RT Journal Article
SR Electronic
T1 Deep-learning-based cell composition analysis from tissue expression profiles
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 659227
DO 10.1101/659227
A1 Menden, Kevin
A1 Marouf, Mohamed
A1 Oller, Sergio
A1 Dalmia, Anupriya
A1 Kloiber, Karin
A1 Heutink, Peter
A1 Bonn, Stefan
YR 2019
UL http://biorxiv.org/content/early/2019/11/18/659227.abstract
AB We present Scaden, a deep neural network for cell deconvolution that uses gene expression information to infer the cellular composition of tissues. Scaden is trained on single cell RNA-seq data to engineer discriminative features that confer robustness to bias and noise, making complex data preprocessing and feature selection unnecessary. We demonstrate that Scaden outperforms existing deconvolution algorithms in both precision and robustness. A single trained network reliably deconvolves bulk RNA-seq and microarray, human and mouse tissue expression data and leverages the combined information of multiple data sets. Due to this stability and flexibility, we surmise that deep learning will become an algorithmic mainstay for cell deconvolution of various data types. Scaden’s comprehensive software package is easy to use on novel as well as diverse existing expression datasets available in public resources, deepening the molecular and cellular understanding of developmental and disease processes.RNA-seqNext Generation RNA SequencingGEPgene expression profile matrixSVRSupport Vector RegressionDNNDeep Neural NetworkscRNA-seqsingle cell RNA-seqsimulated tissuetraining data generated by mixing proportions of scRNA-seq dataPBMCperipheral blood mononuclear cellsCCCconcordance correlation coefficientrPearson’s correlation coefficientCSCIBERSORTCSxCIBERSORTxCPMCell Population Mapping