Abstract
Messenger RNA (mRNA) and long noncoding RNA (lncRNA) are two main subgroups of RNAs participating in transcription regulation. With the development of next generation sequencing, increasing lncRNAs are identified. Many hidden functions of lncRNAs are also revealed. However, the differences in lncRNAs and mRNAs are still unclear. For example, we need to determine whether lncRNAs have stronger tissue specificity than mRNAs and which tissues have more lncRNAs expressed. To investigate such tissue expression difference between mRNAs and lncRNAs, we encoded 9339 lncRNAs and 14,294 mRNAs with 71 expression features, including 69 maximum expression features for 69 types of cells, one feature for the maximum expression in all cells, and one expression specificity feature that was measured as Chao-Shen-corrected Shannon’s entropy. With advanced feature selection methods, such as maximum relevance minimum redundancy, incremental feature selection methods, and random forest algorithm, 13 features presented the dissimilarity of lncRNAs and mRNAs. The 11 cell subtype features indicated which cell types of the lncRNAs and mRNAs had the largest expression difference. Such cell subtypes may be the potential cell models for lncRNA identification and function investigation. The expression specificity feature suggested that the cell types to express mRNAs and lncRNAs were different. The maximum expression feature suggested that the maximum expression levels of mRNAs and lncRNAs were different. In addition, the rule learning algorithm, repeated incremental pruning to produce error reduction algorithm, was also employed to produce effective classification rules for classifying lncRNAs and mRNAs, which gave competitive results compared with random forest and could give a clearer picture of different expression patterns between lncRNAs and mRNAs. Results not only revealed the heterogeneous expression pattern of lncRNA and mRNA, but also gave rise to the development of a new tool to identify the potential biological functions of such RNA subgroups.
Highlights
Ribonucleic acid (RNA) is one of the most significant nucleic acid components in all living creatures except for some viruses [1,2]
RNA contributes to the maintenance and regulation of gene expression and function, regulating the coding, decoding, transcription, and translation of a specific protein, the final functional component of most biological processes; these factors are quite different from the biological functions of other nucleic acid subtypes, such as DNA, as the genetic passenger in the cell nucleus [7]
Each long noncoding RNA (lncRNA) or Messenger RNA (mRNA) was encoded into 71 expression features that are described in detail in SectioEnac4h.1l.nTchReNnA, aoprompuRlNarAfewatausreensceoledcetidoninptoro7c1edeuxprer,emssRioMn Rfematuetrheosdth[a2t5]a,rwe adsesacprpiblieedditnodaentaaliylzine tSheecsteiofnea4t.u1r.eTsh, penro, daupcoinpgultahrefmeaRtuMreRsfeelaetcutrioenlisptr,owchederuerien, tmheR7M1Rfematuetrheos dw[e2r5e]s, owrtaesdaapcpcloierddintogatnoatlhyezier rtehleesveafnecaetutoretsa,rpgreotdvuacriinabglethaenmd RreMduRnfdeaatnucrieeslitsot,owthheerrefeinattuhrees7.1TfheeatoubrteasinweedremsRoMrteRdfaecactuorrdeilnisgt tios pthreesirenreteledvianncTeabtoletaSr1g. et variable and redundancies to other features
Summary
Ribonucleic acid (RNA) is one of the most significant nucleic acid components in all living creatures except for some viruses [1,2]. Among the different subtypes of nucleic acid, RNA is a specific functional component that has specific structures and functions. As for the structures, generally, DNA, as another major component of nucleic acid in our living cells, exists as desoxy-ribonucleic acid of double-strand status with bases as A, G, C, and T in the cell nucleus as the transporter of genetic materials [3]. RNA contributes to the maintenance and regulation of gene expression and function, regulating the coding, decoding, transcription, and translation of a specific protein, the final functional component of most biological processes; these factors are quite different from the biological functions of other nucleic acid subtypes, such as DNA, as the genetic passenger in the cell nucleus [7]
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