Tag: GSEA

Immune-related Prognostic Genes of ccRCC

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…

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Bioinformation Analysis Reveals IFIT1 as Potential Biomarkers in Centr

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…

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GeneTonic: an R/Bioconductor package for streamlining the interpretation of RNA-seq data | BMC Bioinformatics

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,…

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Problem for analysing GSEA and ORA

Problem for analysing GSEA and ORA 0 I analysed two different GEO dataset individually and found DEG for each dataset .After that I compare the two dataset DEG and found some common DEG.Now i want to analyse GSEA and ORA for that common DEG.As far i know for analysing GSEA…

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Identification of lipid metabolism-associated gene signature

Background Female breast cancer has surpassed lung cancer as the most commonly diagnosed cancer. Despite the dramatic improvement in breast cancer prognosis due to recent therapeutic advances, such as more effective adjuvant and neo-adjuvant chemotherapies, together with more radical and safer surgery, advances in early diagnosis and treatment over the…

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Easy differential expression heatmap?

Easy differential expression heatmap? 0 I’m finally getting back to an RNAseq differential expression dataset I analyzed years ago and cannot remember what tool I used to generate these simple heat maps that I really like. I think it was an online interface where I could add/take away genes from…

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Frontiers | Plasma Cell-Free DNA Methylomics of Bipolar Disorder With and Without Rapid Cycling

Introduction Bipolar disorder (BD) features recurrent episodes of mania/hypomania and depression, interspersed with periods of euthymia. Symptoms usually include drastic changes in energy levels, sleep, thinking, and behaviors, which can significantly disrupt the daily life of BD patients (Craddock and Sklar, 2013). A mood cycle is defined as the period…

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GOstats doubts about significant GO terms with small “size”

Hi all, I am trying to perform a GO enrichment analysis on a list of differentially expressed genes and I am having doubts on the robustness of the results. I am using the GOstats package and the organism is Apis mellifera, so I had to make a custom gene universe…

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Genes and Pathways Involved in Postmenopausal Osteoporosis

Introduction Many postmenopausal women suffer from postmenopausal osteoporosis (PMO). A survey of 3247 Italian postmenopausal women found that according to bone mineral density (BMD) diagnostic criteria, the prevalence of osteoporosis was 36.6%.1 PMO patients may suffer from chronic pain and fractures, and as a result their quality of life is…

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Recommended bioinformatic course?

Recommended bioinformatic course? 0 Hello all, I started my PhD in medicine this year, my research includes a lot -omics analysis. Currently I am doing a transcriptomics project, but a proteomic and peptidomic project will certainly follow. Now I have mastered the basic of doing gene differential exppression myself, but…

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Count Matrix from quant.genes.sf files

Count Matrix from quant.genes.sf files 0 Hello everyone, I am having trouble understanding something and would appreciate any help or even a tutorial on this if someone can link it. I got 20 Bulk RNA samples sequenced and the bioinformatics core gave me 20 quant.genes.sf files obtained through DRAGEN RNA…

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Comparing the whole genelist by GSEA GO BP terms to adjusted pvalue genelist by DAVID GO BP terms

Comparing the whole genelist by GSEA GO BP terms to adjusted pvalue genelist by DAVID GO BP terms 0 Say I have done DESeq2 on my RNA-Seq dataset: experimental vs. control DESeq2 has a column for BH – adjusted Pvalues and I plan to take the genes with less than…

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Bioconductor – sparrow

DOI: 10.18129/B9.bioc.sparrow     Take command of set enrichment analyses through a unified interface Bioconductor version: Release (3.14) Provides a unified interface to a variety of GSEA techniques from different bioconductor packages. Results are harmonized into a single object and can be interrogated uniformly for quick exploration and interpretation of…

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replacing ensembl ID with the gene symbol?

Im a noob with a very unclear idea of what I am doing, but I’m doing my best. The other day, the ncbi webpage for downloading genomes and GTF files was down. As a result, I had to do my analysis on this RNA seq data using the ensembl files,…

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Bioconductor – Bioconductor 3.14 Released

Home Bioconductor 3.14 Released October 27, 2021 Bioconductors: We are pleased to announce Bioconductor 3.14, consisting of 2083 software packages, 408 experiment data packages, 904 annotation packages, 29 workflows and 8 books. There are 89 new software packages, 13 new data experiment packages, 10 new annotation packages, 1 new workflow,…

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single gene GSEA

single gene GSEA 0 Hello,I have a candidate gene which I want to check if it is related to important pathways/gene-sets in a dataset that its samples are from one biological group (tumor samples). I came up with two methods: Projecting the expression matrix to gene-set space using ssGSEAProjection and…

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Available GO molecular functions for AlphaFold proteins : bioinformatics

Context I’m currently exploring the AlphaFold 2 dataset. The goal is to use deep learning to generate some embeddings to represent the structures and group structurally similar proteins together using a clustering algorithm. I have my first pass at the clusters of AlphaFold proteins. Assuming that structure and function are…

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A TME-Related Signature as a Biomarker in Liver Cancer

Introduction As one of the most frequent causes of cancer deaths across the globe, liver cancer, characterized by high mortality, recurrence, metastasis and poor prognosis, is the only one of the top five deadliest cancers to have an annual percentage increase in occurrence.1 Surgery, local destructive therapies, and liver transplantation…

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ssGSEA scores correlate with the number of gene counts, should I be worried?

ssGSEA scores correlate with the number of gene counts, should I be worried? 0 I performed a Pearson correlation between the ssGSEA scores for all the 50 Hallmark pathways and the number of gene counts in my data. I noticed that most hallmark ssGSEA scores correlate with the number of…

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Gene Set Enrichment Analysis, KEGG and over representative analysis

Dear Seniors, I am looking to perform GSEA, KEGG and Over Representative Analysis. I found ClusterProfiler interesting and had ago with “GO classification” including groupGo (gene classification based on GO distribution at a specific level) , enrichGO (Over Representative analysis), gseGO (GO Gene Set Enrichment Analysis). ClusterProfiler needs EntrezID. Unfortunately,…

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RNA-seq z-score normalization

RNA-seq z-score normalization 1 Hi! I have RNA-seq data that I have put into DeSeq2 (R) for analysis and I would like to create heatmaps. I have also run my data using the gsea software from the broad institute and I would like to replicate the heatmaps that come out…

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Differential gene abundance analysis with 16s seq data

Differential gene abundance analysis with 16s seq data 0 Hello, Is it possible to do differential gene „abundance“ (I don’t want to say expression because it was not sequenced) analysis from two conditions of 16s RNA seq data (Microbiome analysis)? So basically, by 16s seq we can assign sequences to…

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Convert HTSeq-count, raw count to TPM : bioinformatics

Hi Everyone, I am working with a publicly available RNA-Seq dataset for which only the HTSeq-count data is accessible. I have done differential gene expression already (i.e. between sample analysis) however I am also hoping to obtain TPM count for within-sample analysis such as single-sample GSEA and for this I…

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deseq2 tutorial microbiome

phyloseq Handling and analysis of high-throughput microbiome census data. Detecting the periodontal pathogens at the subgingival plaque requires skilled professionals to collect samples. Import mothur list and group files and return an otu_table. In a randomized, double-blind, placebo-controlled trial, we assessed the effect of Lactobacillus reuteri supplementation, from birth to…

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Exclude pseudogenes and lncRNA’s from DE-analysis?

Hi all, Let’s start off to thank the ones that helped me lately. I almost feel bad for how many questions I have asked in the last weeks, but the answers were always of great help, so thanks for that! And yet I have another question. As described in my…

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Functional succinate dehydrogenase deficiency is a common adverse feature of clear cell renal cancer

Clear cell renal cell carcinoma (ccRCC) is by far the most common type of kidney cancer, accounting for ∼80% of all kidney cancers (1). Despite recent advances, metastatic ccRCC is a generally incurable malignancy, with a 5-y survival rate <20%, highlighting the need for further biologic and therapeutic insights in…

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Proper way(s) to perform enrichment analysis in R

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…

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clusterProfiler won’t read gene list

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…

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Identification of Prognosis-Associated Biomarkers in Thyroid Carcinoma

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

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Classifiers for predicting coronary artery disease

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

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Visualization of GO results using enrichplot

Visualization of GO results using enrichplot 0 Hello I am doing gene set analysis on DNA methylation microarray data (Illumina 450k and EPIC), and use the missMethyl package to do the analysis, and want to keep using that package because it accounts for some biases that occur when extracting the…

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Bioconductor – ttgsea (development version)

DOI: 10.18129/B9.bioc.ttgsea     This is the development version of ttgsea; for the stable release version, see ttgsea. Tokenizing Text of Gene Set Enrichment Analysis Bioconductor version: Development (3.14) Functional enrichment analysis methods such as gene set enrichment analysis (GSEA) have been widely used for analyzing gene expression data. GSEA…

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Filtering relevant Gene Ontology (GO) results from Gene Set Enrichment Analysis (GSEA)

Filtering relevant Gene Ontology (GO) results from Gene Set Enrichment Analysis (GSEA) 1 Hi all, I am new to bioinformatics and am currently learning how to use GSEA. Background: I analyzed my RNA-Seq results using DESeq2, and am now learning to perform GSEA. For my project, in broad terms, I…

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Gene expression profiling of contralateral dorsal root gangl

Introduction Mirror-image pain (MIP) is a mysterious pain phenomenon which is accompanied with many clinical pain conditions.1 MIP develops from the healthy body region which is contralateral to the actual injured site.1–3 MIP is typically characterized by increased mechanical hypersensitivity on the uninjured mirror-image body side.4 It can be triggered…

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gct output in DESeq2

gct output in DESeq2 2 Hi everyone, I’m trying to analyze my counts data with DESeq2 and based on the tutorial of GSEA, DESeq2 has an output format that can be used directly in the GSEA (here). However, I’m reading their workflow and I don’t find how to make this…

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Error in loading files into the GSEA software

Error in loading files into the GSEA software 0 Hi everyone I have some trouble with my RNA-seq file when I try to upload it for analysis with GSEA. I am getting the following error: Can anyone help me fix it? many thanks! —- Full Error Message —- There were…

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Sum of rows for GSEA analysis

Sum of rows for GSEA analysis 0 Hi, I have an issue which looks like easy to solve, but I’m stuck. I have a dataframe composed of columns (significant pathways retrieved from GSEA) and rows (entrez gene ids). In this data frame there are 1 if a gene is present…

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Predicting and characterizing a cancer dependency map of tumors with deep learning

INTRODUCTION The development of novel cancer therapies requires knowledge of specific biological pathways to target individual tumors and eradicate cancer cells. Toward this goal, the landscape of genetic vulnerabilities of cancer, or the cancer dependency map, is being systematically profiled. Using RNA interference (RNAi) loss-of-function screens, Marcotte et al. (1),…

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working with .gmt files

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…

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Performing GSEA using MSigDB gene sets in R

Performing GSEA using MSigDB gene sets in R 2 I am trying to perform a gene set enrichment analysis in r using the gene sets available from msigdb and a list of gene names from my own data set. I am able to to use the msigdbr library to import…

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how to use ESTIMATE to infer tumor purity and stromal score from RNA-seq data?

how to use ESTIMATE to infer tumor purity and stromal score from RNA-seq data? 1 Dear all: Did anyone use ESTIMATE (bioinformatics.mdanderson.org/main/ESTIMATE:Overview) to infer tumor purity and stromal score from RNA-seq before? I am not clear how to use this tool and what is the input file format for this…

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GSEA and over-representation analysis of many genes

GSEA and over-representation analysis of many genes 0 Hello everyone! I’ve been doing some Differential Expression analysis on specific samples. It happens that I found a lot of genes that are DE. In total, of 24000 features, 11000 were up or down regulated in control vs group. Even tough the…

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