Tag: GSEA

Amino acid sequence comparisons between GAS and GBS Cas9 identify orthologous active sites Relationships between the amino acid sequence of GBS Cas9 endonuclease and its molecular functions can be deduced from detailed studies of its GAS ortholog, SpyCas9 (Supplementary Fig. 1). As a first step in locating DNA complementary to a…

GSEA application not launching 0 I’ve been using the GSEA app on my mac (Ventura OS) without issue and all of a sudden it is not launching. I’m guessing something was updated behind the scenes but I’m not sure what (possibly something to do with java?). Can someone point me…

GSEA app not launching all of a sudden 0 I’ve been using the GSEA app on my mac (Ventura OS) just fine up to about a week ago and all of a sudden it is not launching. I’m guessing something was updated but I’m not sure what (possibly something to…

How do I calculate differential expression for RNA-seq values with the “limma” package and the “ebayes” function? 0 So for context, I have a set of TPM values (which I converted to log2(TPM+1) for multiple genes for different samples, and I need to calculate the differential expression for RNA-seq values….

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 &…

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…

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…

fGSEA collapsePathways function not working 0 Hello all, I’m running the package fgsea and I’m having trouble with the collapsePathways function. When not using that function, I get the expected data frame with 8 columns (pathway, pval, NES, etc.) that I can then plot using ggplot. However, when I try…

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…

DOI: 10.18129/B9.bioc.phenoTest     This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see phenoTest. Tools to test association between gene expression and phenotype in a way that is efficient, structured, fast and scalable. We also provide tools to do GSEA (Gene set enrichment analysis)…

Frontier Medicines is seeking a highly motivated and experienced Senior/Principal 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,…

job summary: We are seeking a Bioinformatics Analyst to assist in multi-omics data analysis and setup network biology pipelines for supporting target discovery programs and indication prioritization efforts. The role involves analyzing large collections of bulk and single cell transcriptomic data, performing differential expression analysis and meta-analysis and interpret results…

Cells and cell culture KOPN30, BV173, and K562 are BCR/ABL1-positive leukemia cell lines. All leukemia cell lines, as well as Ba/F3 cells, were maintained in RPMI-1640 medium supplemented with 15% fetal bovine serum (FBS) and penicillin–streptomycin (100 U/mL) at 37 °C in an atmosphere containing 5% CO2. KOPN30 cells were obtained…

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,…

GSEA with duplicate sample 1 Hi all, I have a data which is coming from RNA-Seq and it is composed of 2 replicates for each sample. So when I am trying to run GSEA it gives me an error about “phenotype” option even though I run in “gene set” option….

Identify necroptosis-related lncRNAs in SKCM There are 386 necroptosis-related lncRNAs identified from the data of TCGA and GTEx, as the standard is the coefficients > 0.4 and P < 0.001. After that, flowing the differential expression analysis, 87 necroptosis-related lncRNAs were found to display significantly differential expression with the screen value as |logFC…

About us Everyone should have access to innovative therapies that represent the promise of lasting cures. At Theolytics we are working to transform patients’ lives, through world-leading science, with a great team. Our discovery platforms harness the power of viruses to systematically identify therapies optimised for a chosen patient population,…

scEC&T sequencing A detailed, step-by-step protocol of scEC&T-seq is available on the Nature Protocol Exchange46 and is described below. The duration of the protocol is approximately 8 days per 96-well plate. Cell culture Human tumor cell lines were obtained from ATCC (CHP-212) or were provided by J. J. Molenaar (TR14; Princess…

STAGEs is an interactive web app built using Streamlit (www.streamlit.io), and the running instance of the online app can be accessed via the website (kuanrongchan-stages-stages-vpgh46.streamlitapp.com/). The app can also run locally using the instructions detailed in GitHub (github.com/kuanrongchan/STAGES). Users can directly upload data from Excel spreadsheets, csv or txt files…

Clinical and biochemical characteristics of parathyroid carcinoma In total, 50 thyroid tissues were collected from three groups, 12 parathyroid carcinomas, 28 parathyroid adenomas, and 10 normal parathyroid tissues, for genomic and transcriptomic profiling (Fig. 1). The detailed protocols and quality control procedures are described in the Materials and Methods section….

What statistical test to apply for DE after CibersortX deconvolution 0 I am running CibersortX in high-resolution mode (which yields estimates of gene values per sample). After that, I want to perform DE between two conditions on the resulting gene estimates. What statistical test would one need to apply to…

Cell clusters in ZIKV-infected mouse testis defined by scRNA-Seq To investigate the influence of ZIKV infection on testes, testicular cells from ZIKV-infected (14 dpi.) and uninfected A6 male mice (Ifnar−/− mice) were analyzed by single-cell RNA sequencing (scRNA-Seq). After filtering out poor-quality cells, 11014 cells in control testes and 11974…

Introduction The metabolome is an incredibly diverse collection of small molecules (<1,500 Da) in biological systems involved in virtually every cellular process, including cellular energy production, macromolecule synthesis, epigenetic modifications, cell signalling and more (for recent reviews see [Citation1–6]). It responds rapidly (in seconds) to both internal (signalling, allostery) and external…

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 =…

Study cohort and performance during NMP An overview of the overall study population is presented in Table 1 (individual data are given in Supplementary Table 1). Detailed information on study livers and analysis is provided as workflow scheme in Fig. 1. The decision to apply NMP was based on one or a combination…

Background: FBXW7 is recognized as a critical tumor suppressor gene and a component of the ubiquitin-proteasome system, mediating the degradation of multiple oncogenic proteins, including c-MYC, Cyclin E, c-Jun, Notch, p53. Around 16% of colorectal cancer (CRC) patients carried FBXW7 somatic mutations, while a comprehensive characterization of FBXW7 somatic mutations…

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…

HhS activation is a marker of poor prognosis in BLCA patients First, HhS scores were calculated and its expression characteristics were analyzed for patients in the TGCA-BLCA cohort. The results showed that HhS was overactivated in patients with higher stage and older age (Fig. 2A, B). And there is no significant…

Genome-scale CRISPR screen to identify regulators that maintain mESC pluripotency To establish a function-based PGRN, we first performed a CRISPR-Cas9 mediated genome-wide screen to detect genes essential for self-renewal. mESCs were cultured under Leukaemia inhibitory factors (LIF)/serum condition (L/S), which was commonly used in similar tasks and confer a naïve…

Gene set enrichment analysis for genetic interactions 0 Hi, I have a list of pairs of genes that are simultaneously knocked out which have a corresponding score, for example an effect size and/or a corresponding p-value of the cell’s growth compared to a control, which is better known as the…

Expression of IGFL2 in cancer According to the TIMER2.0 database results, the difference in IGFL2 expression between cancer and normal tissues was significant in most cancers, including BLCA, BRCA, CHOL, COAD, ESCA, GBM, HNSC, KIRC, KIRP, LIHC, LUAD, LUSC, SKCM, HNSC, STAD THCA, and UCEC, while IGFL2 expression was higher…

Introduction Breast cancer is the second most common cancer and is the leading cause of cancer-related death among females worldwide with over 2 million newly diagnosed cases and more than 60 thousand deaths every year.Citation1 Despite advances in treatment, the mortality rate of breast cancer remains high, mainly due to…

Genomics-based consensus tumor purity estimates For TCGA samples, genomic-based consensus tumor purities were computed as a mean of predictions from ABSOLUTE17, AbsCNSeq18, ASCAT15, and PurBayes16 following the approach reported in Ghoshdastider et al. 41. AbsCNSeq and PurBayes estimates are based on mutation variant allele frequency data, and ASCAT and ABSOLUTE…

Differential expression of DDR1 between tumor and normal tissue samples To better understand DDR1 expression levels in various cancer types, we first performed a pan-cancer analysis of 33 cancers in the TCGA database. Excluding cancers without corresponding normal samples, significant differences in DDR1 expression were found between tumor and normal…

Kat5-dependent alterations of gene expression in a cranial neural crest cell line To study the role of Kat5 in cells of the cranial neural crest, we first resorted to mouse O9-1 cells as a suitable and well characterized cellular model.18 In these cells, we used CRISPR/Cas9-dependent genome editing to inactivate…

Bioinformatician position available at NIH (Bethesda, MD) We seek a bioinformatician/data scientist with a strong record of collaborative interactions with biologists. The successful candidate must have a M.S or Ph.D. degree in bioinformatics, computational biology, computer science, or a related field and have the ability to work independently or as…

RNA-seq analysis without replicates 1 We have RNA-seq data for 12 samples for 12 conditions. Unfortunately, we do not have any replicates and each sample corresponds to one condition. For differential gene expression analysis, I will need at least 3 replicates (or patients) for each condition to be able to…

FG spectrum in pediatric AML patients A combinatorial approach, including conventional and next-generation sequencing (NGS)-based assays, was employed to profile the FG landscape (see Methods). FG analysis was feasible for 138 patients (94% of the entire cohort, Supplementary Data 1) from whom suitable testing materials were available. The most common FGs…

Differences between GSVA and GSEA? 0 What are the differences between GSVA and GSEA? I got some idea from a toward data science post (link): “GSVA builds on top of GSEA where a set of genes is characterized between two condition groups defined in the sample. GSEA works on how…

Human samples Placental and decidual samples used for the in vivo and in vitro profiling were obtained from elective terminations from: The MRC and Wellcome-funded Human Developmental Biology Resource (HDBR, www.hdbr.org), with appropriate maternal written consent and approval from the Fulham Research Ethics Committee (REC reference 18/LO/0822) and Newcastle and…

Dealing with very large gene-lists in GSEA 1 I’m using fgsea to do gene-set enrichment using the ENCODE transcription factor targets dataset. However, some of the gene lists are very large and I suspect this is causing my gene-set enrichment to fail to find many significant enrichments due to how…

Exogenous expression of the transcription factors Pdx1, Neurog3, and MafA in human fibroblasts We first sought to examine whether the transcription factors Neurog3, Pdx1, and MafA could induce expression of the INSULIN (INS) gene in human fibroblasts as readout of the capacity of these cells to be transformed toward a…

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…

From GeneSetEnrichmentAnalysisWiki GSEA Home | Downloads | Molecular Signatures Database | Documentation | Contact Introduction With the release of MSigDB 2023.1 we have created a new SQLite database for the fully annotated gene sets in both the Human (2023.1.Hs) and the Mouse (2023.1.Ms) resources. Each ships as a single-file database…

How to create GO Bar Plot using data obtained from DAVID Functional Enrichment Analysis? 0 Hi, I have done DAVID Functional Enrichment Analysis. My objective now is to plot the BP, CC, & MF using a barplot like image i shown here I do read a lot recommend using R,…

collapsePathways function throwing error 2 I am trying to perform GSEA on DESeq2 results by ranking the t stat and successfully ran fgsea to extract a list of enriched pathways. However, when I run the collapsePathway function, I receive this error message: Error in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam, :…

Seeking explanation of the difference between GO term normal vs non-redundant! 0 Hi people, I am trying to do some GO analysis (ORA and GSEA) of my RNA-seq data on the WebGestalt website and while choosing a functional database as geneontology, there are options for GO terms as normal and…

Mice All mice experiments were performed in accordance with the guidelines of the Institutional Animal Care and Use Committee (IACUC) at the Center for Excellence in Molecular Cell Science, Shanghai Institutes of Biological Sciences, Chinese Academy of Science. The approved animal protocol number is SIBCB-S374-1702-001-C1. The CK19-CreER, HNF4α-DreER, R26-tdTomato (R26-tdT),…

Mice Mice were of mixed genetic background C57BL/6 and 129/SvJ. Mice were bred and maintained under specific-pathogen-free conditions at the Breeding Unit (BRU) at the CRUK Cambridge Institute. Fh1fl/fl (ref. 4) and R26-Cre-ERT2 (ref. 5) mice were gifts from E. Gottlieb and D. Winton, respectively. Experimental mice were homozygous for…

Yan Sha,1,&ast; An-qi Mao,1,&ast; Yuan-jie Liu,2 Jie-pin Li,2 Ya-ting Gong,3 Dong Xiao,1 Jun Huang,1 Yan-wei Gao,1 Mu-yao Wu,3 Hui Shen1 1Departments of Dermatology, Zhangjiagang TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Zhangjiagang, People’s Republic of China; 2Department of Oncology, Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu…

DLBCL patients with high expression of PIM kinase family had a poor prognosis The prognostic value of PIM kinase family for DLBCL was verified with the dataset GSE10846. It was found that DLBCL patients with high expression of PIM1, PIM2, and PIM3 all had a poor OS (Fig. 1A–C). The results…

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…

ANKLE1 is the causal gene for breast and ovarian cancer risk in the chr19p13.1 region Expression quantitative trait loci (eQTL) data have revolutionized how geneticists identify candidate causal genes from genome-wide association study (GWAS) loci. We integrated the most recent meta-analysis of breast cancer GWAS10 and Genotype-Tissue Expression (GTEx) project…

Gene Set Enrichment Analysis (GSEA) is an important tool in genetic research because it can help researchers identify key biological pathways and processes that are associated with a particular phenotype or disease. GSEA is usually employed in genetic research in the following ways: Identifying gene signatures: By analyzing gene expression…

Gene Enrichment analysis with EggNog output 0 Hi everyone! I want to perform a gene set enrichment analysis of differently expressed host genes during virus infection. I performed Gene Ontology (GO) annotation with eggnog for the whole host genome and got one .tsv file, an excel file, and two .orthologs…

gseKEGG – no gene can be mapped (RNAseq analysis) 0 Hi all, I have been trying to extract the GSEA results from a list of genes after RNAseq analysis. It looks like my gseKEGG function is giving me problems. I am unable to generate a list of KEGG terms, it…

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,…

Gene concept network plot by using GSEA SOFTWARE output on R 0 Hi Everyone! I am trying to plot a gene concept network with the output from GSEA SOFTWARE. I would like something as cnetplot function provided on R. I tried to plot the result, but it did not work…

How to interpret dotplot from enrichment analysis with gseapy? 0 Hello, I used gseapy for enrichment analysis and I am trying to understand the dotplot figure that is generated. This is what the object after enrichment analysis looks like: Below is the figure they produced. I am trying to understand…

. 2021 Apr;101(4):463-476. doi: 10.1038/s41374-020-00517-x. Epub 2023 Jan 4. Affiliations Expand Affiliations 1 Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China. 2 Department of Pathology, Shanghai First People’s Hospital, Shanghai Jiaotong University School of Medicine, 200032, Shanghai, China….

Using DESeq2 to data normalization 0 Hello, I have a single question in DESeq2 usage. I have multiple groups, but each has a single sample. Therefore, I could not use DESeq2 to obtain the fold change. Alternatively, I have a plan to do GSEA, but GSEA requested a normalized data…

An ENU-induced mutagenesis screening for genes involved in mouse vocalization To identify novel genes involved in mouse vocalization, we set up an ENU-induced mutagenesis screening (Fig. 1a). To this end, we crossed ENU-treated G0 males with untreated C57BL/6 J females, and through the use of an USV detector, identified G1 pups with…

What are the differences between GSVA and ssGSEA (in layman’s term)? 0 I know the Bioconductor vignettes for GSVA has a decent description of the methodological differences between the algorithms. However, I am still confused with the technical terms. May I know if there are any further references that explain…

Background. Oxidative stress (OS) can either lead to leukemogenesis or induce tumor cell death by inflammation and immune response accompanying the process of OS through chemotherapy. However, previous studies mainly focus on the level of OS state and the salient factors leading to tumorigenesis and progression of acute myeloid leukemia…

The original question was GSEApy vs KEGG. The response below is GSEApy. The question has been edited and is now a different question concerning options within GSEApy. Response to original question If GSEApy as described in the publication provides the output you require – that is much, much simpler. KEGG…

Ethics statement All fresh peripheral blood samples were obtained after approval of protocols by the Weizmann Institutional Review Board (IRB application 92-1) and following informed consent from the donors. The study using BAL fluid samples was approved by the Hadassah Medical Organization research ethics committee in accordance with the Declaration…

Single sample GSEA analysis 1 Hi, I sorted specific type of cells by FACS and subjected it to RNA-seq. I want to test the enrichment of target cell type. I want to perform analysis just like GSEA to show the enrichment and get the plot which is common for GSEA…

Hello, I analyzed some data using scanpy and now I want to do some pathway analysis. I have done DE analysis between each cluster and the rest and I want to do the pathway analysis for each cluster but I have a few questions. I initially followed the instructions from…

I am relatively new to R studio, I am attempting to import a .RNK file to run on GSEA. However, the pathway to my working directory is lost and I keep receiving a file, “rt” warning message. When comparing my working directory with my usual windows explorer file, the files…

Recommendations needed for a tool for comparative gene set enrichment analyses via a webserver 1 dear All, I’d like to compare 6 gene expression datasets (multiple conditions / time-points) in terms of joint patterns in the enrichments of the differentially expressed genes. The DEG lists I have prepared (logFC,padj). GO…

Cell culture and treatments Bladder cancer cells lines RT4, MGHU3, RT112, KU19-19, JMSU1, T24 and TCCSup were grown in RPMI-1640 medium (Life Technologies, Carlsbad, CA, USA), supplemented with 10% Fetal Bovine Serum (FBS; Eurobio, Courtaboeuf, France). Normal human urothelium (NHU) cells were from Jennifer Southgate (University of York, UK). NHU were…

Job Posting for Scientist II, Bioinformatics at PTC Therapeutics, Inc. Job Description Summary: The Scientist II, Bioinformatics is responsible for planning and performing scientific experiments that contribute to PTC’s research and drug discovery activities. The Scientist II is also responsible for communicating experimental results to his/her supervisor and…

GSEA on nonmodel organisms 2 Hi, I want to do GSEA analysis in R on significantly differentially expressed genes on nonmodel species (five in total). My research is based on cross-species comparative transcriptomics. And this is what I am doing: I already have species-specific: de novo assemblies, annotations (across 7…

What does it mean in GSEA when HALLMARK_UV_RESPONSE_DN is upregulated ? how it’s down and upregulated? 0 What does it mean in GSEA when HALLMARK_UV_KRAS_SIGNALING_DN is upregulated ? how it’s down and upregulated? GSEA HALLMARK • 27 views • link updated 3 minutes ago by Papyrus &starf; 2.3k • written…

Gene Set Enrichment Analysis, pathway, metabolism 0 Hi friends, I am doing GSEA for specific pathways. I want to analyze my genes with the gene sets in specific pathways, such as the metabolism of carbohydrates, lipids, proteins, etc. I am using the REACTOME database as a source. I also want…

single pathway score 1 Hello, I would like to find out a method for “single pathway” differential analysis (if it exists). For example, our team is focused in KEGG pathway hsa03018 (RNA degradation). Our transcriptome data (Treatment vs Control) underwent differential analysis as usual, and GSEA: I happily obtained a…

How can two contradicted gene sets be enriched in a cancer sample in GSEA analysis? 0 How can two contradicted gene sets be enriched in a cancer sample in GSEA analysis? For example in GSEA analysis of cancer sample vs normal sample, How can HALLMARK_UV_RESPONSE_UP and HALLMARK_UV_RESPONSE_DN be enriched in…

Let’s imagine a single cell experiment in which we have 3 biological replicates, treated (TR) and untreated (UNT). After all the necessary filtering and integration steps, we isolate a cluster of interest (cluster X), for which we want to test differential gene expression (DE) between TR and UNT. Ideally one…

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…

doi: 10.3389/fgene.2022.958641. eCollection 2022. Affiliations Expand Affiliations 1 Laboratório de Ecofisiologia e Bioquímica de Plantas, Núcleo de Conservação da Biodiversidade, Instituto de Pesquisas Ambientais, São Paulo, SP, Brasil. 2 Programa de Pós-Graduação em Biologia Celular e Estrutural, Universidade Estadual de Campinas, Campinas, SP, Brasil. Item in Clipboard Camilla Alves Santos et…

Introduction Stroke is one of the leading causes of death and disability worldwide, which causes substantial economic and social burdens.1 Ischemic stroke is caused by insufficient blood and oxygen supply to the brain,2 accounting for about 85% of the casualties of stroke patients.3 The concept of treatment for ischemic injury…

lncRNA expression according to breast cancer clinicopathological subtypes To identify lncRNAs expressed by specific breast cancer subtypes or associated with clinicopathological features, we analyzed RNA-sequencing data from two large independent breast cancer cohorts: SCAN-B (n = 3455)17 and TCGA-BRCA (n = 1095). We focused on lncRNAs annotated in the Ensembl18 v93 non-coding reference transcriptome…

Reagents, antibodies, viruses and cells LMW-Poly(I:C), LPS, 2′3′-cGAMP and DMXAA (InvivoGen); hydroxyurea, camptothecin and mitomycin C (MCE); GM-CSF, Flt3L (peproTech); lipofectamine 2000 (Invitrogen); polybrene (Millipore); RNAiso Plus (Takara); HT-DNA (Sigma); SYBR (BIO-RAD); dual-specific luciferase assay kit (Promega); ELISA kit for murine Ifn-β (PBL); ELISA kits for murine IP-10 (Biolegend) were…

Cell culture Human glioblastoma cells (U87MG and U87MG-Luc) and human embryonic kidney cells (HEK293) were obtained from the American Type Culture Collection (Manassas, Va.). Cells were cultured in Dulbecco’s Modified Eagle Medium supplemented with 10% fetal bovine serum (Gibco™ Fetal Bovine Serum South America, Thermo Scientific Fisher-US), 2 mM l-glutamine, 50 U/ml…

Cell-type annotation scRNA-seq data were filtered to discard low-quality cells and doublets (Supplementary Fig. 1, Extended Data Fig. 1 and Methods). Supervised clustering (Reference Component Analysis v2 (RCA2)) at low resolution grouped cells into 11 major cell types (Extended Data Fig. 1). To identify epithelial cell subtypes, we initially analyzed…

Dataset MSigDB Cancer Gene Co-expression Modules Category transcriptomics Type co-expressed gene Description tumor necrosis factor (ligand) superfamily, member 10|The protein encoded by this gene is a cytokine that belongs to the tumor necrosis factor (TNF) ligand family. This protein preferentially induces apoptosis in transformed and tumor cells, but does not…

Expression of CD68 in pan-cancer First, to fully clarify the expression of CD68 in pan-cancer, we matched the GTEx normal samples with TCGA tumor samples (Fig. 1A). We found that the levels of CD68 were significantly elevated (P < 0.01) in colon adenocarcinoma (COAD), glioblastoma multiforme (GBM), kidney renal clear cell carcinoma (KIRC),…

This article was originally published here J Oncol. 2022 Apr 19;2022:1802706. doi: 10.1155/2022/1802706. eCollection 2022. ABSTRACT Background. Bladder cancer (BLCA) is a highly malignant tumor that develops in the urinary system. Identification of biomarkers in progression and prognosis is crucial for the treatment of BLCA. BLCA-related differentially expressed genes (DEGs)…

GSEA RNASeq 0 Hi friends For gene set enrichment analysis (GSEA), the software from broad institute does not accept ensemble IDs, I want to do the analysis using entrez ID or hugo ID but about 2000 genes don’t have hugo ID or entrez ID. What should I do? gene enrichment…

Bioinformatics analyses revealed the involvement of m6A modification in cervical cancer progression To better understand whether and how m6A regulators contribute to cervical cancer progression, we first identified 9 m6A writers (WTAP, ZC3H13, METTL3, METTL14, METTL16, VIRMA, RBM15B, RBM15, and CBLL1), 15 m6A readers (FMR1, hnRNPA2B1, hnRNPC, YTHDF1/2/3, YTHDC1/2, LRPPRC,…

Introduction Lung cancer is the major leading cause of tumour-related deaths throughout the world, while lung squamous cell carcinoma (LUSC) as the second most common histological type of lung cancer.1 Each year, almost 1.8 million people are diagnosed with lung cancer worldwide and 400,000 of these die from LUSC.2,3 Due to…

    This package is for version 2.13 of Bioconductor; for the stable, up-to-date release version, see neaGUI. An R package to perform the network enrichment analysis (NEA). Bioconductor version: 2.13 neaGUI is an easy to use R package developed to perform the network enrichment analysis (NEA) proposed by Alexeyenko…

Overview of the transcriptomics-guided drug discovery strategy.(A) Schematic outline of the drug screening strategy. (B) Heatmap shows the gene expression pattern of the druggable genes (www.dgidb.org) identified both in CS-exposed mice and patient with COPD databases. (C) Reactome pathway enrichment analysis of genes differentially expressed from patients with COPD (8)…

This article was originally published here Hematology. 2022 Dec;27(1):280-292. doi: 10.1080/16078454.2022.2040123. ABSTRACT PURPOSE: While the prognosis of multiple myeloma (MM) has significantly improved over the last decade because of new treatment options, it remains incurable. Aetiological explanations and biological targets based on genomics may provide additional help for rational disease…

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 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…

Introduction Tuberculosis (TB) is considered to be one of the top ten causes of death in the world, about a quarter of the world’s population is infected with M. tuberculosis.1 The World Health Organization (WHO) divides tuberculosis into pulmonary tuberculosis (PTB) and extra-pulmonary tuberculosis (EPTB). Although breakthroughs have been made…

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,…