke L. BMC Med Genomics. 2009 Jan 7;!2:1. |
| | 82 | |
| | 83 | === Myers/Human === |
| | 84 | This set includes Genotypes, SNP locations, and Expression data. Also available from !http://labs.med.miami.edu/myers/LFuN/data.html. |
| | 85 | |
| | 86 | * [http://gbic.biol.rug.nl/xgap/data/myers.zip Download data in xgap format (zip)] |
| | 87 | * [http://gbicserver1.biol.rug.nl:8080/xgap4exampledatasets/molgenis.do?__target=molgenis_main_Investigations&__action=filter_set&__filter_attribute=id&__filter_operator=EQUALS&__filter_value=647405 View data on xgap server] |
| | 88 | * [http://www.ncbi.nlm.nih.gov/pubmed/17982457 View pubmed:17982457] - A survey of genetic human cortical gene expression. Myers AJ, Gibbs JR, Webster JA, Rohrer K, Zhao A, Marlowe L, Kaleem M, Leung D, Bryden L, Nath P, Zismann VL, Joshipura K, Huentelman MJ, Hu-Lince D, Coon KD, Craig DW, Pearson JV, Holmans P, Heward CB, Reiman EM, Stephan D, Hardy J. Nat Genet. 2007 Dec;39(12):1494-9. Epub 2007 Nov 4. |
| | 89 | |
| | 90 | === Li/C.elegans === |
| | 91 | Mapping determinants of gene expression plasticity by genetical genomics in C. elegans. This set includes Probe, Gene, Marker, Paired sample and Strain annotations and Genotype and Expression datasets. |
| | 92 | |
| | 93 | * [http://gbic.biol.rug.nl/xgap/data/li.zip Download data in xgap format (zip)] |
| | 94 | * [http://gbicserver1.biol.rug.nl:8080/xgap4exampledatasets/molgenis.do?__target=molgenis_main_Investigations&__action=filter_set&__filter_attribute=id&__filter_operator=EQUALS&__filter_value=601329 View data on xgap server] |
| | 95 | * [http://www.ncbi.nlm.nih.gov/pubmed/17196041 View pubmed:17196041] - Mapping determinants of gene expression plasticity by genetical genomics in C. elegans. Li Y, Alvarez OA, Gutteling EW, Tijsterman M, Fu J, Riksen JA, Hazendonk E, Prins P, Plasterk RH, Jansen RC, Breitling R, Kammenga JE. PLoS Genet. 2006 Dec 29;2(12):e222. Epub 2006 Nov 13. |
