Tag: clusterProfiler

Hunter, D. J. & Bierma-Zeinstra, S. Osteoarthritis. Lancet 393, 1745–1759 (2019). Article  CAS  PubMed  Google Scholar  Puig-Junoy, J. & Ruiz Zamora, A. Socio-economic costs of osteoarthritis: A systematic review of cost-of-illness studies. Semin. Arthritis Rheum. 44, 531–541 (2015). Article  PubMed  Google Scholar  Hunter, D. J., March, L. & Chew, M….

Cell culture Cell lines (MDA-MB-231, 4T1 and RPE-1) were purchased from the American Type Culture Collection (ATCC). TP53-knockout MCF10A, TP53-knockout RPE-1 and Trex1 knockout 4T1 cells were gifts from the Maciejowski laboratory at the Memorial Sloan Kettering Cancer Center (MSKCC). OVCAR-3 cells were a gift from J. D. Gonzales. All…

What statistical test should I use to analyse my two set of transcriptomique data? 0 I have an assembled transcriptome. I performed analyses on this transcriptome to extract candidate sequences involved in the production of a substance. Then, I annotated both sets of data using the Eggnog Mapper tool. This…

Job Description Overall Position Summary and Objectives Under this task order, the contractor will provide support services to satisfy the overall operational objectives. The primary objective is to provide services and deliverables through bioinformatics support services as part of an existing bioinformatics team. Minimum EducationMaster’s Resume Max Pages15 Certifications &…

Hi everyone First of all thank you for making rna-seq data much more accessible to an average clinical doctor through the DEseq2 packages and vignettes. I am though running into some trouble: I have a dataset of Nanostring mRNA-data from clinical study, which later was followed up. I therefore have…

Dot Plot using KEGG 2 Hi, I´m trying to do a dotplot using data from KEGG. I have my data represented, but I don´t want the species name in the X axis. My comand is: kegg_gene_list = sort(kegg_gene_list, decreasing = TRUE) kegg_gene_list = sort(kegg_gene_list, decreasing = TRUE) kegg_organism = “mmu”…

1 Introduction Stroke is the leading cause of permanent disability (Diener and Hankey, 2020). The latest global burden of disease (GBD) study (GBD 2019 Diseases and Injuries Collaborators, 2020) indicated that stroke is the leading cause of death in the Chinese population. The overall lifetime risk of stroke in China…

Screening for pivotal genes in diabetic peripheral neuropathy In screening the DEGs, a total of 6 DPN samples and 6 control samples were included in the GEO dataset GSE95849, and this dataset was normalised. A principal component analysis (PCA) of GSE95849 was conducted to demonstrate clustering using scatter plots. Each…

DOI: 10.18129/B9.bioc.methylGSA     This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see methylGSA. Gene Set Analysis Using the Outcome of Differential Methylation Bioconductor version: 3.13 The main functions for methylGSA are methylglm and methylRRA. methylGSA implements logistic regression adjusting number of probes as…

Podlesny-Drabiniok, A., Marcora, E. & Goate, A. M. Microglial phagocytosis: a disease-associated process emerging from Alzheimer’s disease genetics. Trends Neurosci. 43, 965–979 (2020). Article  CAS  PubMed  PubMed Central  Google Scholar  Calsolaro, V. & Edison, P. Neuroinflammation in Alzheimer’s disease: current evidence and future directions. Alzheimers Dement. 12, 719–732 (2016). Article …

fgsea/clusterProfiler Packages for nCounter data enrichment analysis 0 Hi there guys. I have gene expression data collected from nCounter with a panel of around 700 genes (Pancancer immune profiling panel). I performed differential expression analysis and now I want to see which immune-related pathways are over or under expressed in…

Preuss TM. The human brain: rewired and running hot. Ann N Y Acad Sci. 2011;1225 Suppl 1(Suppl 1):E182-191. Article  PubMed  Google Scholar  Roth G, Dicke U. Evolution of the brain and intelligence in primates. Prog Brain Res. 2012;195:413–30. Article  PubMed  Google Scholar  Laland K, Seed A. Understanding human cognitive uniqueness….

bitr() doesn’t recognize the keys I’ve entered as valid gene symbols for my organism’s database (‘SYMBOL’). 0 Hello, In trying to re-run my pathway analysis with a DEG set annotated with gene symbols. I have encountered this error while wanting to retrieve Entrez IDs for clusterProfiler. This is a new…

I was using R in RStudio under a conda environment with various bioconductor packages. But suddenly I ran into this error when I tried to load a package: ImportError: /home/user/anaconda3/envs/dmcgb/bin/../lib/libstdc++.so.6: version `GLIBCXX_3.4.30′ not found (required by /lib/x86_64-linux-gnu/libLLVM-13.so.1) It is not the first time that I have this error so I…

Introduction Liver cancer is the third most common cause of cancer death globally with hepatocellular carcinoma (HCC) accounting for the majority of liver cancer.1,2 Early HCC (stage I/II) treatment mainly includes radical surgical resection, radiofrequency ablation and liver transplantation.3,4 However, there is a lack of typical clinical symptoms with early-stage…

selection of GO terms manually 0 I am new to RNAseq analysis. I am performing GO analysis using Clusterprofiler in r and get some 100 GO terms, all within the cutoff of 0.05 set (gene list has more than 3K genes). Can I manually select 10 GO terms and plot…

How to see gene names in goProfiler2 functional enrichment analysis 0 Hi guys!! I would like to use goProfiler2 package in R for my GO and KEGG enrichment analysis, yet the output does not contain the name of the genes that involve in a specific pathway. Instead, it only shows…

Litman, G. W., Cannon, J. P. & Dishaw, L. J. Reconstructing immune phylogeny: New perspectives. Nat. Rev. Immunol. 5, 866–879 (2005). Article  CAS  PubMed  PubMed Central  Google Scholar  Criscitiello, M. F. & de Figueiredo, P. Fifty shades of immune defense. Heitman J, editor. PLoS Pathog. 9, e1003110 (2013). Article  CAS …

DOI: 10.18129/B9.bioc.scFeatures   This is the development version of scFeatures; for the stable release version, see scFeatures. scFeatures: Multi-view representations of single-cell and spatial data for disease outcome prediction Bioconductor version: Development (3.18) scFeatures constructs multi-view representations of single-cell and spatial data. scFeatures is a tool that generates multi-view representations…

Hello! I’m having problems with lfcShrink in my DESeq2 workflow. I’m trying to do a differential expression analysis (with only one comparison term: “MULTIseq_ID_call2”) on my single-cell data. However when I do lfcShrink I get an error that I cannot interpret. Can you help me? dds <- DESeq(dds, test =…

Gene Set Enrichment Analysis 1 Once I come to Gene Set analysis, I have faced some confusing about the differences between ORA, GSEA, Pathway analysis . In addition about difference gene set databases: Which once shall I start first and using which tools ? for examples there are clusterProfile package,…

DOI: 10.18129/B9.bioc.multiSight   Multi-omics Classification, Functional Enrichment and Network Inference analysis Bioconductor version: Release (3.17) multiSight is an R package providing functions to analyze your omic datasets in a multi-omics manner based on Stouffer’s p-value pooling and multi-block statistical methods. For each omic dataset you furnish, multiSight provides classification models…

DOI: 10.18129/B9.bioc.mastR   Markers Automated Screening Tool in R Bioconductor version: Release (3.17) mastR is an R package designed for automated screening of signatures of interest for specific research questions. The package is developed for generating refined lists of signature genes from multiple group comparisons based on the results from…

Home Bioconductor 3.17 Released April 26, 2023 Bioconductors: We are pleased to announce Bioconductor 3.17, consisting of 2230 software packages, 419 experiment data packages, 912 annotation packages, 27 workflows and 3 books. There are 79 new software packages, 7 new data experiment packages, no new annotation packages, 2 new workflows,…

Performing GO analysis from Differential Peaks 0 Hello everyone, I called for FindMarkers() in order to find differential peaks between two biological conditions and the following was output (“diff.peaks”). My question is how would I generate a nice chart for GO analysis from this? My current code is: install.packages(“JASPAR2022”) library(JASPAR2022)…

Different results between clusterProfiler and Enrichr 0 Hi, I first used enrichr and found an intesresting pathway enriched in my geneset. Then I wanted to use clusterProfiler with the same geneset but this time including background genes. My issue is that clusterProfiler gives completely different results compared to enrichr even…

Hello everyone, Initially I express that I am not very expert in bioinformatics analysis. I have the TMP from RNAseq data. These data come from Arabidopsis seeds infected with a fungal inoculum. I select the data by calculating the zscore. Thanks to the tutorials and the forums I have managed…

A large portion of gene ID cannot be mapped when running the “bitr” command of the “clusterProfiler” package 0 Hello everyone, When I run the bitr command, I get warning message saying that 58.9% of input gene IDs are fail to map…, like the following: library(ggplot2) library(clusterProfiler) > gs.up =…

enrichKEGG function error 1 @d4a334e3 Last seen 4 hours ago Germany Hello, I was trying to check kegg enrichment analysis for my Bulk RNAseq DGE results, and I am getting this error –> No gene can be mapped…. –> Expected input gene ID:–> return NULL… could you kindly tell what…

Introduction Gout is an inflammatory disease caused by the deposition of monosodium urate (MSU) crystals in joints and other non-joint tissues. The main clinical manifestations of gout include recurrent joint redness, swelling, heat and pain, and even joint mutilation, urinary acid nephropathy and renal failure.1,2 The incidence and prevalence of…

1Department of Gastroenterology, Zhongnan Hospital, Wuhan University, Wuhan, Hubei, 430071, China; 2Hubei Clinical Centre and Key Laboratory of Intestinal and Colorectal Diseases, Zhongnan Hospital, Wuhan University, Wuhan, Hubei, 430071, China Background: Ulcerative colitis (UC) is a chronic inflammatory disease of the colon and rectum that has no exact cause and…

DOI: 10.18129/B9.bioc.eegc     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see eegc. Engineering Evaluation by Gene Categorization (eegc) Bioconductor version: 3.12 This package has been developed to evaluate cellular engineering processes for direct differentiation of stem cells or conversion (transdifferentiation) of somatic…

Seeking feedback on RNA-seq analysis with low sample size and custom pathways 0 I am a first year PhD student and I am new to RNA-seq analysis. I have some questions about the validity and feasibility of the analysis that my mentor asked me to do. I would appreciate any…

Customizable pvalue scales in clusterprofiler 0 Hello I used clusterprofiler for GO enrichment analysis. For each ontology, it gives plots with “different” p.adj scaling value. For BP ontology dot plot, padj value ranges from 0.001 to 0.01 . While for CC ontology, dotplot gives p.adj scale value from 0.01 to…

Hello everyone in biostars. I’m trying to do a go, kegg analysis. But I’m having an error. I’m using the following code. reference from github library(AnnotationHub) ah <- AnnotationHub() query(ah,’Oryza_sativa’) rice <- ah[[‘AH107684’]] rice library(clusterProfiler) setwd(“C:/Users/R”) deseqas <- read.csv(‘deg.csv’) as <- deseqas$gene geneList = sort(as, decreasing = TRUE) IDtable <-…

Nakamura, T. et al. Molecular mechanisms underlying the exceptional adaptations of batoid fins. Proc. Natl Acad. Sci. USA 112, 15940–15945 (2015). Article  ADS  CAS  PubMed  PubMed Central  Google Scholar  Turner, N. et al. The evolutionary origins and diversity of the neuromuscular system of paired appendages in batoids. Proc. Biol. Sci….

Is the same order when using p value or q value for compareCluster analysis? 1 Hey, I’m so confused about a simple question, hope you guys could help me! So I do a GO analysis using compareCluster as I compared my downregulated genes and upregulated genes. I’m wondering whether the…

Roy, S. et al. Celebrating 20 years of genetic discoveries in legume nodulation and symbiotic nitrogen fixation. Plant Cell 32, 15–41 (2020). Article  CAS  PubMed  Google Scholar  Roux, B. et al. An integrated analysis of plant and bacterial gene expression in symbiotic root nodules using laser‐capture microdissection coupled to RNA…

Comput Struct Biotechnol J. 2023; 21: 2276–2285. ,a,1 ,a,1 ,a ,b,c and a,b,⁎ Leiming Jiang aComputational Systems Biology Laboratory, Department of Bioinformatics, Shantou University Medical College (SUMC), 515041 Shantou, China Shijia Hao aComputational Systems Biology Laboratory, Department of Bioinformatics, Shantou University Medical College (SUMC), 515041 Shantou, China Lirui Lin aComputational…

Hi! Apologies for the stupid question! but I think I am doing something wrong but i do not understand what. I would like to do ORA analysis on bulk-RNAseq dataset so I tried both clusterProfiler and also genekitr.` However, despite getting the same terms, but I have different p-adjusted value…

ClusterProfiler : What is GeneRatio and BgRatio? 3 Question is in the title. GeneRatio is like M/N where M is the number of genes from your input list that match the GO term. But I don’t see what is N ? BgRatio is like A/B where B is all genes…

C. elegans strains All strains were cultured under standard conditions78 and were always incubated at 20 °C during the experiments. The strains used were N2 (Bristol; WT): DREAM: MT8839 lin-52(n771) III, MT10430 lin-35(n745) I, MT15107 lin-53(n3368) I/hT2 [bli-4(e937) let-?(q782) qIs48] (I;III), MT8879 dpl-1(n2994) II, MT11147 dpl-1(n3643) II, JJ1549 efl-1(se1) V, BJS634…

How to sort graph based on fold change and instead of activated and suppressed, how to add up and downregulated in graph header? 0 BiocManager::install(“clusterProfiler”, version = “3.16”) BiocManager::install(“pathview”) BiocManager::install(“enrichplot”) library(clusterProfiler) library(enrichplot) # we use ggplot2 to add x axis labels (ex: ridgeplot) library(ggplot2) # reading in data from deseq2…

Emapplot Pie Graphic Legend Interferes with Map 0 Enrichment Map using emapplot Below is my code to populate the plot. I have tried various ways to remove or make the pie legend (bottom left corner) smaller…to no avail. I appreciate any help with this issue. IBU_REACTForm_res <- pairwise_termsim(IBU_REACTForm_res) par(mar =…

Stephenson, W. et al. Single-cell RNA-seq of rheumatoid arthritis synovial tissue using low-cost microfluidic instrumentation. Nat. Commun. 9(1), 791 (2018). Article  ADS  PubMed  PubMed Central  Google Scholar  Schmidt, C. J. et al. Infection with Clostridioides difficile attenuated collagen-induced arthritis in mice and involved mesenteric Treg and Th2 polarization. Front. Immunol….

I am trying to use the gseKEGG function in the R package clusterProfiler with the KEGG database entries for Streptomyces coelicolor. This code snippet confirms that KEGG supports this organism, with kegg_code of ‘sco’. search_kegg_organism(‘sco’, by=’kegg_code’) returns kegg_code scientific_name common_name 2810 scon Streptococcus constellatus subsp. pharyngis C232 <NA> 2811 scos…

Introduction Coronary heart disease (CHD) is the most common heart condition worldwide and the leading cause of death of elderly men and women (1). Despite recent declines in developed countries, both CHD morbidity and mortality continue to increase rapidly in developing countries. Various factors are involved in CHD pathogenesis, including…

Objects To evaluate the hsa_circ_0001445 level in peripheral blood leukocytes of patients with coronary heart disease (CHD) and its related clinical factors, and predict its circRNA-miRNA-mRNA regulatory network in CHD pathogenesis via bioinformatics analysis. Methods Peripheral blood leukocytes were isolated from the whole blood samples of 94 CHD patients (aged…

Error when running getGDCprojects() 0 @4bb5d1af Last seen 3 hours ago Sweden Hello everyone, I’m trying to run some very basic code which worked just a couple of days ago. Now when I run it I get an error message instead. library(“TCGAbiolinks”) library(“limma”) library(“edgeR”) library(“glmnet”) library(“factoextra”) library(“FactoMineR”) library(“caret”) library(“SummarizedExperiment”) library(“gplots”)…

Introduction Chronic obstructive pulmonary disease (COPD) is a common chronic respiratory condition that mostly occurs in middle-aged and elderly people. COPD manifests as a progressive airflow limitation associated with an abnormal lung inflammatory response.1 As a disease with high incidence, disability rate, long disease course, and multiple comorbidities, COPD has…

Case selection In this prospective case‒control study, we enrolled PD patients and healthy controls at Asan Medical Center (AMC), Seoul, South Korea, between 2018 and 2020. PD diagnosis was based on the UK PD Society Brain Bank criteria15. Batch 1 (n = 210) and 2 (n = 100) PD cohorts were recruited from January…

Hi Biostar users, I am working with clusterprofiler enrichKegg function KEGG_all = enrichKEGG(regulated.gene$entrez, organism=”human”) I have used library(org.Hs.eg.db) to convert gene names(Symbols) to Entrez ID which is the possible input to use this function. However I am seeing strange message and I am not sure what could be the reason?…

Hello There! I am doing the enrichment analysis based on kegg. The analysis is based on zebrafish entrezid/ncbi-geneid Clusterprofiler seems to work for this example. data(geneList, package=”DOSE”) de <- names(geneList)[1:100] yy <- enrichKEGG(de, pvalueCutoff=0.01) head(yy) But when I tried my code, it does not work. I did it for my…

Problem with universe argument in enrichKEGG 0 Hi all, I am trying to do KEGG enrichment with enrichKEGG, I was wondering if I need to specify universe argument. Could you please help me with it? In the documentation, it says “universe: background genes. If missing, the all genes listed in…

Hi there! I would like to perform KEGG enrichment with some differentially expressed gene data from RNAseq data. I am working on a non-model organism. I have 1) KEGG to GeneName Mapping head(expr5_FS_final) KEGG unigene_FS 1 K02727 FS_gene_1 2 K17277 FS_gene_3 3 K17307 FS_gene_10 4 K14453 FS_gene_11 5 K14700 FS_gene_11…

Introduction Melanoma is the deadliest type of skin cancer, with a rising yearly incidence.1,2 Despite the rapid development of checkpoint immunotherapy and targeted therapies, the main melanoma treatment methods include surgical resection and chemotherapy.3,4 Recent immunosuppressive agents increase the one-year survival rate of melanoma patients to more than 50%. However,…

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 (2021). Article  PubMed  Google Scholar  Sanli, O. et al. Bladder cancer. Nat. Rev. Dis. Prim. 3, 17022 (2017). Article  PubMed  Google Scholar  International…

Hi, I’m currently trying to assess fold change when comparing two different sample types using DESeq2 package and I’m getting weird Cook’s distance values which are causing major problems. The two different samples have different amounts of replicates (6 replicates vs 5 replicates) which might be the reason for these…

Issues with clusterProfiler and WikiPathways 0 Hello, are there any known issues with WikiPathways-related functions in clusterProfiler v. 4.0.5? I’m not able to retrieve even the list of supported organism using the get_wp_organisms() because I’m returned with: “Error in file(con, “r”) : cannot open the connection”. I had experienced similar…

Hi, I’m doing an Over Representation Analysis using the clusterProfiler package. When I used the enrichGO function, I obtained a dataframe with the following columns: _ONTOLOGY: BP (in my case) _ID: GO ID. _Description: Description of the Biological Process. _GeneRatio: ratio of input genes that are annotated in a term….

Hunter, D. J. & Bierma-Zeinstra, S. Osteoarthritis. Lancet 393, 1745–1759 (2019). Article  CAS  Google Scholar  Hunter, D. J., March, L. & Chew, M. Osteoarthritis in 2020 and beyond: A Lancet Commission. Lancet 396, 1711–1712 (2020). Article  Google Scholar  Puig-Junoy, J. & RuizZamora, A. Socio-economic costs of osteoarthritis: A systematic review…

Taylor, J. P., Hardy, J. & Fischbeck, K. H. Toxic proteins in neurodegenerative disease. Science 296, 1991–1995 (2002). Article  CAS  Google Scholar  Spires-Jones, T. L., Attems, J. & Thal, D. R. Interactions of pathological proteins in neurodegenerative diseases. Acta Neuropathol. 134, 187–205 (2017). Article  CAS  Google Scholar  Gan, L., Cookson,…

Ou A, Yung WKA, Majd N. Molecular mechanisms of treatment resistance in glioblastoma. Int J Mol Sci. 2021;22(1):351. CAS  Google Scholar  Wang G-M, Cioffi G, Patil N, Waite KA, Lanese R, Ostrom QT, et al. Importance of the intersection of age and sex to understand variation in incidence and survival…

WHO. Autism spectrum disorders and other developmental disorders: From raising awareness to building capacity. Geneva: World Health Organization; 2013. Google Scholar  Sahin M, Sur M. Genes, circuits, and precision therapies for autism and related neurodevelopmental disorders. Science. 2015;350:6263. Kim JY, Son MJ, Son CY, Radua J, Eisenhut M, Gressier F,…

Cell culture IMR90 (CCL-186) and WI38 (AG06814-N) fibroblasts were purchased from ATCC and the Coriell Institute for Medical Research, respectively. IMR90 and WI38 fibroblasts were grown under 7.5% CO2 and 3% O2 in GlutaMax-DMEM (Gibco, 10569-010) supplemented with 0.1 mM non-essential amino acids (Corning, 25-025-Cl) and 15% fetal bovine serum (VWR/Seradigm,…

Yu, Z., Loisel, J., Brosseau, D. P., Beilman, D. W. & Hunt, S. J. Global peatland dynamics since the Last Glacial Maximum. Geophys. Res. Lett. 37, L13402 (2010). van Breemen, N. How Sphagnum bogs down other plants. Trends Ecol. Evol. 10, 270–275 (1995). Article  Google Scholar  Johnson, M. G. et…

Forum:Pathway Analysis for Cancer Spatial Transcriptomics Characterization 0 Hello all, I am currently working on a spatial transcriptomics project on a cancer sample. I have gone through the workflow to cluster regions of my tissue and have obtained marker genes that are differentially expressed between clusters. I am interested in…

Luo, M. C. et al. Synteny analysis in rosids with a walnut physical map reveals slow genome evolution in long-lived woody perennials. BMC Genom. 16, 707 (2015). Article  Google Scholar  Martinez-Garcia, P. J. et al. The walnut (Juglans regia) genome sequence reveals diversity in genes coding for the biosynthesis of…

Hi, I failed to install clusterProfiler on Mac M1. May I ask the solution >BiocManager::install(“clusterProfiler”) Bioconductor version 3.14 (BiocManager 1.30.19), R 4.1.3 (2022-03-10) Installing package(s) ‘clusterProfiler’ also installing the dependencies ‘fgsea’, ‘DOSE’, ‘enrichplot’, ‘GOSemSim’ Warning: unable to access index for repository bioconductor.org/packages/3.14/bioc/bin/macosx/big-sur-arm64/contrib/4.1: cannot open URL ‘https://bioconductor.org/packages/3.14/bioc/bin/macosx/big-sur-arm64/contrib/4.1/PACKAGES’ Warning: unable to access…

Dear Community, I am trying to show pathway expression in 6 clusters that I identified in disease and control and would like to compare the corresponding clusters. I followed this post 438466 and used Pratik ‘s solution. Which gives me a plot only for the disease. However, I would like…

Materials Medakamo hakoo 311 was obtained from the personal aquarium of Prof. Kuroiwa (Kagurazaka, Tokyo, Japan)4. The M. hakoo strain was cultured in 0.05% HYPONeX (HYPONeX Japan Corp., Ltd., Osaka, Japan) liquid medium and on 0.05% HYPONeX gellan gum-based solid medium in plates. Cyanidioschyzon merolae 10D (Toda et al. 1995)…

Error in UseMethod(“rescale”) 0 @2528ae94 Last seen 17 hours ago United States While using cnetplot to plot enrichGo results, I am getting the following error. It used to work before, but now I am constantly getting this error. I am using clusterprofiler package gse <- enrichGO(gene = deGenes, ont =…

DOI: 10.18129/B9.bioc.EasyCellType     Annotate cell types for scRNA-seq data Bioconductor version: Release (3.16) We developed EasyCellType which can automatically examine the input marker lists obtained from existing software such as Seurat over the cell markerdatabases. Two quantification approaches to annotate cell types are provided: Gene set enrichment analysis (GSEA)…

Sample preparation and sequencing The method of sample collection and processing is described in a companion article (ref. 23). Sequencing and basic bioinformatic processing of DNA-, RNA- and ATAC-seq data are included there as well. Gene expression normalization and filtering The number of non-ribosomal protein-coding genes on the 23 canonical chromosome pairs…

The incidence of lung adenocarcinoma (LUAD), the most common subtype of lung cancer, continues to make lung cancer the largest cause of cancer-related deaths worldwide. Long noncoding RNAs (lncRNAs) have been shown to have a significant role in both the onset and progression of lung cancer. In this study, we…

Zhou, G. et al. Global comparison of gene expression profiles between intramuscular and subcutaneous adipocytes of neonatal landrace pig using microarray. Meat. Sci. 86(2), 440–450 (2010). CAS  PubMed  Article  Google Scholar  Alfaia, C. M. et al. Current feeding strategies to improve pork intramuscular fat content and its nutritional quality. Adv….

Martincorena, I. et al. Somatic mutant clones colonize the human esophagus with age. Science 362, 911–917 (2018). CAS  PubMed  PubMed Central  Google Scholar  Yizhak, K. et al. RNA sequence analysis reveals macroscopic somatic clonal expansion across normal tissues. Science 364, eaaw0726 (2019). CAS  PubMed  PubMed Central  Google Scholar  Yokoyama, A….

Biological materials RAW264.7, 293T and HeLa cells were obtained from ATCC. RAW264.7 cells with Tnf-mCherry reporter and relA-GFP fusion protein (RAW-G9 clone) were kindly provided by I.D.C. Fraser (National Institutes of Health). The IBA cell line derived from the stromal vascular fraction of interscapular brown adipose tissue of young male…

Acute lung injury (ALI) is a severe form of sepsis that is associated with a high rate of morbidity and death in critically ill individuals. The emergence of ALI is the result of several factors at work. Case mortality rates might range from 40% to 70%. Researchers have discovered that…

Introduction Endometriosis (EMS) is a chronic gynecological disease defined as implantation and periodic growth of the endometrial glands and stroma outside the uterine cavity, causing chronic pelvic pain, severe dysmenorrhea, and infertility in 10% reproductive-age women, among which the infertility rate is approximately 30–50%.1,2 Surgical excision is commonly used for…

Rawla, P., Sunkara, T., Muralidharan, P. & Raj, J. P. Update in global trends and aetiology of hepatocellular carcinoma. Contemp. Oncol. (Poznan, Poland) 22, 141–150 (2018). CAS  Google Scholar  Kong, D. et al. Current statuses of molecular targeted and immune checkpoint therapies in hepatocellular carcinoma. Am. J. Cancer Res. 10,…

Rosen, E. D. & Spiegelman, B. M. What we talk about when we talk about fat. Cell 156, 20–44 (2014). CAS  PubMed  PubMed Central  Google Scholar  Kahn, S. E., Hull, R. L. & Utzschneider, K. M. Mechanisms linking obesity to insulin resistance and type 2 diabetes. Nature 444, 840–846 (2006)….

Introduction Chronic obstructive pulmonary disease (COPD) will become the third leading cause of death worldwide.1,2 The incidence of COPD worldwide is 13.1%3 and is 13.7% in the Chinese population over 40 years of age.4 Emphysema is one of the most common phenotypes.1 Over the past few decades, we have conducted…

Cluster Profiler output not the same as Enrichr output 0 @angkoo-23537 Last seen 18 hours ago United Kingdom Hi there, I have am getting different outputs after running enrichGO on cluster profiler when I put the same genes into enrichR (by Maayan Lab) website. Example here using Biological Process 2021…

Introduction Rotator cuff tear (RCT) is a common shoulder disorder causing shoulder pain and disability. The prevalence of full-thickness RCT is 20.7% in the general population, and increased with age.1 Rotator cuff play essential roles in shoulder function and the treatment of proximal humeral fractures.2,3 It is important to repair…

INTRODUCTION Mammalian life starts with the fusion of two terminally differentiated gametes, sperm and oocyte, resulting in a totipotent zygote. After going through preimplantation development, the zygote reaches blastocyst before implantation. The two most important events taking place during preimplantation development are zygotic genome activation (ZGA) and the first cell…

Introduction Kidney cancer is one of the most commonly diagnosed tumors around the globe.1 According to the statistics from the World Health Organization, annually, there are more than 140,000 RCC-related deaths.2 ccRCC is the most typical subtype of kidney cancer and contributes to the majority of kidney cancer-related deaths.3,4 Until…

1. Van den Berge K, Hembach KM, Soneson C, Tiberi S, Clement L, Love MI, Patro R, Robinson MD. RNA sequencing data: Hitchhikers guide to expression analysis. Annu Rev Biomed Data Sci. 2019;2(1):139–73. doi.org/10.1146/annurev-biodatasci-072018-021255. Article  Google Scholar  2. Conesa A, Madrigal P, Tarazona S, Gomez-Cabrero D, Cervera A, McPherson A,…

Introduction Renal cell carcinoma (RCC) accounts for approximately 2–3% of all malignant tumors, and its prevalence is rising. Metastatic RCC accounts for 25–30% of all RCC cases, and has an exceedingly poor prognosis.1 In 2020, among approximately 430,000 newly discovered cases of RCC, 179,000 died.2 Clear cell renal cell carcinoma…

Introduction Alzheimer’s disease (AD) ranks first among the common dementia type of the world. According to epidemiological investigation from the International Alzheimer’s disease association, about 45 million people has been suffered from AD, and the number is expected to increase to 131 million in 2050.1 Despite the widespread prevalence of…

I am not sure what is the proper way to carry out over-representation analysis (and also gene set enrichment analysis) for RNAseq data. Ideally, the analysis can be performed in R, otherwise, if the software/ platform can export the output file (also include all the non-statistical-significant term) will also be…

What is the codification in genestrand 1 and 2? 0 Hi there, I’m doing some peak annotation using ChIPseeker library(ChIPseeker) library(TxDb.Hsapiens.UCSC.hg38.knownGene) library(clusterProfiler) library(annotables) library(org.Hs.eg.db) txdb <- TxDb.Hsapiens.UCSC.hg38.knownGene peaks= readPeakFile(“peaks_”, header = F) peakAnno <- annotatePeak(peaks, tssRegion=c(-3000, 3000), TxDb=txdb, annoDb=”org.Hs.eg.db”) peaks_annot <- as.data.frame(peakAnno) In my annotation file “geneStrand” is codified as…

clusterProfiler won’t read gene list 0 So I have a list of DE genes that I would like to analyse for enriched GO and KEGG terms. I was going to use clusterProfiler for this, but I can’t seem to get past constructing the gene list. I have followed the vignette…

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…

DOI: 10.18129/B9.bioc.conclus     ScRNA-seq Workflow CONCLUS – From CONsensus CLUSters To A Meaningful CONCLUSion Bioconductor version: Release (3.13) CONCLUS is a tool for robust clustering and positive marker features selection of single-cell RNA-seq (sc-RNA-seq) datasets. It takes advantage of a consensus clustering approach that greatly simplify sc-RNA-seq data analysis…

clusterProfiler: number of GO terms in results 0 I am working with a non-model organism. So I constructed TERM2GENE and TERM2NAME files and used enricher to run GO enrichment analysis. The code I used was below. Finally, I got 71 GO terms in the result. But actually, there are 99…

Can cnetplot plot points change shape in clusterprofiler? 0 I have a cnetplot and I am wondering if it is possible for me to do further categorising of the plot by point shape? I have a cnetplot of genes and their interacting pathways, but the genes also have a few…

Sorry for lateness, I wanted to do something similar. This is what I did for reference: Using a Seurat generated gene list for input into ClusterProfiler to see the GO or KEGG terms per cluster. I’ll keep the meat and potatoes of the Seurat vignette in this tutorial: library(dplyr) library(Seurat)…

FindMarkers for ClusterProfiler 1 Hi, I recently ran FindMarkers to compare DEG between two different clusters in a single-cell RNA-seq analysis This is my code: markers= FindMarkers(obj, ident.1=c(4), ident.2 = c(5)) head(markers) dim(markers) table(markers$avg_log2FC > 0) table(markers4v5$p_val_adj < 0.05 & markers$avg_log2FC > 0) I would like to run ClusterProfiler to…

working with .gmt files 3 Hi! I have downloaded a pathway data set in .gmt format form the GSEA website. I’m wondering how can I properly read this data set in R. Could anyone help me? Thank you!   myposts • 9.5k views • link updated 2 hours ago by…