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Keygenes specifications

Information


Unique identifier OMICS_26771
Name Keygenes
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


Maintainer


  • person_outline Susana Chuva de Sousa Lopes

Information


Unique identifier OMICS_26771
Name Keygenes
Software type Application/Script, Toolkit/Suite
Interface Command line interface
Restrictions to use None
Output data A file with a heatmap containing the identity scores, a file containing a matrix with the identity scores, a text file with the queried samples and the sample in the training set with the highest identity score and a file containing the list of classifier genes per sample.
Output format PDF+TXT+TXT+TXT
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Requirements
limma, ggplot2, gplots, glmnet
Maintained Yes

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Versioning


No version available

Documentation


Maintainer


  • person_outline Susana Chuva de Sousa Lopes

Publication for Keygenes

Keygenes citations

 (3)
library_books

Human pluripotent stem cell derived HLC transcriptome data enables molecular dissection of hepatogenesis

2018
Sci Data
PMCID: 5848791
PMID: 29533390
DOI: 10.1038/sdata.2018.35

[…] included in the publication by Matz et al.. Several clusters were representative for distinct differentiation stages. Genes from cluster#9 were employed to make a tissue type prediction via the tool KeyGenes (). Based on the normalized gene expression data of these genes KeyGenes predicted the tissue type “liver” for HLC, fetal liver and PHH samples. demonstrates that genes from cluster#9 have m […]

library_books

Dynamics of lineage commitment revealed by single cell transcriptomics of differentiating embryonic stem cells

2017
Nat Commun
PMCID: 5653659
PMID: 29061959
DOI: 10.1038/s41467-017-01076-4

[…] with non-zero average expression across all time points. Differences in the L2 norm between time points are reported in Supplementary Fig. .To reveal the identity of sorted subpopulations (Fig. ) the KeyGenes algorithm was used with a panel of pre-/peri-implantation tissues as training set. Since there were 3 replicates per tissue in the training set, leave-one-out cross-validation had to be used […]

call_split

A three dimensional model of human lung development and disease from pluripotent stem cells

2017
Nat Cell Biol
PMCID: 5777163
PMID: 28436965
DOI: 10.1038/ncb3510
call_split See protocol

[…] RNAseq data obtained from d170 LBOs from RUES2, C12, HDF SV and HDF mRNA lines was compared to different first and second trimesters and adult organs, including the lungs, using KeyGenes. Hierarchical clustering of 12 samples of the d170 LBOs and 75 samples from 19 organs from second trimester was performed using Cluster 3.0 and viewed by TreeView. The 87 classifier genes wer […]

Citations

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Keygenes institution(s)
Department of Anatomy and Embryology, Leiden University Medical Center, Leiden, the Netherlands; Leiden Genome Technology Center, Leiden University Medical Center, Leiden, the Netherlands; Sequence Analysis Support Core, Leiden University Medical Center, Leiden, the Netherlands; Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden, the Netherlands; Department of Nephrology, Leiden University Medical Center, Leiden, the Netherlands; Hubrecht Institute, Utrecht, the Netherlands; Department for Health Evidence, Radboud University Medical Center, Nijmegen, the Netherlands; Department for Reproductive Medicine, Ghent University Hospital, Ghent, Belgium

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