Tag: lncRNA

In Rett Models, Regulatory RNAs Appear To Be Altered

Regulatory RNAs involved in nerve cell signaling and structure were altered in cell and mouse models of Rett syndrome, with these changes also evident in tissue from deceased patients, a study reported. These findings aid in understanding the biological processes impaired in Rett and may reveal potential biomarkers to help…

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Identification of Novel Diagnostic Biomarkers in Prostate Adenocarcinoma Based on the Stromal-Immune Score and Analysis of the WGCNA and ceRNA Network

This article was originally published here Dis Markers. 2022 Jan 15;2022:1909196. doi: 10.1155/2022/1909196. eCollection 2022. ABSTRACT Prostate cancer is still a significant global health burden in the coming decade. Novel biomarkers for detection and prognosis are needed to improve the survival of distant and advanced stage prostate cancer patients. The…

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Novel diagnostic biomarkers for keloid based on GEO database

Introduction Keloid is excessive fibrosis of the skin that extends beyond the area of injury and does not regress.1 Keloid can occur in the joints and mouth after several years of severe injury, including burns, chemical injury, wound, and surgical incision.2 Keloids on the joints affect the quality of life,…

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Long non-coding RNA MSTRG.81401 short hairpin RNA relieves diabetic neuropathic pain and behaviors of depression by inhibiting P2X4 receptor expression in type 2 diabetic rats

1. Nicodemus JM, Enriquez C, Marquez A, Anaya CJ, Jolivalt CG (2017) Murine model and mechanisms of treatment-induced painful diabetic neuropathy. Neuroscience 354:136–145. doi.org/10.1016/j.neuroscience.2017.04.036 CAS  Article  PubMed  Google Scholar  2. Morimoto SS, Kanellopoulos D, Manning KJ, Alexopoulos GS (2015) Diagnosis and treatment of depression and cognitive impairment in late life….

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Comprehensive Analysis of mRNA, lncRNA, circRNA, and miRNA Expression Profiles and Their ceRNA Networks in the Longissimus Dorsi Muscle of Cattle-Yak and Yak

doi: 10.3389/fgene.2021.772557. eCollection 2021. Chun Huang  1 , Fei Ge  1 , Xiaoming Ma  1 , Rongfeng Dai  1 , Renqing Dingkao  2 , Zhuoma Zhaxi  3 , Getu Burenchao  3 , Pengjia Bao  1 , Xiaoyun Wu  1 , Xian Guo  1 , Min Chu  1 , Ping Yan  1 , Chunnian Liang  1 Affiliations Expand Affiliations 1 Key Laboratory of…

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Omics advanced 07 | transcriptome mRNA | miRNA | lncrna

A brief introduction mRNA,miRNA,lncRNA And circRNA Principle of genome sequencing 、 Routine analysis of Shengxin . Catalog Introduction to transcriptome sequencing mRNA|miRNA|lncRNA|circRNA Introduction to analysis mRNA Group miRNA Group lncRNA Group circRNA Group mRNA|miRNA|lncRNA|circRNA Correlation analysis Reference Introduction to transcriptome sequencing Transcriptome (Transcriptome) Is a single or group of cells…

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ncRNA | Free Full-Text | Common Features in lncRNA Annotation and Classification: A Survey

CONC 2006 SVM Eukaryotes (both protein-coding and non-coding genes) peptide length, amino acid composition, predicted secondary structure content, mean hydrophobicity, percentage of residues exposed to solvent, sequence compositional entropy, number of homologues, alignment entropy 10-fold CV on protein-coding: F1-score: 97.4% ☼ Precision: 97.1% ☼ Recall: 97.8% ◙ On non-coding: F1-score:…

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Science Papers Describe NanoProCas9 System, Inflammatory Protein Biomarkers, LncRNA Affects Muscle Tissue Formation in Aging

A conditionally activatable CRISPR-Cas9 prodrug system that can be leveraged for precision medicine is described in this week’s Science Advances. While CRISRP-Cas9 genome editing holds great therapeutic potential, the nonspecific distribution of Cas9 raises safety concerns relating to off-target activity at the tissue level. Aiming to overcome this limitation, Zhejiang…

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Poly A vs total RNA

Poly A vs total RNA – Which is better for extracting noncoding RNA information 0 Hi everyone, In scRNAseq ,I want to extract lncRNA,miRNA etc Extracted molecule -polyA RNA or total RNA Since polyA RNA will not give much information about noncoding counterpart,will it be fruitful to go on with…

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miRNAs and mRNAs in intestinal ischemia-reperfusion injury

Introduction Intestinal ischemia-reperfusion (II/R) injury is a severe clinical complication common in the Intensive Care Unit (ICU). It is associated with high morbidity and mortality.1 Usually, this problem is followed by various causes, including sepsis, shock, trauma, and so on.2 Intestinal ischemia-reperfusion injury destroys intestinal tissue and impairs the function…

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Omics data collection and merging of datasets from different studies

Omics data collection and merging of datasets from different studies 0 Hi! I’m going to do omics analysis on skin basal cell carcinoma. I’m currently trying to find publicly available data to use to make a data collection. I have looked after RNA-seq(high throughput) in GEO and found some studies…

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Identification of Prognosis-Associated Biomarkers in Thyroid Carcinoma

Introduction Thyroid cancer (TC) is a common endocrine malignancy with a rapidly increasing incidence worldwide, and the estimated new cases and deaths are notably higher in women than in men.1 Papillary thyroid carcinoma (PTC) is identified as the most common pathological type of TC, and accounts for approximately 80–85% of…

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Classifiers for predicting coronary artery disease

Introduction Coronary artery disease (CAD) is a complex pathology associated with behavioral and environmental factors.1–3 CAD shows high prevalence and is associated with a high fatality rate among cardiovascular diseases. The main manifestations of CAD are stable or unstable angina pectoris and identifiable or unrecognized myocardial infarction.4 The main risk…

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Running htseq-count to “grab” long non coding gene_id names

Running htseq-count to “grab” long non coding gene_id names 0 hi all, new to bioinformatics. so bare with me.. I am trying find long non coding RNA from RNA-seq data. As i checked the human gtf file there are 2 different types of long non coding RNA, “lnc_RNA” and “lncRNA”,…

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Looking up Gene IDs in R

Looking up Gene IDs in R 1 Hello, Given a list of gene names, I need to create a table containing the Ensemble ID, chromosome, start, end of that gene. Example: ## ens_id gene view chr start end ## 1: ENSG00000243485 MIR1302-2HG Gene Expression chr1 29553 30267 ## 2: ENSG00000237613…

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Finding differentially expressed lncRNA

Finding differentially expressed lncRNA 0 Hi all, I’m trying to diff. expressed lncRNAs between two groups (of humans). I wanted to use the following pipeline: trimmomatic –> stringtie/cufflinks –> Cuffmerge/stringtie merge –> FEELnc to find lncRNAs. To find diff. expressed transcripts I want to use the following pipeline: trimmomatic –>…

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How do I check the expression level of a unannotated lncRNA in RNAseq dataset?

How do I check the expression level of a unannotated lncRNA in RNAseq dataset? 2 I plan to check a lncRNA expression level in RNAseq dataset, but the lncRNA was just identified and not annotated yet.Only I know is its position in chromatin and the sequence of it. so how…

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normalization two different datasets tcga vs gtex

normalization two different datasets tcga vs gtex 0 using tcga and gtex to look for lncrna DE (using raw files) – what are the best ways to normalize? deseq2 and edger? also if i want to look at lncrnas of specific chromosomes, how should i approach normalization? tcga gtex normalization…

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