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We developed a Semi-Supervised Mouse data Deconvolution (SSMD) method to study the mouse tissue microenvironment. SSMD is featured by (i) a novel nonparametric method to discover data set-specific cell type signature genes; (ii) a community detection approach for fixing cell types and their marker genes; (iii) a constrained matrix decomposition method to solve cell type relative proportions that is robust to diverse experimental platforms. In summary, SSMD addressed several key challenges in the deconvolution of mouse tissue data, including: (i) varied cell types and marker genes caused by highly divergent genotypic and phenotypic conditions of mouse experiment; (ii) diverse experimental platforms of mouse transcriptomics data; (iii) small sample size and limited training data source and (iv) capable to estimate the proportion of 35 cell types in blood, inflammatory, central nervous or hematopoietic systems. In silico and experimental validation of SSMD demonstrated its high sensitivity and accuracy in identifying (sub) cell types and predicting cell proportions comparing with state-of-the-arts methods. A user-friendly R package and a web server of SSMD are released via https:\/\/github.com\/xiaoyulu95\/SSMD.<\/jats:p>","DOI":"10.1093\/bib\/bbaa307","type":"journal-article","created":{"date-parts":[[2020,10,12]],"date-time":"2020-10-12T07:11:04Z","timestamp":1602486664000},"source":"Crossref","is-referenced-by-count":5,"title":["SSMD: a semi-supervised approach for a robust cell type identification and deconvolution of mouse transcriptomics data"],"prefix":"10.1093","volume":"22","author":[{"given":"Xiaoyu","family":"Lu","sequence":"first","affiliation":[{"name":"Department of BioHealth Informatics, Indiana University\u2212Purdue University Indianapolis"}]},{"given":"Szu-Wei","family":"Tu","sequence":"additional","affiliation":[{"name":"Department of BioHealth Informatics, Indiana University\u2212Purdue University Indianapolis"}]},{"given":"Wennan","family":"Chang","sequence":"additional","affiliation":[{"name":"Department of Electrical and Computer Engineering, Purdue University"}]},{"given":"Changlin","family":"Wan","sequence":"additional","affiliation":[{"name":"Department of Electrical and Computer Engineering, Purdue University"}]},{"given":"Jiashi","family":"Wang","sequence":"additional","affiliation":[{"name":"Biomedical Data Research Data (BDRD) Lab at Indiana University School of Medicine"}]},{"given":"Yong","family":"Zang","sequence":"additional","affiliation":[{"name":"Department of Biostatistics and a member of the Center for Computational Biology and Bioinformatics, Indiana University School of Medicine"}]},{"given":"Baskar","family":"Ramdas","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, Indiana University School of Medicine"}]},{"given":"Reuben","family":"Kapur","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, Indiana University School of Medicine"}]},{"given":"Xiongbin","family":"Lu","sequence":"additional","affiliation":[{"name":"Department of Medical and Molecular Genetics, Indiana 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