Categories
Tag: lncRNA
LncRNA pipeline
Forum:LncRNA pipeline 0 HI ALL, I AM WORKING ON FINDING LNCRNA, I WOULD LIKE TO CHECK IF MY PIPELINE IS RIGHT FIRST I MAP USING STAR AND THEN SORT IT AND THEN GO FOR HTSEQ -GET THE COUNT DATA AND DO DESEQ. FOR LNCRNA EXTRACTION FROM RNA SEQ, I AM…
Progress of circRNA/lncRNA-miRNA-mRNA axis in atrial fibrillation [PeerJ]
Introduction The incidence and mortality rates of AF are continuously increasing, leading to serious complications such as heart failure and stroke (Fig. 1) (Sagris et al., 2021). The occurrence and development of AF involve different mechanisms and interactions (Kornej et al., 2020). AF often progresses from paroxysmal to persistent (Nattel…
LncRNA/circRNA-mRNA networks in CARAS | JIR
Introduction Combined allergic rhinitis and asthma syndrome (CARAS), a new terminology introduced by the World Allergy Organization (WAO) in 2004, is an allergic reaction that occurs in the respiratory tract, including upper respiratory tract allergy (allergic rhinitis, AR) and lower respiratory tract allergy (asthma, AS).1,2 The incidence of AS in…
PRRG4 regulates mitochondrial function and promotes migratory behaviors of breast cancer cells through the Src-STAT3-POLG axis | Cancer Cell International
Sung H, Ferlay J, Siegel RL, Laversanne M, Soerjomataram I, Jemal A, Bray F. Global cancer statistics 2020: GLOBOCAN estimates of incidence and mortality Worldwide for 36 cancers in 185 countries. CA Cancer J Clin. 2021;71(3):209–49. doi.org/10.3322/caac.21660. Article PubMed Google Scholar Hu G, Chong RA, Yang Q, Wei Y, Blanco…
Fatty Acid Metabolism-Related lncRNAs as Biomarkers for SKCM
Introduction Skin cutaneous melanoma (SKCM), as one of the most aggressive types of cancer due to its elevated degree of heterogeneity, has gained increasing attention during the past few decades.1 Also known as “the cancer that rises with the sun”,2 melanoma originates from cancerous melanocytes due to molecular or genetic…
Special Issue : Extracellular Vesicles and ncRNA
Dear Colleagues, Over the past two decades, the biological science arena has witnessed the emergence and rapid advancement of two distinct research domains: noncoding RNA (ncRNA) and extracellular vesicles. Presently, the significance of ncRNA in the biology of virtually all living organisms is beyond dispute, and our comprehension of its…
How an immune response is driven by one lette
One-letter difference in our DNA determines whether BCG vaccine provides good protection against tuberculosis or not. Researchers at Radboudumc have elucidated how that one letter difference affects the activation and deactivation of the immune system. The discovery, published in Nature Genetics, not only provides more insight into interleukin-driven inflammatory responses,…
Just a One Letter Difference in DNA Affects the Activation of the Immune System
Register for free to listen to this article Thank you. Listen to this article using the player above. ✖ Want to listen to this article for FREE? Complete the form below to unlock access to ALL audio articles. One-letter difference in our DNA determines whether BCG vaccine…
Transition of allele-specific DNA hydroxymethylation at regulatory loci is associated with phenotypic variation in monozygotic twins discordant for psychiatric disorders | BMC Medicine
Lichtenstein P, Yip BH, Bjork C, Pawitan Y, Cannon TD, Sullivan PF, Hultman CM. Common genetic determinants of schizophrenia and bipolar disorder in Swedish families: a population-based study. Lancet. 2009;373(9659):234–9. Article PubMed Google Scholar Maurano MT, Humbert R, Rynes E, Thurman RE, Haugen E, Wang H, Reynolds AP, Sandstrom R,…
ncRNA | Free Full-Text | Regulation of Macrophage Polarization in Allergy by Noncoding RNAs
1. Introduction Allergies affect millions of people worldwide and are characterized by an excessive type 2 immune response to normally harmless substances, generally known as antigens or allergens, specifically [1,2]. Consequently, this response leads to the development of various allergic symptoms, including asthma, allergic rhinitis, and atopic dermatitis. In the…
Shotgun Metagenomic Sequencing | Psomagen, Inc.
More Sequencing Possibilities Choose from our wide range of sequencing options — whole genome to single-cell transcriptomics — to support your project. Genomics The most comprehensive way to investigate an entire genome.Get the whole story, including exons, introns, and untranslated regions (UTR). Transciptomics A more complete picture of various disease…
A chromosome-level genome assembly for the Silkie chicken resolves complete sequences for key chicken metabolic, reproductive, and immunity genes
Friedman-Einat, M. & Seroussi, E. Avian leptin: bird’s-eye view of the evolution of vertebrate energy-balance control. Trends Endocrinol. Metab. 30, 819–832 (2019). Article CAS PubMed Google Scholar International Chicken Genome Sequencing C. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 432, 695–716 (2004)….
In-depth analyses of lncRNA and circRNA expression in the hi… : NeuroReport
Zhang, Yongcanga,*; Tang, Liangb,c,*; Wang, Yanb; Zhu, Xiaoyana; Liu, Lana Author Information aMedical College, Tibet University, Lhasa, Tibet bDepartment of Basic Medicine, Changsha Medical University cHunan Provincial University Key Laboratory of the Fundamental and Clinical Research on Neurodegenerative Diseases, Changsha Medical University, Changsha, People’s Republic of China Received 19…
Research progress in the role of non-coding RNAs and embryo implantation
Non-coding RNA (ncRNA) refers to RNA that lack the ability to encode protein. Based on their distinct biological characteristics, ncRNA are mainly classified into microRNA (miRNA), long non-coding RNA (lncRNA), and circular RNA (circRNA). NcRNA plays a crucial regulatory role in various biological processes. Pregnancy is a highly intricate physiological…
Identification and validation of key miRNAs for colon cancer
Introduction With nearly 2 million new cases and 1 million deaths worldwide in 2020, colorectal cancer is the third-most common cancer and the second leading cause of cancer-related deaths.1 According to data from the US Surveillance, Epidemiology and End Results program and the National Program of Cancer Registries program, the…
01 | Ribo-off rRNA depletion kit (Plant) Anawa
The Ribo-off rRNA depletion kit (Plant) is designed to deplete rRNA (including 5S, 18S and 25S rRNA) from total RNA of plant roots, seeds and leaves and to obtain mRNA and other non-coding RNA. This kit is suitable for removing rRNA from 1 μg – 5μg of plant total RNA….
Chapter 6 GGHH 2023 – notes – Chapter 6. Expression Quantitative Trait Loci (eQTL) Learning Outcomes
Chapter 6. Expression Quantitative Trait Loci (eQTL) Learning Outcomes Define an eQTL Summarise the methodology of RNAseq Understand the reason for expressing RNAseq outcomes as transcripts per million (TPM) Explain why patterns of H3K4me3 and H3K27ac can be used as markers of transcriptionally active genes Incorporate this data into a…
m6A-related lncRNAs as potential biomarkers and the lncRNA ELFN1-AS1/miR-182-5p/BCL-2 regulatory axis in diffuse large B-cell lymphoma
doi: 10.1111/jcmm.18046. Online ahead of print. Affiliations Expand Affiliations 1 Department of General Surgery, Guizhou Provincial people’s Hospital, Guiyang, China. 2 Department of Infectious Diseases, Guizhou Provincial people’s Hospital, Guiyang, China. Item in Clipboard Qinglong Yang et al. J Cell Mol Med. 2023. Show details Display options Display options Format AbstractPubMedPMID…
Transcriptome analysis reveals pituitary lncRNA, circRNA and mRNA affecting fertility in high-and low-yielding goats
1South China Agricultural University, China The final, formatted version of the article will be published soon. Notify me Receive an email when it is updated You just subscribed to receive the final version of the article The pituitary gland serves as the central…
Salpa genome and developmental transcriptome analyses reveal molecular flexibility enabling reproductive success in a rapidly changing environment
Loeb, V. et al. Effects of sea-ice extent and krill or salp dominance on the Antarctic food web. Nature 387, 897–900 (1997). Article ADS CAS Google Scholar Atkinson, A., Siegel, V., Pakhomov, E. & Rothery, P. Long-term decline in krill stock and increase in salps within the Southern Ocean. Nature…
Functions Support the New RNA Gene Paradigm
Photo credit: THAVIS 3D via Unsplash. In recent days I have covered a new paper published in BioEssays by Australian molecular biologist John Mattick who cites the need for a “paradigm shift” in biology away from the concept of junk DNA (see here, here, and here). I recounted how this shift is being driven by…
How should I run ssgsea analysis ?
How should I run ssgsea analysis ? 1 I have TPM expression data from RNA-seq data analysis. The data comprises of not only protein coding genes but also several other biotypes like miRNA, lncRNA, pseudogene etc making the matrix genes around 60,000. Here, should I filter by data with biotype=”protein…
How to identify the 300 kb upstream and downstream genes of lncRNAs?
How to identify the 300 kb upstream and downstream genes of lncRNAs? 3 Hi I have a list of human lncRNAs expressed in the blood sample. I want to know the upstream and downstream of genes in the range of ± 300 kb. please guide me on how to find…
Integrative lncRNA, circRNA, and mRNA analysis reveals expression profiles of six forensic body fluids/tissue
RNAs have attracted much attention in forensic body fluid/tissue identification (BFID) due to their tissue-specific expression characteristics. Among RNAs, long RNAs (e.g., mRNA) have a higher probability of containing more polymorphic sites that can be used to assign the specific donor of the body fluid/tissue. However, few studies have characterized…
Analysis of nucleoporin 107 overexpression
Introduction Lung cancer is one of the most common types of cancer worldwide and the leading cause of cancer death.1 The main category of lung cancer is non-small cell lung cancer, accounting for about 85%, and lung adenocarcinoma, as a kind of non-small cell lung cancer, is the most frequently…
how to get ER, PR and HER2 data from TCGA BRCA
how to get ER, PR and HER2 data from TCGA BRCA 2 Hi I have dowloaded the BRCA data from TCGA using TCGABiolinks I have done this: BRCARnaseqSE <- GDCprepare(query.a, directory = “BRCA_all”) sample.info <- SummarizedExperiment::colData(BRCARnaseqSE) Now I want to get data on ER, PR and HER2 – positive, negative…
CRISPR-Cas13d screens identify KILR a breast cancer risk-associated lncRNA that regulates DNA replication and repair.
Abstract Long noncoding RNAs (lncRNAs) have surpassed the number of protein-coding genes, yet the majority have no known function. We previously discovered >800 lncRNAs at regions identified by breast cancer genome-wide association studies (GWAS). Here, we performed a pooled CRISPR-Cas13d RNA knockdown screen to identify which of these lncRNAs altered…
ncRNA | Free Full-Text | Ethanol
Received: 14 July 2023 / Revised: 23 October 2023 / Accepted: 3 November 2023 / Published: 17 November 2023 Round 1 Reviewer 1 Report Comments and Suggestions for Authors Rizavi and colleagues present a study describing the effects of alcohol and PARP inhibitor on the lncRNA ribosomal binding. The study…
standalone blastx of queries without NR annotations
standalone blastx of queries without NR annotations 0 I have to identify long non-coding RNA transcripts in Arabidopsis thaliana using expressed sequence tags. For that I have downloaded ESTs from dbEST NCBI. Next I need to blastx ESTs to nr database but can not be done through online database due…
Conceptual question about open reading frames
Conceptual question about open reading frames 0 Many publications state that typical way to classify mRNA vs. lncRNA is based off whether they have an open-reading frame, and that typical open-reading frames must be 300 nucleotides long. If that is the case (or at least typical assumption), why do many…
ncRNA | Free Full-Text | An Overview of the Immune Modulatory Properties of Long Non-Coding RNAs and Their Potential Use as Therapeutic Targets in Cancer
Non-Coding RNA 2023, 9(6), 70; doi.org/10.3390/ncrna9060070 (registering DOI) Non-Coding RNA 2023, 9(6), 70; doi.org/10.3390/ncrna9060070 (registering DOI) Received: 27 June 2023 / Revised: 25 October 2023 / Accepted: 8 November 2023 / Published: 11 November 2023 Round 1 Reviewer 1 Report Comments and Suggestions for Authors In the current manuscript, Moises et al….
The Bib Theorists: Exploring the Extensive Effects of SARS-CoV-2 Infection on Host Systems
Title: COVID-19’s Impact on the Cardiovascular System: Uncovering the Mechanisms The Bib Theorists As the world continues to grapple with the effects of the COVID-19 pandemic, researchers are uncovering more about the virus’s impact on various bodily systems. Among them, the cardiovascular system has emerged as a significant player in…
vcf – VEP annotation INFO field Ensembl IDs and locations
I have a vcf file that I annoteted with VEP, for human data. I have run VEP to annotate my files with some additional parameters (as shown below in the ##VEP-command-line). However, my output is rather strange (mainly the INFO column). ##VEP=”v108″ time=”2023-04-27 15:13:08″ cache=”workflow/resources/variants/cache_vep/homo_sapiens/108_GRCh38″ ensembl-funcgen=108.56bb136 ensembl-variation=108.a885ada ensembl-io=108.58d13c1 ensembl=108.d8a9c80 1000genomes=”phase3″…
Bioinformatics analysis and experimental validation of tumorigenic role of PPIA in gastric cancer
Expression of PPIA in pan-cancer and prognostic value of PPIA in GC To assess the effects of PPIA on the genesis of human tumor, TCGA database was utilized to detect the mRNA levels of PPIA in 33 types of cancer. The findings demonstrated that the levels of PPIA were upregulated…
Non-coding RNA-mediated endothelial-to-mesenchymal transition in human diabetic cardiomyopathy, potential regulation by DNA methylation | Cardiovascular Diabetology
Raghavan S, Vassy JL, Ho Y, Song RJ, Gagnon DR, Cho K, et al. Diabetes mellitus-related all-cause and cardiovascular mortality in a national cohort of adults. J Am Heart Assoc. 2019;8(4): e011295. Article PubMed PubMed Central Google Scholar Jia G, Whaley-Connell A, Sowers JR. Diabetic cardiomyopathy: a hyperglycaemia—and insulin-resistance-induced heart…
ncRNA | Free Full-Text | Dysregulation of Non-Coding RNAs: Roles of miRNAs and lncRNAs in the Pathogenesis of Multiple Myeloma
4. Dysregulation of lncRNAs in MM In recent years, numerous studies have focused on the role of lncRNAs in MM pathogenesis. Since then, the role of aberrantly expressed lncRNAs in MM has been reported, highlighting the potential in clinical applications. For instance, lncRNAs participate in the differentiation of erythroid, myeloid,…
Researchers develop curated and integrated biomarker knowledgebase for animals
Graphical Abstract. Credit: Nucleic Acids Research (2023). DOI: 10.1093/nar/gkad873 Biological markers, commonly referred to markers or biomarkers, serve as quantifiable and measurable indicators of certain biological states in normal and pathogenic processes, as well as potential pharmacologic responses to therapeutics. They serve as the foundation for diagnostic analysis, the identification…
Conversion of Gene Name to Ensembl ID
Using Enembl REST API: rest.ensembl.org/lookup/symbol/homo_sapiens/A1CF assembly_name: GRCh38 biotype: protein_coding db_type: core description: APOBEC1 complementation factor [Source:HGNC Symbol;Acc:HGNC:24086] display_name: A1CF end: 50885675 id: ENSG00000148584 logic_name: ensembl_havana_gene_homo_sapiens object_type: Gene seq_region_name: 10 source: ensembl_havana species: homo_sapiens start: 50799409 strand: -1 version: 15 rest.ensembl.org/lookup/symbol/homo_sapiens/A1CF?content-type=application/json {“strand”:-1,”assembly_name”:”GRCh38″,”version”:15,”species”:”homo_sapiens”,”end”:50885675,”description”:”APOBEC1 complementation factor [Source:HGNC Symbol;Acc:HGNC:24086]”,”source”:”ensembl_havana”,”db_type”:”core”,”object_type”:”Gene”,”id”:”ENSG00000148584″,”seq_region_name”:”10″,”display_name”:”A1CF”,”start”:50799409,”logic_name”:”ensembl_havana_gene_homo_sapiens”,”biotype”:”protein_coding”} Look up multiple symbols at…
Identification of hub genes associated with gastric cancer
Introduction GC is a common malignant tumor of digestive system. According to the International Agency for Research on Cancer (IARC) of the World Health Organization, there were 19.29 million new cancer cases and 9.96 million deaths worldwide in 2020, of which the number of new cases of GC was 1089,103…
HOXC-AS3 as an Oncological Biomarker and Therapeutic Target
1Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, 330008, People’s Republic of China; 2Department of General Surgery, Jiujiang Hospital of Traditional Chinese Medicine, Jiujiang, Jiangxi, 332007, People’s Republic of China; 3Queen Mary School, Nanchang University, Nanchang, Jiangxi, 330038, People’s Republic of China Correspondence: Hongliang Luo,…
Genome-wide analyses identify NEAT1 as genetic modifier of age at onset of amyotrophic lateral sclerosis | Molecular Neurodegeneration
van Es MA, Hardiman O, Chio A, Al-Chalabi A, Pasterkamp RJ, Veldink JH, van den Berg LH. Amyotrophic Lateral Sclerosis. Lancet (London England). 2017;390:2084–98. Article PubMed Google Scholar Liu MS, Cui LY, Fan DS. Age at onset of Amyotrophic Lateral Sclerosis in China. Acta Neurol Scand. 2014;129:163–7. Article CAS PubMed …
How do I write a correctly formatted gff3 file in R?
Dear all, I am trying to annotate non-coding RNA in a small RNA-seq dataset. The RNACentral gff3 file that I am using has different chromosome identifiers than the genome assembly. I have loaded the gff3 file in R where I changed the chromosome identifiers using the the assembly report and…
Macrophage polarization and metabolism in atherosclerosis
Organization WH the top 10 causes of death. www.who.int/news-room/fact-sheets/detail/the-top-10-causes-of-death, 2019. Rana JS, Khan SS, Lloyd-Jones DM, Sidney S. Changes in mortality in Top 10 causes of death from 2011 to 2018. J Gen Intern Med. 2021;36:2517–8. Article PubMed Google Scholar Libby P. The changing landscape of atherosclerosis. Nature. 2021;592:524–33. Article …
Transcriptional regulation and overexpression of GST cluster enhances pesticide resistance in the cotton bollworm, Helicoverpa armigera (Lepidoptera: Noctuidae)
Bras, A., Roy, A., Heckel, D. G., Anderson, P. & Green, K. K. Pesticide resistance in arthropods: ecology matters too. Ecol. Lett. 25, 1746–1759 (2022). Article PubMed PubMed Central Google Scholar Chen, Y. H. & Schoville, S. D. Editorial overview: ecology: ecological adaptation in agroecosystems: novel opportunities to integrate evolutionary…
RNA Targeting Small Molecule Drug Discovery Market Size, Share And Growth Analysis For 2023-2032
(MENAFN– EIN Presswire) RNA Targeting Small Molecule Drug Discovery Global Market Report 2023 – Market Size, Trends, And Market Forecast 2023-2032 The Business Research Company’s RNA Targeting Small Molecule Drug Discovery Global Market Report 2023 – Market Size, Trends, And Market Forecast 2023-2032 The Business Research Company’s global market reports…
Pseudogene MAPK6P4-encoded functional peptide promotes glioblastoma vasculogenic mimicry development
Gusyatiner, O. & Hegi, M. E. Glioma epigenetics: from subclassification to novel treatment options. Semin. Cancer Biol. 51, 50–58 (2018). Article PubMed Google Scholar Kunnakkat, S. & Narayana, A. Bevacizumab in the treatment of high-grade gliomas: an overview. Angiogenesis 14, 423–430 (2011). Article PubMed Google Scholar Luo, Q. et al….
Identification of a lncRNA/circRNA-miRNA-mRNA ceRNA Network in Alzheimer’s Disease
Background: Alzheimer’s disease (AD) occurs in the elderly and pre-elderly, characterized by decline of memory, cognitive dysfunction, impairment of learning capacity, and motor dysfunction. Recently a competitive endogenous RNA (ceRNA) network has been found to be related to AD progression, but there is still little understanding of the ceRNA regulatory…
Figure 5 | lncRNA DLX6-AS1 Promotes Myocardial Ischemia-Reperfusion Injury through Mediating the miR-204-5p/FBXW7 Axis
Mediators of Inflammation/ 2023/ Article/ Fig 5 / Research Article Figure 5 DLX6-AS1 promoted FBXW7 expression by sponging miR-204-5p. (a) The predicted binding sites between miR-204-5p and FBXW7 were presented. (b) The interaction between miR-204-5p and FBXW7 in H9c2 cells was verified by luciferase reporter assay. (c) H9c2 cells were…
Investigation of LGALS2 expression in the TCGA database reveals its clinical relevance in breast cancer immunotherapy and drug resistance
Bray, F., Laversanne, M., Weiderpass, E. & Soerjomataram, I. The ever-increasing importance of cancer as a leading cause of premature death worldwide. Cancer 127, 3029–3030. doi.org/10.1002/cncr.33587 (2021). Article PubMed Google Scholar Xia, C. et al. Cancer statistics in China and United States, 2022: Profiles, trends, and determinants. Chin. Med. J….
LncRNA/CircRNA-miRNA-mRNA Axis in Atherosclerotic Inflammation: Research Progress
Title:LncRNA/CircRNA-miRNA-mRNA Axis in Atherosclerotic Inflammation: Research Progress Volume: 25 Author(s): Nuan Lv, Yilin Zhang, Luming Wang, Yanrong Suo, Wenyun Zeng, Qun Yu, Bin Yu and Xijuan Jiang* Affiliation: School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China Keywords: Atherosclerosis, Inflammation, LncRNA, CircRNA, miRNA, mRNA. Abstract: Atherosclerosis is…
rs67047829 genotypes of ERV3-1/ZNF117 are associated with lower body mass index in the Polish population
Datamining showed that most (80/137 = 58%) of the high-frequency PTC-SNPs, defined as having minor-allele frequencies (MAFs) between 1 and 99%, including rs67047829, had MAFs > 5%, indicating most likely near-neutral selection (Supplementary Table S1). Initial regression models for several PTC-SNPs versus BMI gave low p-values (Supplementary Table S3), suggesting possible future studies, but…
ncRNA | Free Full-Text | A Small De Novo CNV Deletion of the Paternal Copy of FOXF1, Leaving lncRNA FENDRR Intact, Provides Insight into Their Bidirectional Promoter Region
Received: 28 August 2023 / Revised: 3 October 2023 / Accepted: 6 October 2023 / Published: 9 October 2023 Round 1 Reviewer 1 Report Dear authors, After consideration, I have some recommendations and concerns that I believe will improve the quality and impact of your manuscript. While the manuscript provides…
Investigation of lncRNA PART1 SNP (rs8176070) polymorphism in Turkey knee osteoarthritis patient population by DNA sequence analysis
Author links open overlay panelIlkay Piskin a, Gulben Akcan a 1, Ahmet Firat b 2, Ahmet Cevik Tufan a 3 Show more doi.org/10.1016/j.humgen.2023.201224Get rights and content Highlights • Osteoarthritis (OA) is a chronic disease that causes damage to cartilage and bone. • The world of long non-coding RNAs is still…
lncRNA SNHG8 regulates stress granule formation by modifying TIA1 protein levels in tauopathies
Neurology/Psychiatric Dominantly inherited mutations in the MAPT gene, which encodes the tau protein, result in a subset of tauopathies named frontotemporal lobar degeneration with tau pathology (FTLD-tau). However, the mechanisms by which MAPT mutations cause disease remain unclear. In a recent study, researchers from Washington University in St. Louis aimed…
Functional analysis of differentially expressed circular RNAs in sheep subcutaneous fat | BMC Genomics
Chikwanha, O. C., P. Vahmani, V. Muchenje, M. E. R. Dugan and C. Mapiye (2018). Nutritional enhancement of sheep meat fatty acid profile for human health and wellbeing. Food research international (Ottawa, Ont.) 104: 25–38. doi.org/10.1016/j.foodres.2017.05.005. Khan R, Raza SHA, Schreurs N, Xiaoyu W, Hongbao W, Ullah I, et al….
small RNAseq analysis of non human samples
small RNAseq analysis of non human samples 0 Hello all, Please share a workflow/pipeline for RNAseq analysis focused on small RNA of insects such as roaches. Since annotation is available for protein coding only, in this scenario how do i deal with question of regulation of small RNA Any help…
Progress and challenges in completing the human gene catalogue
In a recent review published in Nature, a group of authors reviewed the progress and challenges in annotating the human genome, including protein-coding genes, isoforms, and non-coding ribonucleic acids (RNAs), and advocated for a universal annotation standard for clinical use. Study: The status of the human gene catalogue. Image Credit:…
The status of the human gene catalogue
Understanding our Genetic Inheritance: The US Human Genome Project, The First Five Years 1991-1995 (US Department of Health and Human Services, US Department of Energy, 1990). Nurk, S. et al. The complete sequence of a human genome. Science 376, 44–53 (2022). Describes the first complete gap-free assembly and annotation of…
Histone regulator KAT2A acts as a potential biomarker related to tumor microenvironment and prognosis of diffuse large B cell lymphoma | BMC Cancer
Zhang Y, Tan H, Daniels JD, Zandkarimi F, Liu H, Brown LM, et al. Imidazole Ketone Erastin induces ferroptosis and slows Tumor Growth in a mouse lymphoma model. Cell Chem Biol. 2019;26(5):623–33e9. Article CAS PubMed PubMed Central Google Scholar Hartert KT, Wenzl K, Krull JE, Manske M, Sarangi V, Asmann…
Unveiling Wheat’s Long Non-Coding RNAs: Grain Development Leap
Wheat is a global staple food and plays a pivotal role in the livelihoods of billions of people. Although long non-coding RNAs (lncRNAs) have been recognized as crucial regulators of numerous biological processes, our knowledge of lncRNAs associated with wheat (Triticum aestivum) grain development remains minimal. Seed Biology published an…
ncRNA | Free Full-Text | The Intergenic Type lncRNA (LINC RNA) Faces in Cancer with In Silico Scope and a Directed Lens to LINC00511: A Step toward ncRNA Precision
CRC Upregulated 153-5p HIF-1 activates LINC00511, targeting HIF-1’s 3-UTR and +ve feedback loop [78] Oncogene Human CRC tissues vs. paired adjacent non-tumor and CRC cell lines HT29, LOVO, SW620, SW480 vs. normal colon epithelial FHC cell line and athymic BALB/c nude mice for implantation – HNF4 promotes LINC00511 transcription, interaction…
Reconstructing the cytokine view for the multi-view prediction of COVID-19 mortality | BMC Infectious Diseases
Li H, Liu SM, Yu XH, Tang SL, Tang CK. Coronavirus disease 2019 (COVID-19): current status and future perspectives. Int J Antimicrob Agents. 2020;55(5):105951. Article CAS PubMed PubMed Central Google Scholar . virusncov.com/. Iwendi C, Bashir AK, Peshkar A, Sujatha R, Chatterjee JM, Pasupuleti S, et al. COVID-19 Patient Health…
Genome-Wide Association Study of Alopecia Areata in Taiwan
Introduction Alopecia areata (AA) is one of Taiwan’s most common autoimmune hair diseases and incidence rate of AA is 0.22%.1–3 The main symptoms of AA are rapid, non-scarring hair loss that affects body hair, facial hair, eyelashes, and brows.1,2 In the United States, the prevalence of AA is estimated to…
Total Flavonoids of Rhizoma Drynariae Treat Osteoarthritis
Introduction Osteoarthritis (OA) is a common degenerative joint disease characterized by chronic pain and ambulation limitation, affecting about 250 million people worldwide.1 With increased aging population, the OA incidence rapidly increases and OA has become a major cause of disability.2,3 The morbidity of OA is closely related to articular cartilage,…
ncRNA | Free Full-Text | Long Non-Coding RNA TUG1 Gene Polymorphism and TUG1 Expression Level as Molecular Biomarkers of Systemic Lupus Erythematosus and Lupus Nephritis
1. Introduction Systemic lupus erythematosus (SLE) is a chronic autoimmune disease with a wide variety of manifestations ranging from mild cutaneous to organ failure as lupus nephritis (LN) and cardiopulmonary complications [1]. SLE is mainly present among young women, with a greater incidence in certain ethnic groups, such as Asian,…
Competitive endogenous network of circRNA, lncRNA, and miRNA in osteosarcoma chemoresistance
Review doi: 10.1186/s40001-023-01309-x. Affiliations Expand Affiliations 1 Department of Medical Imaging, Tongji Hospital, Tongji University School of Medicine, Xincun Road No. 389, Shanghai, 200065, China. 2 Department of Orthopedics, Shanghai General Hospital of Shanghai Jiaotong University, Wujin Road No. 85, Shanghai, 200080, China. drmachunhui@163.com. 3 Department of Medical Imaging, Tongji…
Genome-wide identification of lncRNA & mRNA for T2DM
Department of Biotechnology, College of Science, Taif University, Taif, 21944, Saudi Arabia Correspondence: Sarah Albogami, Department of Biotechnology, College of Science, Taif University, P.O. Box 11099, Taif, 21944, Saudi Arabia, Email [email protected] Purpose: According to the World Health Organization, Saudi Arabia ranks seventh worldwide in the number of patients with…
Cas13d-mediated isoform-specific RNA knockdown with a unified computational and experimental toolbox
Abstract Alternative splicing is an essential mechanism for diversifying proteins, in which mature RNA isoforms produce proteins with potentially distinct functions. Two major challenges in characterizing the cellular function of isoforms are the lack of experimental methods to specifically and efficiently modulate isoform expression and computational tools for complex experimental…
CircRNA PGAM1 Promotes the Migration and Invasion of Pancreatic Adenocarcinoma Cells by Activating the AKT/mTOR Signaling Pathway
Atay, S. (2020). Integrated transcriptome meta-analysis of pancreatic ductal adenocarcinoma and matched adjacent pancreatic tissues. PeerJ, 8, e10141. Article PubMed PubMed Central Google Scholar Sung, H., Ferlay, J., Siegel, R. L., Laversanne, M., Soerjomataram, I., Jemal, A., Global Cancer Statistics, et al. (2021). GLOBOCAN estimates of incidence and mortality worldwide…
Integrated bioinformatics analysis of noncoding RNAs with tumor immune microenvironment in gastric cancer
Sung, H. et al. Global Cancer Statistics 2020: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries. CA Cancer J. Clin. 71, 209–249. doi.org/10.3322/caac.21660 (2021). Article PubMed Google Scholar Siegel, R. L., Miller, K. D., Fuchs, H. E. & Jemal, A. Cancer statistics, 2022. CA A…
RNA-sequencing and bioinformatics analysis | COPD
Introduction COPD, a common preventable and treatable disease characterized by persistent airflow limitation and respiratory symptoms, is associated with exposure to harmful environments. COPD is currently the third leading cause of death globally. The high incidence and mortality of COPD, which seriously threaten human health, represent a public health problem…
Role of the cGAS-STING pathway in radiotherapy for non-small cell lung cancer | Radiation Oncology
Sung H, Ferlay J, Siegel RL, et al. Global Cancer Statistics 2020: GLOBOCAN estimates of incidence and Mortality Worldwide for 36 cancers in 185 countries. CA Cancer J Clin. 2021;71(3):209–49. doi.org/10.3322/caac.21660 Article PubMed Google Scholar Duma N, Santana-Davila R, Molina JR. Non-Small Cell Lung Cancer: Epidemiology, Screening, diagnosis, and treatment….
ncRNA | Free Full-Text | Non-Coding RNAs: Foes or Friends for Targeting Tumor Microenvironment
Received: 27 June 2023 / Revised: 17 August 2023 / Accepted: 22 August 2023 / Published: 28 August 2023 Round 1 Reviewer 1 Report This is a very comprehensive treatment of the topic of ncRNAs in cancer therapy. There is definitely a need for this work to be published but…
ncRNA | Free Full-Text | Systematic Analysis of Long Non-Coding RNAs in Inflammasome Activation in Monocytes/Macrophages
Received: 7 August 2023 / Revised: 21 August 2023 / Accepted: 23 August 2023 / Published: 25 August 2023 Round 1 Reviewer 1 Report There are a few errors that must be corrected before the manuscript is accepted. 1) In Figure 1C the green ovals are mislabeled. They should…
Novel epigenetic molecular therapies for imprinting disorders
Surani MA, Barton SC, Norris ML. Development of reconstituted mouse eggs suggests imprinting of the genome during gametogenesis. Nature. 1984;308:548–50. Article CAS PubMed Google Scholar McGrath J, Solter D. Completion of mouse embryogenesis requires both the maternal and paternal genomes. Cell. 1984;37:179–83. Article CAS PubMed Google Scholar Barlow DP, Stoger…
KGETCDA: an efficient representation learning framework based on knowledge graph encoder from transformer for predicting circRNA-disease associations
doi: 10.1093/bib/bbad292. Online ahead of print. Affiliations Expand Affiliations 1 School of Automation Science and Engineering, Xi’an Jiaotong University, 710049, Shaanxi, China. 2 Research Institute of Xi’an Jiaotong University, 311200, Zhejiang, China. 3 Sichuan Digital Economy Industry Development Research Institute, 610036, Sichuan, China. Item in Clipboard Jinyang Wu et al. Brief…
What is the next step in preventative therapi
image: In a chronic inflammatory context, epigenetic changes occur in LPCs: (1) through a sustained stimulation by cytokines that either promotes dedifferentiation and transformation of LPCs to CSCs (IL-17, TNF-α and IL-6), or in contrast avoiding their transformation (IFN-γ, IL-27); (2) by hosting small non-coding RNAs transferred by exosomes coming from…
MD Anderson Research Highlights for August 16, 2023
Newswise — HOUSTON ― The University of Texas MD Anderson Cancer Center’s Research Highlights showcases the latest breakthroughs in cancer care, research and prevention. These advances are made possible through seamless collaboration between MD Anderson’s world-leading clinicians and scientists, bringing discoveries from the lab to the clinic and back. Recent…
Animals | Free Full-Text | Integrated Comparative Transcriptome and circRNA-lncRNA-miRNA-mRNA ceRNA Regulatory Network Analyses Identify Molecular Mechanisms Associated with Intramuscular Fat Content in Beef Cattle
1. Introduction Intramuscular fat (IMF), also known as marbling, has a major role in various meat quality traits. The composition of fatty acids in IMF, especially polyunsaturated fatty acids (PUFA), affects beef quality, with IMF closely related to various sensory characteristics, including taste, juiciness, and tenderness [1,2,3,4]. A critical aspect…
ncRNA | Free Full-Text | Investigation into the Role of Long-Non-Coding RNA MIAT in Leukemia
1. Introduction Recent advances in RNA-based approaches and Next Generation Technologies have unveiled the existence of non-coding RNAs (ncRNA), transcripts that lack the ability to code for proteins [1,2]. ncRNAs typically lack an open reading frame (ORF) and are subdivided into housekeeping and regulatory transcripts. Housekeeping ncRNAs are usually 50–500…
Bioinformatics analysis of hedgehog interacting protein in colorectal cancer: a study based on GEO data and TCGA data | BMC Gastroenterology
HHIP was lowly expressed in CRC tissues and HHIP expression was associated with cancer patient prognosis We acquired the RNA-sequencing data of CRC from TCGA public database. To pursue possible roles of HHIP in carcinostasis, we first analyzed HHIP expression in 33 types of human cancers. As shown in Fig. 1A,…
LncRNA FENDRR suppresses melanoma growth
Introduction Cutaneous melanoma is a kind of highly aggressive and metastatic cancer.1 It only occurs in 5% of all skin cancers but causes more than 75% of deaths.2,3 Melanoma can be cured by surgical removal at an early stage.4 However, when the disease progresses to an advanced stage (stage IV),…
Integrative Transcriptomic Profiling of mRNA, miRNA, circRNA, and lncRNA in Alveolar Macrophages Isolated from PRRSV-Infected Porcine
1Sun Yat-sen University, China 2Sun Yat-sen Memorial Hospital, China 3Henan University of Science and Technology, China The final, formatted version of the article will be published soon. Notify me Receive an email when it is updated You just subscribed to…
CircRNA-0100 positively regulates the differentiation of cashmere goat SHF-SCs into hair follicle lineage via sequestering miR-153-3p to heighten …
Original study Arch. Anim. Breed., 65, 55–67, 2022 Open Access doi.org/10.5194/aab-65-55-2022 © Author(s) 2022. This work is distributed under Archives Animal Breeding the Creative Commons Attribution 4.0 License. CircRNA-0100 positively regulates the differentiation of cashmere goat SHF-SCs into hair follicle lineage via sequestering miR-153-3p to heighten the KLF5 expression Junyin…
Identification of immuno-inflammation-related biomarkers | JIR
Introduction Acute myocardial infarction (AMI) is the sudden irreversible necrosis of heart muscle, which commonly results from atherosclerotic plaque disruption and subsequent interruption of blood flow.1 It is one of the heart diseases with the highest prevalence and incidence and brings enormous health and financial burdens.2 Despite the rapid development…
Transcriptomic risk scores for attention deficit/hyperactivity disorder
Song P, Zha M, Yang Q, Zhang Y, Li X, Rudan I. The prevalence of adult attention-deficit hyperactivity disorder: A global systematic review and meta-analysis. J Glob Health. 2021;11:1–9. Article Google Scholar Faraone SV, Asherson P, Banaschewski T, Biederman J, Buitelaar JK, Ramos-Quiroga JA, et al. Attention-deficit/hyperactivity disorder. Nat Rev…
ncRNA | Free Full-Text | Long Non-Coding RNA Signatures in Lymphopoiesis and Lymphoid Malignancies
The most common types of B-cell lymphomas include chronic lymphocytic leukemia (CLL), mantle-cell lymphoma (MCL), Burkitt’s lymphoma (BL), follicular lymphoma (FL), and diffuse large B-cell lymphoma (DLBCL). Several studies have identified differently expressed lncRNAs in B-cell NHLs by using datasets that confirm the findings in tissue samples or cell lines…
ncRNA | Free Full-Text | Crosstalk between Long Non-Coding RNA and Spliceosomal microRNA as a Novel Biomarker for Cancer
3.1.1. HAGLR (HOXD Antisense Growth-Associated Long Non-Coding RNA) HAGLR, known also as HOXD-AS1, is located between the HOXD1 and HOXD3 genes on chromosome 2q31.1 (Figure 1A) and has been reported to play a critical role in the development and progression of different human cancers, including bladder, cervical, colorectal, gastric, ovarian,…
class codes x , lncRNA
class codes x , lncRNA 0 can anyone help me from getting class codes X from lnc rna filtering. i am getting very less transcripts of class codes x. is there anything to do with the stringtie or cuffcompare options inorder to get class codes x. tq codes X lncRNA…
Gtf or GFF with target genes regulated by ncRNAs
Gtf or GFF with target genes regulated by ncRNAs 0 I was wondering if there is a gtf containing target genes regulated by ncRNAs. In databases like GENECODE i can download a gff/gtf with the gene_ids which corresponds to the id of the lncRNA. Is it possible to find or…
Immune Cell Infiltration and Novel Biomarkers of CAD
Introduction Coronary artery disease (CAD) is a major cause of death and disability worldwide,1 and has been proved to be triggered by the interaction of environmental and genetic risk factors. It is considered to be a systemic, progressive inflammatory disease. The atherosclerotic plaque formed in CAD accumulates chronically in the…
reference annotation for the human and mouse genomes in 2023
D942–D949 Nucleic Acids Research, 2023, Vol. 51, Database issue Published online 24 November 2022 doi.org/10.1093/nar/gkac1071 GENCODE: reference annotation for the human and mouse genomes in 2023 Adam Frankish 1,* , Sı́lvia Carbonell-Sala2 , Mark Diekhans 3 , Irwin Jungreis 4,5 , Jane E. Loveland 1 , Jonathan M. Mudge1 ,…
[Intervention effect of Chuanxiong-Chishao herb pair on circRNA/lncRNA expression profile in a myocardial infarction-atherosclerosis model]
This study aimed to explore the intervention effect of Chuanxiong-Chishao herb pair(CX-CS) on a myocardial infarction-atherosclerosis(MI-AS) mouse model and investigate its effect on the expression profile of circular RNAs(circRNAs)/long non-coding RNAs(lncRNAs) in ischemic myocardium and aorta. Sixty male ApoE~(-/-) mice were randomly assigned to a model group, high-, medium-, and…
miRNA, lncRNA and circRNA: targeted molecules with therapeutic promises in Mycoplasma pneumoniae infection
Review . 2023 Jul 21;205(8):293. doi: 10.1007/s00203-023-03636-3. Affiliations Expand Affiliations 1 The Affiliated Nanhua Hospital, Department of Clinical Laboratory, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China. 2 Department of Public Health Laboratory Sciences, School of Public Health, Hengyang Medical School, University of South China, Hengyang, Hunan,…
Integrated analysis of circRNA, lncRNA, miRNA and mRNA to reveal the ceRNA regulatory network of postnatal skeletal muscle development in Ningxiang pig
Introduction: The development of skeletal muscle is regulated by regulatory factors of genes and non-coding RNAs (ncRNAs). Methods: The objective of this study was to understand the transformation of muscle fiber type in the longissimus dorsi muscle of male Ningxiang pigs at four different growth stages (30, 90, 150, and…
The complementarity of DDR, nucleic acids and anti-tumour immunity
Decout, A., Katz, J. D., Venkatraman, S. & Ablasser, A. The cGAS–STING pathway as a therapeutic target in inflammatory diseases. Nat. Rev. Immunol. 21, 548–569 (2021). Article CAS PubMed PubMed Central Google Scholar Martincorena, I. & Campbell, P. J. Somatic mutation in cancer and normal cells. Science 349, 1483–1489 (2015)….
Integrated analysis of copy number variation-associated lncRNAs identifies candidates contributing to the etiologies of congenital kidney anomalies
Study design We aimed to investigate the potential contribution of lncRNAs to the pathogenicity of CAKUT associated CNVs. 19 recurrent CAKUT-associated CNVs were identified based on clinical researches of congenital anomalies of the kidney and urinary tracts (CAKUT) cases3,4,12,13 (Table 1). We retrieved lncRNAs located within these genomic regions as candidate…
Senior Bioinformatics Scientist – HAYA Therapeutics SA
Position Summary We are seeking highly motivated candidates to join our R&D team in San Diego and contribute to the development and application of advanced technologies in RNA-based therapeutics. You will be an early member of a highly dynamicscientific team generating and executing experiments on actionable, pioneering hypotheses to drive…
Help understanding enhancer and promoter annotation
Hello everyone, I am creating this post because I feel a bit overwhelmed and confused regarding the concept of “annotation”. I will provide some context for you to understand where is my confusion arising from. First of all, I understand that in bioinformatics, when you have a .bed file that…
rna seq – DE analysis tool and method for non-coding features
I am currently working with the non-coding features of A. thaliana, and trying to get the DE features. Among the three DE test methods in edgeR such as exactTest(), glmFit() and glmLRT(), glmQLFit() and glmQLFTest(), which is/are the one(s) most suitable for running DE tests on miRNA, snRNA, snoRNA, pseuogenes,…