Tag: GSEA

Database Of Space Life Science Investigations And Bioinformatics Of Microbiology In Extreme Environments Biological experiments performed in space crafts like space stations, space shuttles, and recoverable satellites has enabled extensive spaceflight life investigations (SLIs). In particular, SLIs have revealed distinguished space effects on microbial growth, survival, metabolite production, biofilm formation,…

Animals C57BL/6-Tg (Pf4-icre) Q3Rsko/J (Pf4-Cre) mice were purchased from the Jackson Laboratory (Bar Harbor, ME, USA). B6;129-Tmem173tm1(flox)Smoc (Stingfl) mice were purchased from Shanghai Model Organisms Center, Inc. (Shanghai, China). C57BL/6J-Ifnar1em1(flox)Cya (Ifnar1fl) mice were purchased from Cyagen Biosciences (Guangzhou, China). Stingcko and Ifnar1cko mice were generated by crossing Pf4-Cre mice with…

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…

Hello! I’m having issues generating an adequate geneList for running gseGO in clusterProfiler, using keytype = “GO” Similar issues have been described here: No gene mapped gseGO code is: gse <- gseGO(geneList = gene_List, ont = “ALL”, #ont one of “BP”, “MF”, “CC” or “ALL” OrgDb = OrgDb, minGSSize =…

Hello everyone, I am an absolute beginner on sequencing analysis and DESeq2, so please forgive me for possibly mundane questions. I have tried to look up different methods, but couldn’t find a fitting answer yet. I am currently working with sequencing data derived from an Illumina sequencer. The data is…

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…

Pig-tailed macaques can be reliably infected with purified cryopreserved PkSPZ This study was designed to evaluate PTM as potential alternative hosts for malaria vaccine studies, with the aim of further characterizing the parasitological and veterinary health outcomes after infectious PkSPZ challenge. The study was conducted in two pilot cohorts. Cohort…

Identification of DRGs in PCa Figure 1a showed the flow chart of this study. To explore the role of DRGs in PCa, we analyzed the gene expression profiles of these 15 DRGs in PCa patients. As shown in Fig. 1b, for ACTN4, TLN1, IQGAP1, CD2AP, FLNA, MYH9, MYL6, and ACTB genes, the…

Collection and handling of biospecimens obtained from participants in the randomized controlled clinical study of the efficacy of MDCF-2 The human study entitled ‘Community-based clinical trial with microbiota-directed complementary foods (MDCFs) made of locally available food ingredients for the management of children with primary moderate acute malnutrition (MAM)’ was approved…

mTORC1 signaling in bladder cancer Initially, we assessed the mTORC1 signaling scores of both normal and bladder cancer samples. We analyzed the TCGA dataset and observed that the mTORC1 signaling score in normal tissues was considerably lower than that in breast cancer tissue samples (Fig. 2A). We analyzed the expression of…

Selection of 152 ALI-related genes (ALIRGs) by weighted gene co-expression network analysis (WGCNA) The samples of the GSE16409, GSE18341 and GSE102016 datasets were discretely distributed before merging, and the sample data (ALI = 21 and control = 14) was uniform after batch processing (Supplementary Fig. 1a,b). To identify the ALIRGs, the WGCNA was performed in…

fgsea leading edge genes 1 I’m using fgsea to find enriched genes/pathways. The returned leading edges contain many overlapping genes, which I understand. What I don’t understand is that many seem to be in the same order. Are the leading edges arranged by significance? E.g. [1] “RPLP0” “RPS2” “RPL28” “RPS17″…

News:Course. – Gene Set Enrichment Analysis in R/Bioconductor – ONLINE, 22-25 January 0 Dear all, there are still 5 seats for the next edition of the online course on “Gene Set Enrichment Analysis in R/Bioconductor” taking place from January 22nd to January 25th, 2024. This course will cover popular GSEA…

recommend gene ranking methods when doing GSEA 0 Dear guys, Do you recommend to use t to rank gene or log2FC or sign(log2FC) * -log10(Pvalue) to rank gene? The fgsea use t to rank the gene. fgsea rank gene Rscript While when looking the distribution of the DEGs, t is…

DESeq2 : stat or lfcshrink for GSEA analysis 1 @0318a29a Last seen 19 hours ago France Hi, I see the advantage of using lfcshrink in DESeq2 analysis for getting a more “realistic” FC that takes into account the variance of the data. I have a question regarding what variable generated…

Cell line and growth assays Cell lines were grown in Roswell Park Memorial Institute-1640 medium (RPMI-1640) with 1% penicillin–streptomycin (10,000 U ml−1) and 10% FBS or in Iscove’s modified Dulbecco’s medium (IMDM) with 1% penicillin–streptomycin (10,000 U ml−1), l-glutamine (200 mM) and 10% FBS in a humidified incubator with 5% CO2 maintained at 37 °C. Drugs…

Introduction Lung cancer remains the leading cause of cancer-related mortality worldwide, and the majority are non-small-cell lung cancer (NSCLC).1,2 Genetic variation is a typical feature of NSCLC that drives cancer initiation and progression.3 Understanding the role of mutated genes in NSCLC is the basis of the development of novel treatment…

I am not able to connect to the mSigDB gene sets database on the Run GSEA tab. I keep getting an error that says it’s timed out and it may be due to firewall rules. But I also tried to connect using my home network which isn’t firewalled and still…

How can we use the organism database created by makeorgPackageFromNCBI to KEGG and GO analysis using clusterprofiler package. 0 @3e18707b Last seen 10 hours ago India I have transcriptome data of an inhouse sequenced bacterial genome. I made the database for my bacteria using makeOrgPackageFromNCBI command. How can I use…

GO categorization 0 Hi all, I am working on a non-model organism. I finished annotation of the transcriptome using trinotate and now I want to do gene set enrichment analysis. How to do GSEA for non-model organisms? I saw many posts and it doesn’t seem to solve the problem? How…

Introduction Fibromyalgia (FM) and Chronic Fatigue Syndrome (CFS) are characterized by chronic pain, fatigue, and weakness. Patients with these symptoms also suffer from sleep abnormalities and report affected cognitive processes such as memory. The diagnosis of these two syndromes is challenging and is based on questionnaires that make the diagnosis…

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…

Introduction The potential role of opioids used in oncology patients has been controversial. Epidemiological and retrospective studies have demonstrated that lower opioid doses and regional anesthesia (epidural, intrathecal, or paravertebral) for breast,1 colon,2 or melanoma3 are linked to lower rates of cancer recurrence, while general anesthesia with high opioid doses…

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…

Doxo and Abe promote cellular senescence accompanied by an altered profile of senescence-related genes in breast cancer cells Doxo and Abe were used to treat breast cancer cells (human triple-negative breast cancer cell line MDA-MB-231 and human luminal A subtype breast cancer cell line MCF-7) for 24 h, without a robust…

Ref seq/Gene bank accession to Entrez id for cluster profiler 1 I have a list id of GenBank accession (protein) for different bacterial species (these are non model bacterial species). The next step is to do GSEA for these proteins. I tried to convert GenBank accession to entrez id, But…

Gene Ontology enrichment with BINGO and ClueGO 0 Hi, I would like to run some GO BP enrichment analysis in Cytoscape (not GSEA based on expression or rankings, just hypergeometric tests on shortlist vs. reference). There are two conditions I would like to fulfill when carrying it out: 1-To be…

A database in the Gene Set Enrichment Analysis (GSEA; www.gsea-msigdb.org/gsea/msigdb/index.jsp) platform10,11 was used to identify 134 GLN metabolism-associated genes. Weighted gene co-expression network analysis (WGCNA) and module screening GLN-associated gene sets were investigated using WGCNA. The results demonstrated that when the weighted value was 24 (Fig. 1A), scale independence was greater…

Both MPH and ATX increase the locomotor activity of wild-type Drosophila To investigate the cell type-specific molecular mechanisms of ADHD drugs in the brain at single-cell resolution, we conducted behavioral experiments and scRNASEQ in wild-type (WT) adult male Drosophila melanogaster following exposure to MPH, ATX, and control treatment. Here, we…

Selecting a subset of MSigDB database for GSEA 0 Hi all I am analyzing bulk RNA-seq data with GSEA and MSigDB to identify significantly enriched pathways. I am interested in which signaling pathways are enriched, so I am planning on using “C2: curated gene sets”, its subcollection “CP: Canonical pathways”,…

error uploading gct file to gsea 0 Hello everyone I’m trying to upload my gct file of the normalized RNAseq counts for mouse into GSEA. I get errors that the last line in my gt file has bad info. I have changed the number of probes in the gct file,…

I was reviewing some GSEA results and noticed something strange with respect of the following 2 genesets : My comparison of interest is of similar nature (similar type of tumor vs normal) and my “UP” regulated genes appear enriched in the DODD_NASOPHARYNGEAL_CARCINOMA_DN set while my “DOWN” list appear enriched in…

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…

Errors in Functional Enrichment Analysis with Clusterprofiler 0 library(clusterProfiler)library(org.Hs.eg.db) library(tidyverse) library(DOSE) library(ReactomePA) library(enrichplot) library(fgsea) library(data.table) library(ggplot2) keytypes(org.Hs.eg.db) res = read.csv(“coex.Csv”) head(res) original_gene_list = res$correlation names(original_gene_list) <- res$gene gene_list<-na.omit(original_gene_list) gene_list = sort(gene_list, decreasing = TRUE) gse <- gseGO(geneList=gene_list, ont =”ALL”, keyType = “ENSEMBL”, minGSSize = 3, maxGSSize = 800, pvalueCutoff =…

GSEA test 0 Hi everyone, I’m trying to test and interpret some GSEA result (e.g. 100 genes between grA and grB). Usually, when we use some carefully designed gene sets on public database, the graph will be in a bell-like shape. If it is left-up skew -> upregulated in grA…

I am using the GUI version of GSEA. The samples are of mice. I prepared the required files (.gct) and phenotypelabel (.cls), as required. Expression dataset (partial, feature used are normalized counts) 409 5 NAME description CF355 CF328 WT316 WT351 WT354 ENSMUSG00000025902.14 NA 77 61 110 76 54 ENSMUSG00000102269.2 NA…

Single-cell RNA sequencing reveals cellular heterogeneity among young and aged lungs post-influenza infection In order to investigate age-induced alterations in the host response to influenza A virus (IAV) infection, we infected groups of three young (16–18-week-old) and three aged (80–82-week-old) female C57Bl/6 mice intranasally with 50 PFU of the PR8…

Models for single-cell ATAC-seq data In single-cell ATAC-seq data, \(x_{ij}\) is the number of unique reads mapping to peak or region j in cell i. Although \(x_{ij}\) can take non-negative integer values, it is common to “binarize” the accessibility data (e.g., [19, 74, 133,134,135]), meaning that \(x_{ij} = 1\) when…

Extracting most significant core enrichment genes after performing GSEA 0 Dear all, I am trying to extract a list of the 10 most significant leading-edge/core enrichment genes after performing GSEA, and visualizing the gene sets with the highest NES, is there any way to do it? I managed to extract…

Figure 1. ZEN concentration screening and transcriptome data validation. (A) The growth status of sheep oocytes cultured in vitro after 36 h of exposure to different concentrations of ZEN(CK,10 μM, 20 μM, and 30 μM) (10×, 100 μm), (B) qRT-PCR results of SOD1, CCNB1, GPX1, CAT, CDK1, and SOD2 in…

Introduction Crohn’s Disease (CD) is a typical group of inflammatory bowel disease, a chronic intestinal disease with an unclear cause that fluctuates between clinical remission and relapse. The disease may affect the entirety of the gastrointestinal tract, frequently manifesting as segmental, asymmetric, and transmural lesions. 21–47% of patients present with…

PHF5A expression analysis Figure 1A demonstrated that PHF5A expression level was compared between tumor and corresponding normal tissues using TIMER2 tool. As compared to normal tissues, PHF5A expression was considerably elevated in Bladder urothelial carcinoma (BLCA), Breast invasive carcinoma (BRCA), Cholangiocarcinoma (CHOL), Colon adenocarcinoma (COAD), Esophageal carcinoma (ESCA), Head and neck…

Patients’ tumor tissues and clinical data This study recruited 125 breast cancer patients for immunohistochemical (IHC) analysis and 10 breast cancer patients for RNA-seq analysis from the Affiliated Tumor Hospital of Nantong University. Tumor tissues collected from surgical patients were fixed with formalin and embedded with paraffin and then examined….

Max Pay $49.95/hour W2. W2 Candidates only, C2C not possible. Our company offers our consultants a suite of benefits after a qualification period including health, vision, dental, life and disability insurance. 100% remote role, no expectation of onsite work. Description Seeking a Strong scientific understanding and experience in bioinformatics Will…

Job Title: Bioinformatics Scientist III (Remote) Duration: 12 Months Note: Looking for a remote or local candidate for this role. Local to Ridgefield, CT 06877. Pay Rate starts from $50/hr on W2 Duties And Responsibilities Strong scientific understanding and experience in bioinformatics Design, implement and/or deploy data analysis workflows for…

Cell culture and treatments Human embryonic lung MRC5 fibroblasts (ATCC) and IMR90 fibroblasts (ATCC) were grown in Dulbecco’s modified Eagle’s medium (Sigma-Aldrich, D5796) supplemented with 10% heat-inactivated fetal bovine serum (FBS), 100 U ml−1 penicillin, 100 μg ml−1 streptomycin and 2 mM l-glutamine and maintained at 37 °C under 5% CO2. MRC5 fibroblasts were cultured in…

Max Pay $49.95/hour W2. W2 Candidates only, C2C not possible. Our company offers our consultants a suite of benefits after a qualification period including health, vision, dental, life and disability insurance. 100% remote role, no expectation of onsite work. Description Seeking a Strong scientific understanding and experience in bioinformatics Will…

Technical roadmap Figure 1. Fig. 1 Analysis of endometriosis-related differentially expressed genes Using the limma package, we first normalized the expression profile data of the endometriosis datasets, GSE7305 and GSE11691. The data distribution before and after standardized treatment is revealed in a box plot (Figs. 2A–D). We found that the data after…

GSEA analysis for phosphoproteins 1 Hi, I did the GSEA analysis . However, none of the pathways follows the FDR cutoff score 0<.25 and p-value. Can I use the data for publication? Such as one of my pathway showing nominal p-value is 0.87 and FDR q-value is 0.89. GSEA •…

In a recent article published in EMBO Molecular Medicine, researchers investigated cellular, molecular, and spatiotemporal heterogeneity of glioblastoma (GBM), a malignant and highly aggressive primary brain tumor. Study: Single-cell profiling and zebrafish avatars reveal LGALS1 as immunomodulating target in glioblastoma. Image Credit: Triff/Shutterstock.com They performed single-cell ribonucleic acid sequencing (scRNA-seq) of…

GSEApy plot TypeError 0 I’m using GSEApy to do my enrichment analysis. I sorted my pre_res based on nes. I was trying to get GSEA plot for the first term, which is the most enriched. The most enriched was ‘Mitotic G2/M Transition Checkpoint (GO:0044818)’. Here is the code I attempted…

Mapping eQTLs in patients with psoriasis We obtained longitudinal lesional and non-lesional skin biopsies from participants at baseline, during treatment, and at the time of psoriasis relapse after study medication withdrawal over a course of 22 months. We used genome-wide genotyping and RNA-seq to assay samples. After stringent quality control,…

How to decide what gene set libraries to use in your GSEA analysis 0 This is probably more of a philosophical question. I’m sure you could probably choose whichever library you want (i.e. Hallmark, Reactome, Kegg etc.), but I’m curious whether there are known benefits of using one (or a…

Pipelines and parameters used to process data on the BioBox platform   Pipeline for processing public data to sample gene counts SRA-Toolkit is used to fetch the raw files using fasterq-dump -e 3 The files are passed to Kallisto for quantification using kallisto quant -t 3 If the sample is…

Name Last modified Size Description Parent Directory   –   2anova1.jpg 2011-09-09 05:55 121K   4.3.1.jpg 2011-09-09 05:55 117K   4.4.1.jpg 2011-09-09 05:55 63K   4.6.1.jpg 2011-09-09 05:55 38K   4.7.1.jpg 2011-09-09 05:55 56K   4.10.1.jpg 2011-09-09 05:55 63K   4.11.1.jpg 2011-09-09 05:55 112K   4.12.1.jpg 2011-09-09 05:55 55K  …

Lack of IFNβ/IFNAR signaling causes mtDNA oxidization and mutation in a hotspot in complex I respiratory chain subunits mimicking PD brain pathology We analyzed transcriptomic datasets from sPD patients [28] to identify molecular pathways related to the disease pathology. Dysregulated oxidative phosphorylation (OXPHOS) emerged as the top-ranked pathway in sPDD, patients with…

News:Course – Gene Set Enrichment Analysis in R/Bioconductor 0 Dear all, registrations are open for the next edition of the online course on “Gene Set Enrichment Analysis in R/Bioconductor” taking place from January 22nd to January 25th, 2024. This course will cover popular GSEA tools, both online-based and R packages,…

Hello! I am currently analyzing some data that was provided to me. It consists of more than 150 microarray samples from a single kind of tumor. The data is already normalized and background corrected, and in theory I should be able to find differences in gene expression among patients that…

Which function is best for pathway analysis? 1 Hi Biostars, I found there are many function to perform pathway analysis such as fgsea(), gseGO(), gseKEGG(), enrichGO() which made me quite confuse which result I should focus on. Getting a correct background gene set is important. However, how can we find…

Introduction The KCNQ (potassium voltage-gated channel subfamily Q) family of ion channels encode potassium transporters (1). KCNQ proteins typically repolarise the plasma membrane of a cell after depolarisation by allowing the export of potassium ions, and are therefore involved in wide-ranging biological functions including cardiac action potentials (2), neural excitability…

Ties in reranked list 0 I’m trying to perform GSEA with the fgsea package in R: fgseaRes<-fgsea(pathways=pathwaysH,stats=new_res_important) However, I receive the error: Warning message: In preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam, : There are ties in the preranked stats (5.02% of the list). The order of those tied genes will be…

High pvalues when using clusterProfiler for seurat 0 Hi, I am trying to run clusterProfiler::GSEA version 4.8.3 for each cluster of my SeuratObj When ranking the DEG based on logFC I get decent ES/NES scores however my q/p values are usually > 0.05 sometimes even >0.5. However, when I re-run…

GSEA Result Visualization in R 1 Hello, I have performed GSEA analysis using the Broad’s GSEA software. I now want to create a running enrichment score figure that includes my top 4 gene sets using the ‘enrichplot’ package in R. (example picture below) However, I cannot figure out how to…

Experimental procedures Plasmid design and cloning AAV genome plasmids (Fig. 1a and Extended Data Figs. 1a,g,h and 5a) were based on Addgene plasmid 60231 (ref. 12). To achieve widespread transgene expression, the hSyn promoter was replaced by the ubiquitous CBh promoter (pAS088). For the triple-colour experiments (Extended Data Fig. 1a),…

Find potential important genes from bulk-RNA seq experiment 0 Hi Biostars, After finding DEG genes, I try to find important genes that may cause for a disease so I do pathway analysis with GSEA and find pathway with highest enrichment score using gseKEGG() and gseGO(). Is that genes in the…

Braun, J. & Sieper, J. Ankylosing spondylitis. Lancet 369, 1379–1390. doi.org/10.1016/S0140-6736(07)60635-7 (2007). Article  PubMed  Google Scholar  Lai, S. W., Kuo, Y. H. & Liao, K. F. Incidence of inflammatory bowel disease in patients with ankylosing spondylitis. Ann. Rheum. Dis. 80, e144. doi.org/10.1136/annrheumdis-2019-216362 (2021). Article  PubMed  Google Scholar  Bukowski, B. R….

Genomic analysis and cohort description We generated whole-exome sequencing (WES) and RNA sequencing (RNA-Seq) data from tumors and blood samples from 27 advanced urothelial cancer patients treated with anti-PD-1/PD-L1 ICIs at Hospital del Mar (Fig. 1a). WES data was obtained from the tumors before treatment as well as from blood samples,…

The rise of full transcriptome acquisition technologies has fueled the rapid proliferation of molecular-level biological data. These large datasets require interpretation beyond the single-gene level to connect them to meaningful biology and clinical impacts. In 2003, we pioneered the gene set enrichment analysis (GSEA) approach1 to enable the identification of…

Data collection and bioinformatic analysis GSE10846, GSE19246, GSE32918, GSE50721, GSE64820, and GSE94669, were downloaded from the Gene Expression Omnibus database (www.ncbi.nlm.nih.gov/geo/). DLBCL datasets from the GEPIA (Gene Expression Profiling Interactive Analysis) (gepia.cancer-pku.cn) and the TCGA (The Cancer Genome Atlas) (xenabrowser.net/datapages/) were also used in this study. A total of 284…

Bioconductor is an open-source software project that provides tools for the analysis and comprehension of high-throughput genomic data. It’s a powerful tool, widely used in bioinformatics and computational biology to process and analyze intricate biological data. Bioconductor’s strength lies in its vast array of packages specifically tailored for genomics research,…

Identification and functional enrichment analysis of common DEGs Batch effects had been eliminated with Rank-In in all samples from the AD combined dataset and GSE98895 dataset, as shown in Fig. 2A,B. The 3023 DEGs (1376 up- and 1647 down-regulated) were screened between AD and control subjects using the ‘limma’ package in…

Abstract Long interspersed element 1 (L1) are a family of autonomous, actively mobile transposons that occupy ~17% of the human genome. The pleiotropic effects L1 induces in host cells (promoting genome instability, inflammation, or cellular senescence) are established, and L1’s associations with aging and aging diseases are widely recognized. However,…

Animals The animal experiments were approved by the Institutional Animal Care and Use Committee of Jinling Hospital (Nanjing, China), in accordance with the approved guidelines of the Institutional Animal Care and Use Committee of Jinling Hospital. 7 weeks old male wild-type (wt) and leptin receptor-deficient (db/db) mice on the C57BLKS/J…

Infection mortality, observations of manipulation, and LC–MS/MS Similar to previous laboratory infections with O. camponoti-floridani24, we collected C. floridanus displaying manipulated summiting between four hours before (zeitgeber time, ZT 20) to half an hour after dawn (ZT 0.5), beginning three weeks after infection (Fig. 1). Sham-treated healthy ants showed no mortality…

Introduction OA is a degenerative joint disease that primarily affects the elderly population. It is a multifactorial disorder with a complex pathogenesis, involving a variety of joint tissues. In addition to the well-established degradation of articular cartilage, OA encompasses a comprehensive joint pathology, encompassing the synovial membrane, subchondral bone, menisci,…

Frontier Medicines is seeking a highly motivated and experienced Scientist/Sr. Scientist in Bioinformatics or Computational Biology to join an emerging Bioinformatics group embedded in our growing Data Sciences team. The ideal candidate has proven experience in the analysis of high-dimensional omics data derived from multiple platforms (such as RNA-seq, Chip-seq,…

Abstract Background/Aim: The immunogenic cell death (ICD) pathway plays a crucial prognostic role in lung adenocarcinoma (LUAD) therapy. The cyclic GMP–AMP synthase (cGAS)-stimulator of interferon genes (STING) pathway is an upstream mechanism that drives ICD activation, but the interaction of hub genes remains unclear. The present study aimed to investigate…

DOI: 10.18129/B9.bioc.GSEABase   This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see GSEABase. Gene set enrichment data structures and methods Bioconductor version: 3.16 This package provides classes and methods to support Gene Set Enrichment Analysis (GSEA). Author: Martin Morgan, Seth Falcon, Robert Gentleman Maintainer:…

What is a GMT File? A GMT file, also known as Gene Matrix Transposed, is a specific type of file that is extensively used in the field of genomics and bioinformatics. Derived from the title, when a file carries a .gmt extension, it signifies that the file contains a matrix…

Can be used GSEA over geneset instead of the entire genome? 0 Hi! I have a dataset of 1500 gene counts in which I applied the limma voom pipeline, I understand that ORA should be used instead of GSEA when the gene set does is not the entire set of…

Introduction Immune checkpoint inhibitors (ICIs) have revolutionized the treatment pattern of various cancers, including melanoma and non-small cell lung cancer (NSCLC).1–3 However, there are still a considerable proportion (40%–60%) of patients who do not respond or do not achieve durable responses to these drugs.4 Thus, it is urgent clinical need…

Cell culture IMR90, 4T1, CT26, RAW264.7 and B16F10 cell lines were purchased from the American Type Culture Collection and cultured in MEM (IMR90), DMEM (B16F10, RAW264.7) or RPMI (4T1, IMR90, CT26) supplemented with 10% FBS in the presence of penicillin (50 U ml−1) and streptomycin (50 μg ml−1). All cells were found to be…

Overview of the sequencing information To explore the presence of circRNAs during spleen development, we assessed circRNAs expression in the spleen tissues of Meishan pigs at various developmental stage. We prepared and sequenced ribo-depleted total RNA-seq libraries, as shown in the flow chart (Fig. 1). Table S2 presents our rudimentary sequencing…

KDM6A inactivation in an autochthonous SCLC mouse model promotes NEUROD1 expression leading to SCLC tumors that express both ASCL1 and NEUROD1. a, Schematic of the adenovirus used for IT injection into the lungs of LSL-Cas9 mice to generate autochthonous SCLC tumors that are Kdm6a inactivated or Kdm6a WT. RPP: sgRb1,…

In a recent study posted to the medRxiv* preprint server, researchers reconstructed gut bacterial genomes. The study identified metabolic pathways that are differentially expressed in response to a microbiota-directed complementary food prototype (MDCF-2) in metagenome-assembled genomes (MAGs) related to changes in weight-for-length Z scores (WLZ). They also evaluated the impact…

Identification and functional analysis of 73 DEMRGs A total of 73 DEMRGs were identified between N0 samples and N1/N2/N3 samples of LSCC, including 59 up-regulated and 14 down-regulated genes in N0 samples relative to N1/N2/N3 samples (Fig. 1a, Supplementary Table 1). The expressions of DEMRGs were present in the heatmap (Fig. 1b)….

UKB The UKB is a population-based prospective cohort study of more than 500,000 subjects. More detailed information on the UKB is given elsewhere34,35. The study received ethics approval from the North West Multi-center Research Ethics Committee. All participants signed written informed consent before participating. WES data for 450,000 subjects were…

Over Representation Analysis over one specific pathway 0 Hi! Let’s say I would like to analyse if a particular pathway is enriched how would I do that given that I have a set of DGE genes resulting from 1500 genes of RNA Seq? I do not want to analise any…

Al , first head to the msigdb website, and take a look at the annotations that belong to set C1: www.gsea-msigdb.org/gsea/msigdb/human/collections.jsp#C1. Note that, while C1 contains gene sets defined based on position, the others are quite different (e.g. C2 is “curated”, C8 is “cell type signatures”) and so forth. the…

Gene set enrichment analysis / Kegg analysis 0 Hi all, I recently did differential gene expression of Daphnia magna using DESeq2 in R studio. It was my first time doing the analysis. Now the next step is to conduct Kegg analysis or Gene set enrichment analysis of the differentially expressed…

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,…

Sample collection The individuals of self-reported African (AFB) and European (EUB) descent studied are part of the EVOIMMUNOPOP cohort18. In brief, 390 healthy male donors (188 AFB and 202 EUB) were recruited between 2012 and 2013 in Ghent (Belgium), thus, before the COVID-19 pandemic. Blood was obtained from the healthy…

How to perform functional enrichment of Metabolites? 0 I have a dataframe containg about 140 metabolites and and 20 samples of two groups. The data is from gallus gallus (gga). How do I perform functional enrichment of metabolites? My data looks as follows: ID Group Creatinine Gly Ala Ser Histamine…

How ti identify genes per terms in with topGO for scRNAseq dataset 0 Hi all, I want to to perform Gene Ontology (GO) Enrichment of Genes Expressed in specific clusters and I am following this tutorial but in the output I cannot find which genes are associated per terms. How…

SF3B1 MUT cells show selective sensitivity to PARP inhibitors To identify candidate therapeutic targets for cancers with SF3B1 hotspot mutations, we utilized the leukemia K562K700E (SF3B1K700E) and parental (SF3B1WT) isogenic cells1, to model one of the most prevalent SF3B1 hotspot mutations seen in patients8,19,20 (Fig. 1a,b and Supplementary Fig. 1a)….

How to analyse a particular pathway after doing DGE? 0 Let’s say I have a set of RNA-seq of 1500 genes and I did DGE over two groups and got a list os DGE genes. GSEA is out of question due to the 1500 gene set. I have done already…

Enrichment methods to differentiate ORA pathways state 0 It is know that some enrichment methods (Over representation analysis) methods do not take into account that downregulated genes in a pathway could result in the pathway being more active (see this answer for example). I’m curious if there is a better…

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…

Enrichment analysis on scRNSseq on which genes/clusters perform ReactomeGSA and GSEA? 0 Hi all, I have a question about gene ontology/GSEA and reactome analyses on scRNAseq dataset. I don’t understand on which genes/clusters is correct to perform these analyses? Do I have to perform these analysis on all clusters (post…

Tumor samples from patients Biopsies of primary breast tumors and breast tumors that had metastasized to the brain were obtained from patients with TNBC at the National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital of the Chinese Academy of Medical Sciences and Peking Union Medical College. Single-cell RNA sequencing…