Toward a Reference Gene Catalog of Human Primary Monocytes.
Transcriptome analyses based on high-throughput RNA sequencing (RNA-Seq) provide powerful and quantitative characterization of cell types and in-depth understanding of biological systems in health and disease. In this study, we present a comprehensive transcriptome profile of human primary monocytes, a crucial component of the innate immune system. We performed deep RNA-Seq of monocytes from six healthy subjects and integrated our data with 10 other publicly available RNA-Seq datasets of human monocytes. A total of 1.9 billion reads were generated, which allowed us to capture most of the genes transcribed in human monocytes, including 11,994 protein-coding genes, 5558 noncoding genes (including long noncoding RNAs, precursor miRNAs, and others), 2819 pseudogenes, and 7034 putative novel transcripts. In addition, we profiled the expression pattern of 1155 transcription factors (TFs) in human monocytes, which are the main molecules in controlling the gene transcription. An interaction network was constructed among the top expressed TFs and their targeted genes, which revealed the potential key regulatory genes in biological function of human monocytes. The gene catalog of human primary monocytes provided in this study offers significant promise and future potential clinical applications in the fields of precision medicine, systems diagnostics, immunogenomics, and the development of innovative biomarkers and therapeutic monitoring strategies.
1 Faculty of Science, Institute of Biological Sciences, University of Malaya , Kuala Lumpur, Malaysia .
Hoda
H
Mirsafian
2 Allergy and Immunology Research Centre, Institute for Medical Research , Jalan Pahang, Kuala Lumpur, Malaysia .
Adiratna Mat
AM
Ripen
3 Centre of Research for Computational Sciences and Informatics in Biology, Bioindustry, Environment, Agriculture and Healthcare (CRYSTAL), University of Malaya , Kuala Lumpur, Malaysia .
Thamilvaani
T
Manaharan
1 Faculty of Science, Institute of Biological Sciences, University of Malaya , Kuala Lumpur, Malaysia .|3 Centre of Research for Computational Sciences and Informatics in Biology, Bioindustry, Environment, Agriculture and Healthcare (CRYSTAL), University of Malaya , Kuala Lumpur, Malaysia .
Saharuddin Bin
SB
Mohamad
1 Faculty of Science, Institute of Biological Sciences, University of Malaya , Kuala Lumpur, Malaysia .|3 Centre of Research for Computational Sciences and Informatics in Biology, Bioindustry, Environment, Agriculture and Healthcare (CRYSTAL), University of Malaya , Kuala Lumpur, Malaysia .
Amir Feisal
AF
Merican
D000328:Adult; D005260:Female; D020869:Gene Expression Profiling; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D008297:Male; D035683:MicroRNAs / Q000235:genetics / Q000378:metabolism; D008969:Molecular Sequence Data; D009000:Monocytes / Q000378:metabolism*; D061251:Primary Cell Culture; D011506:Proteins / Q000235:genetics; D011544:Pseudogenes; D062085:RNA, Long Noncoding / Q000235:genetics / Q000378:metabolism; D017423:Sequence Analysis, RNA; D014157:Transcription Factors / Q000235:genetics*; D059467:Transcriptome
D035683:MicroRNAs; D011506:Proteins; D062085:RNA, Long Noncoding; D014157:Transcription Factors
RNA-Seq; gene catalogue; multi-omics; personalized medicine; postgenomics; transcriptome