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Exploration of the involvement of LncRNA in HIV-associated encephalitis using bioinformatics

BACKGROUND: HIV-associated encephalitis (HIVE) is one of the common complications of HIV infection, and the pathogenesis of HIVE remains unclear, while lncRNA might be involved it. In this study, we made re-annotation on the expression profiling from the HIVE study in the public database, identified...

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Autores principales: Li, Diangeng, Bao, Pengtao, Yin, Zhiwei, Sun, Lei, Feng, Jin, He, Zheng, Jin, Meiling, Liu, Changting
Formato: Online Artículo Texto
Lenguaje:English
Publicado: PeerJ Inc. 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6187992/
https://www.ncbi.nlm.nih.gov/pubmed/30345171
http://dx.doi.org/10.7717/peerj.5721
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author Li, Diangeng
Bao, Pengtao
Yin, Zhiwei
Sun, Lei
Feng, Jin
He, Zheng
Jin, Meiling
Liu, Changting
author_facet Li, Diangeng
Bao, Pengtao
Yin, Zhiwei
Sun, Lei
Feng, Jin
He, Zheng
Jin, Meiling
Liu, Changting
author_sort Li, Diangeng
collection PubMed
description BACKGROUND: HIV-associated encephalitis (HIVE) is one of the common complications of HIV infection, and the pathogenesis of HIVE remains unclear, while lncRNA might be involved it. In this study, we made re-annotation on the expression profiling from the HIVE study in the public database, identified the lncRNA that might be involved in HIVE, and explored the possible mechanism. METHODS: In the GEO public database, the microarray expression profile (GSE35864) of three regions of brain tissues (white matter, frontal cortex and basal ganglia brain tissues) was chosen, updated annotation was performed to construct the non-cording-RNA (ncRNA) microarray data. Morpheus was used to identify the differential expressed ncRNA, and Genbank of NCBI was used to identify lncRNAs. The StarBase, PITA and miRDB databases were used to predict the target miRNAs of lncRNA. The TargetScan, PicTar and MiRanda databases were used to predict the target genes of miRNAs. The GO and KEGG pathway analysis were used to make function analysis on the targets genes. RESULTS: Seventeen differentially expressed lncRNAs were observed in the white matter of brain tissues, for which 352 target miRNAs and 6,659 target genes were predicted. The GO function analysis indicated that the lncRNAs were mainly involved in the nuclear transcription and translation processes. The KEGG pathway analysis showed that the target genes were significantly enriched in 33 signal pathways, of which 11 were clearly related to the nervous system function. DISCUSSION: The brand-new and different microarray results can be obtained through the updated annotation of the chips, and it is feasible to identify lncRNAs from ordinary chips. The results suggest that lncRNA may be involved in the occurrence and development of HIVE, which provides a new direction for further research on the diagnosis and treatment of HIVE.
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spelling pubmed-61879922018-10-19 Exploration of the involvement of LncRNA in HIV-associated encephalitis using bioinformatics Li, Diangeng Bao, Pengtao Yin, Zhiwei Sun, Lei Feng, Jin He, Zheng Jin, Meiling Liu, Changting PeerJ Bioinformatics BACKGROUND: HIV-associated encephalitis (HIVE) is one of the common complications of HIV infection, and the pathogenesis of HIVE remains unclear, while lncRNA might be involved it. In this study, we made re-annotation on the expression profiling from the HIVE study in the public database, identified the lncRNA that might be involved in HIVE, and explored the possible mechanism. METHODS: In the GEO public database, the microarray expression profile (GSE35864) of three regions of brain tissues (white matter, frontal cortex and basal ganglia brain tissues) was chosen, updated annotation was performed to construct the non-cording-RNA (ncRNA) microarray data. Morpheus was used to identify the differential expressed ncRNA, and Genbank of NCBI was used to identify lncRNAs. The StarBase, PITA and miRDB databases were used to predict the target miRNAs of lncRNA. The TargetScan, PicTar and MiRanda databases were used to predict the target genes of miRNAs. The GO and KEGG pathway analysis were used to make function analysis on the targets genes. RESULTS: Seventeen differentially expressed lncRNAs were observed in the white matter of brain tissues, for which 352 target miRNAs and 6,659 target genes were predicted. The GO function analysis indicated that the lncRNAs were mainly involved in the nuclear transcription and translation processes. The KEGG pathway analysis showed that the target genes were significantly enriched in 33 signal pathways, of which 11 were clearly related to the nervous system function. DISCUSSION: The brand-new and different microarray results can be obtained through the updated annotation of the chips, and it is feasible to identify lncRNAs from ordinary chips. The results suggest that lncRNA may be involved in the occurrence and development of HIVE, which provides a new direction for further research on the diagnosis and treatment of HIVE. PeerJ Inc. 2018-10-12 /pmc/articles/PMC6187992/ /pubmed/30345171 http://dx.doi.org/10.7717/peerj.5721 Text en ©2018 Li et al. http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited.
spellingShingle Bioinformatics
Li, Diangeng
Bao, Pengtao
Yin, Zhiwei
Sun, Lei
Feng, Jin
He, Zheng
Jin, Meiling
Liu, Changting
Exploration of the involvement of LncRNA in HIV-associated encephalitis using bioinformatics
title Exploration of the involvement of LncRNA in HIV-associated encephalitis using bioinformatics
title_full Exploration of the involvement of LncRNA in HIV-associated encephalitis using bioinformatics
title_fullStr Exploration of the involvement of LncRNA in HIV-associated encephalitis using bioinformatics
title_full_unstemmed Exploration of the involvement of LncRNA in HIV-associated encephalitis using bioinformatics
title_short Exploration of the involvement of LncRNA in HIV-associated encephalitis using bioinformatics
title_sort exploration of the involvement of lncrna in hiv-associated encephalitis using bioinformatics
topic Bioinformatics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6187992/
https://www.ncbi.nlm.nih.gov/pubmed/30345171
http://dx.doi.org/10.7717/peerj.5721
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