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Xspecies specifications

Information


Unique identifier OMICS_33840
Name Xspecies
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Erik Kristiansson

Publication for Xspecies

Xspecies citations

 (10)
library_books

Identification of Gene Modules Associated with Low Temperatures Response in Bambara Groundnut by Network Based Analysis

2016
PLoS One
PMCID: 4747569
PMID: 26859686
DOI: 10.1371/journal.pone.0148771

[…] atives such as comprehensive RNA sequencing—while becoming more affordable—can still be costly, prohibiting routine large-scale experiments. One possible solution for this problem is a cross-species (Xspecies) microarray approach [], involving the hybridisation between the cRNA of the species of interest and a closely related species for which a custom microarray chip is available. This approach h […]

library_books

Diversity in global gene expression and morphology across a watercress (Nasturtium officinale R. Br.) germplasm collection: first steps to breeding

2015
PMCID: 4591680
PMID: 26504575
DOI: 10.1038/hortres.2015.29

[…] protcol adapted from Doyle.Hybridisation to X species chip. DNA from the control line (C) was sent to the National Arabidopsis Stock Centre (NASC) for hybridisation to the X species ATH1 genome array.Xspecies chip analysis – creation of probe mask (.cdf) files. Oligonucleotide GeneChip probes with low/no hybridisation to watercress transcripts were removed using the gDNA probe masking strategy dev […]

library_books

DNA microarray global gene expression analysis of influenza virus infected chicken and duck cells

2015
Genom Data
PMCID: 4535746
PMID: 26484178
DOI: 10.1016/j.gdata.2015.03.004

[…] ities above an experimentally set threshold. Selection was performed using a cel file parser script written in the Perl programming language (X-species Version 2.1, http://affymetrix.arabidopsis.info/xspecies/). After installing Active Perl software for windows (Active Perl version 5.10.1.1007 for Windows), CDF_masking.zip was downloaded and unzipped to a chosen location on the computer (http://af […]

library_books

Maternal protein energy malnutrition during early pregnancy in sheep impacts the fetal ornithine cycle to reduce fetal kidney microvascular development

2014
PMCID: 4216596
PMID: 25077559
DOI: 10.1096/fj.14-255364

[…] in which the perfect match (PM) probe has a gDNA hybridization intensity greater than the user-defined threshold and were selected using a .cel file parser script (http://affymetrix.arabidopsis.info/xspecies/), which produces a probe mask file (.cdf) compatible with a range of microarray analysis packages (e.g., Genespring; Agilent Technologies). Probe mask files (.cdf) were produced using gDNA h […]

library_books

Analysis of ripening related gene expression in papaya using an Arabidopsis based microarray

2012
BMC Plant Biol
PMCID: 3562526
PMID: 23256600
DOI: 10.1186/1471-2229-12-242

[…] fruit []. Commercial oligo-chips are not currently available for these organisms and comprehensive RNA sequencing can still be costly often prohibiting routine experiments. However, a cross-species (XSpecies) microarray is an alternative approach that has been successfully used to study the transcriptomes of non-model organisms [,].Papaya is a member of family Caricaceae within the Brassicales, t […]

call_split

Geological Substrates Shape Tree Species and Trait Distributions in African Moist Forests

2012
PLoS One
PMCID: 3419707
PMID: 22905127
DOI: 10.1371/journal.pone.0042381
call_split See protocol

[…] We investigated the main axes of variation in species composition and underlying patterns of species distribution with correspondence analysis (CA) of the plots (n = 56,445)×species (n = 31) abundance matrix. CA, also known as reciprocal averaging, produces a simultaneous ordination of plots and species . It is a robust method for identifying compositional gradients with […]

Citations

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Xspecies institution(s)
Department of Mathematical Statistics, Chalmers University of Technology/University of Gothenburg, Gothenburg, Sweden; Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden; Institute of Neuroscience and Physiology, the Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden; Sahlgrenska Cancer Center, Department of Pathology, Sahlgrenska Academy at The University of Gothenburg, Gothenburg, Sweden; Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
Xspecies funding source(s)
Supported by the Life Science Area of Advance at Chalmers University of Technology, Sweden, the Swedish Research Council (VR), the Foundation for Strategic Environmental Research (MISTRA), the Swedish Research Council for Environment, Agricultural Sciences and Spatial Planning (FORMAS), Swedish Society for Medical Research (SSMF) and the Gothenburg Bioinformatics Network (GOTBIN).

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