Abstract
Many diseases and adverse drug reactions exhibit tissue specificity. To better understand the tissue-specific expression characteristics of transcripts in different human tissues, we deeply sequenced RNA samples from 14 different human tissues. After filtering many lowly expressed transcripts, 24,729 protein-coding transcripts and 1,653 noncoding transcripts were identified. By analyzing highly expressed tissue-specific protein-coding transcripts (TSCTs) and noncoding transcripts (TSNTs), we found that testis expressed the highest numbers of TSCTs and TSNTs. Brain, monocytes, ovary, and heart expressed more TSCTs than the rest tissues, whereas brain, placenta, heart, and monocytes expressed more TSNTs than other tissues. Co-expression network constructed based on the TSCTs and TSNTs showed that each hub TSNT was co-expressed with several TSCTs, allowing functional annotation of TSNTs. Important biological processes and KEGG pathways highly related to the specific functions or diseases of each tissue were enriched with the corresponding TSCTs. These TSCTs and TSNTs may participate in the tissue-specific physiological or pathological processes. Our study provided a unique data set and systematic analysis of expression characteristics and functions of both TSCTs and TSNTs based on 14 distinct human tissues, and could facilitate future investigation of the mechanisms behind tissue-specific diseases and adverse drug reactions.
Highlights
Different transcripts are expressed in diverse tissues or cell types, as well as in different developmental stages or diseases
We found that testis expressed the highest numbers of TSCTs and TSNTs
Each hub TSNT was co-expressed with several TSCTs
Summary
Different transcripts are expressed in diverse tissues or cell types, as well as in different developmental stages or diseases. Noncoding RNAs (ncRNAs) are involved in many biological processes and are increasingly seen as important regulatory molecules They regulate gene expression via sequence-specific interactions with regulatory regions at the level of transcription, RNA processing, and translation. The SEQC consortium described the landscape of tissue-specific gene expression based on 320 RNA-seq from 11 organs of both sexes of rats[22]. Public data sets such as the Illumina Human BodyMap 2.0 data set[18] and more recently the Genotype-Tissue Expression Project (GTEx) data set[23,24] included expression profiles of many different human tissue types, providing unique opportunities to comprehensively characterize the human transcriptomes across tissues. These TSCTs and the enriched biological processes closely associated with the specific functions or diseases of each tissue
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