lncRNAs with specific tissue expression involved in the diagnosis and prognosis of various cancers

سال انتشار: 1399
محل انتشار: بیست و یکمین کنگره ملی و نهمین کنگره بین المللی زیست شناسی ایران
کد COI اختصاصی: BIOCONF21_0750
زبان مقاله: انگلیسی
تعداد مشاهده: 223

نویسندگان

Department of Biochemistry, Payame Noor University, Isfahan, Iran,

Department of Cellular Biotechnology at Cell Science Research Center, Royan Institute of Biotechnology, ACECR, Isfahan, Iran,

Kamran Ghaedi

Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science & Technology, University of Isfahan, Isfahan, Iran.

چکیده

lncRNAs have been shown to be involved in cellular processes. One of their prominent features is the special and specific expression of tissue. In present study, using RNAseq data from the TCGA database for ۱۹ most common cancers, we identified lncRNAs with specific expression for each cancer as good candidates for diagnosis and prognosis for respective cancer. Therefore, RNAseq data for all ۱۹ common cancers were downloaded as raw data (HTSeq-count) and initial preprocessing and data normalization were performed with limma, edgeR and NOIseq packages. A CPM criterion of less than ۰.۵ was chosen to filter out genes with zero expression(Abbas-Aghababazadeh F et al, ۲۰۱۸). A list of all lncRNAs was obtained from the HGNC database and all the lncRNAs expressed in each cancer were extracted. The expression network showed that there are a large number of lncRNAs that have specific expression only in specific cancer, such as: breast, cervix, kidney, liver, lung, prostate, and thyroid. Also, the expression level differences between them compared to counterpart normal samples. Many of them had high diagnostic potency in distinguishing cancer samples from normal ones. Such as breast, colon, kidney, liver, lung (AUC> ۰.۹ and P < ۰.۰۰۱). Also, some of them were related to the survival of patients in terms of expression, such as breast, neck and neck, kidney, liver, lung, prostate and thyroid (HR> ۱, HR < ۱, P < ۰.۰۰۱). Taken together, these lncRNAs could be used as a diagnostic and prognostic biomarkers. They can also be good candidates for identifying specific and common pathways in cancers and can be a good therapeutic target in cancer treatment.

کلیدواژه ها

Bioinformatics, R software, cytoscape, Prism, Long non coding RNA

مقالات مرتبط جدید

اطلاعات بیشتر در مورد COI

COI مخفف عبارت CIVILICA Object Identifier به معنی شناسه سیویلیکا برای اسناد است. COI کدی است که مطابق محل انتشار، به مقالات کنفرانسها و ژورنالهای داخل کشور به هنگام نمایه سازی بر روی پایگاه استنادی سیویلیکا اختصاص می یابد.

کد COI به مفهوم کد ملی اسناد نمایه شده در سیویلیکا است و کدی یکتا و ثابت است و به همین دلیل همواره قابلیت استناد و پیگیری دارد.