Tag: GEO

Novel diagnostic biomarkers for keloid based on GEO database

Introduction Keloid is excessive fibrosis of the skin that extends beyond the area of injury and does not regress.1 Keloid can occur in the joints and mouth after several years of severe injury, including burns, chemical injury, wound, and surgical incision.2 Keloids on the joints affect the quality of life,…

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[BioC] problem with GEOquery

Hi to everybody, i have a little problem with GEOquery .i when I’m trying to download the GSE2841 dataset I encounter the gse <- getGEO(“GSE2841”) try with URL‘ftp.ncbi.nih.gov/pub/geo/data/geo/by_series/GSE2841_family.soft.gz’Error in downloading the.file(myurl, destfile, mode = mode) :impossible to open URL‘ftp.ncbi.nih.gov/pub/geo/data/geo/by_series/GSE2841_family.soft.gz'&#8221; why???????????? Please help me Best regards Dr Alberto GoldoniMedical Genetics UnitS….

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The role of ATXR6 expression in modulating genome stability and transposable element repression in Arabidopsis

Significance The plant-specific H3K27me1 methyltransferases ATXR5 and ATXR6 play integral roles connecting epigenetic silencing with genomic stability. However, how H3K27me1 relates to these processes is poorly understood. In this study, we performed a comprehensive transcriptome analysis of tissue- and ploidy-specific expression in a hypomorphic atxr5/6 mutant and revealed that the…

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ChromoMap: an R package for interactive visualization of multi-omics data and annotation of chromosomes | BMC Bioinformatics

1. Buels R, Yao E, Diesh CM, Hayes RD, Munoz-Torres M, Helt G, Goodstein DM, Elsik CG, Lewis SE, Stein L, et al. JBrowse: a dynamic web platform for genome visualization and analysis. Genome Biol. 2016;17:66. Article  Google Scholar  2. Minio A, Lin J, Gaut BS, Cantu D. How single…

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Bioconductor – GSE13015

DOI: 10.18129/B9.bioc.GSE13015     GEO accession data GSE13015_GPL6106 as a SummarizedExperiment Bioconductor version: Release (3.14) Microarray expression matrix platform GPL6106 and clinical data for 67 septicemic patients and made them available as GEO accession [GSE13015](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE13015). GSE13015 data have been parsed into a SummarizedExperiment object available in ExperimentHub. This data data…

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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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Identification of differentially expressed genes in AF

Defeng Pan,1,&ast; Yufei Zhou,2,&ast; Shengjue Xiao,1,&ast; Yue Hu,3,&ast; Chunyan Huan,1 Qi Wu,1 Xiaotong Wang,1 Qinyuan Pan,1 Jie Liu,1 Hong Zhu1 1Department of Cardiology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, 221004, People’s Republic of China; 2Department of Cardiology, Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital and Institutes of…

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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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Getting peak heights from TF chIP-seq data (wig file)

Getting peak heights from TF chIP-seq data (wig file) 1 Hello everyone, I have TF ChIP seq data from NCBI GEO in wig format. I converted wig to bedgraph and then used MACS peak caller to get bed narrowpeak files.I further uploaded file on genome browser to get graphical map…

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Crosstalk between Venous Thromboembolism and Periodontal Diseases: A Bioinformatics Analysis

This article was originally published here Dis Markers. 2021 Dec 10;2021:1776567. doi: 10.1155/2021/1776567. eCollection 2021. ABSTRACT BACKGROUND: This current study applied bioinformatics analysis to reveal the crosstalk between venous thromboembolism (VTE) and periodontitis, as well as the potential role of immune-related genes in this context. METHODS: Expression data were downloaded…

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Adrenal aldosterone-producing adenoma | IJGM

Background Primary hyperaldosteronism (PA) is characterized by spontaneous secretion of excessive aldosterone and inhibition of plasma renin activity.1 The pathogenesis of adrenal aldosterone-producing adenoma (APA) involves the abnormal proliferation of adrenal cortex cells and the excessive secretion of aldosterone, accounting for nearly 30% of PA. Excessive secretion of aldosterone can…

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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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Prognosis Biomarkers via WGCNA in HCC

Introduction According to the cancer statistics reported in 2020, hepatocellular carcinoma (HCC) is the main type of Primary Carcinoma of the Liver and the second leading causes of cancer-related death globally, with a five-year survival rate < 20%.1 Currently, surgical resection, a standard therapy for HCC, contributes to the prognosis…

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Intersecting Roadmap’s Histone ChIP-seq data using BedTools?!?!??!

Intersecting Roadmap’s Histone ChIP-seq data using BedTools?!?!??! 0 Hi all, I want to prioritise my list of 112 SNPs by looking at those that lie within open chromatin regions and/or active promoter/enhancer histone marks In order to do that I have downloaded several Histone modification ChIP-seq data from Roadmap epigenomics…

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How to convert cloupe files to mtx

How to convert cloupe files to mtx 1 I have 2 cloupe files from a project on GEO. I need to reprocess this data but cannot find a way to extract the gene expression table from the cloupe files. I tried Loupe Browser from cell ranger but this only allows…

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Identification of Hub Genes in Patients with Alzheimer Disease and Obs

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…

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Identification of circRNA-miRNA-mRNA Regulatory Network and Autophagy Interaction Network in Atrial Fibrillation Based on Bioinformatics Analysis

Background: Circular RNA (circRNA) has been receiving increased attention in the research of atrial fibrillation (AF). Our study aims to find potential circRNAs and identify the circRNA-miRNA-mRNA regulatory network in AF based on bioinformatics analysis. Methods: GSE129409 was retrieved from the Gene Expression Omnibus (GEO) database, and we used R…

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Dropseq, GSE124872 and structure of the reads in the FastQ files

Hello I am confused by the structure of the reads in a FastQ File I downloaded via GEO. The data is stored in GEO GSE124872, GSM3557675. According the SRA Run Selector, there is one FastQ file per sample, but the paper* and SRA mention that the data is paired end….

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Comment: Importing GEO dataset

my sessionInfo() output is R version 4.1.1 (2021-08-10) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Big Sur 11.2.2 Matrix products: default LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] compiler_4.1.1 tools_4.1.1 Read more here: Source…

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Potenial biomarker in Crohn’s diease via bioinformatics

Introduction Crohn’s disease (CD) and ulcerative colitis are chronic inflammatory disorders of the gastrointestinal tract, with symptoms evolving in a relapsing and remitting manner that comprise the term inflammatory bowel disease (IBD).1 CD is characterized by the involvement of all parts of the intestine, the most common being the terminal…

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What is a count matrix for input into Seurat supposed to look like?

Hello, I hope you are safe and well. Could someone share what a count matrix for input into Seurat is supposed to look like? I have count matrices however they each cells count matrix is in a separate file. This is the data I want to analyze in Monocle 3:…

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Genome Size Estimation with Jellyfish and Genome Scope is Unexpectedly Small

I used jellyfish to count kmers and the obtained histograms were analyzed using Genome scope (qb.cshl.edu/genomescope/) in order to estimate effective genome size. However the resulting bp estimation of 61,351 bps is unexpectedly small for human data. The paired-end data was obtained from a Chip-seq experiment on Geo (GSE72141). Additionally,…

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The Construction and Comprehensive Analysis of a ceRNA Immunoregulator

1Department of Cardiology, Xiangtan Central Hospital, Xiangtan, Hunan, People’s Republic of China; 2Department of Cardiology, Guangxi Cardiovascular Institute, The First Affiliated Hospital of Guangxi Medical University, Guangxi, People’s Republic of China; 3Department of Critical Care Medicine, Zhuzhou Central Hospital, Zhuzhou, Hunan, People’s Republic of China Correspondence: Yiqian ZengDepartment of Critical…

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Comprehensive analysis of ceRNA networks to determine genes related to prognosis, overall survival, and immune infiltration in clear cell renal carcinoma

Comput Biol Med. 2021 Nov 20:105043. doi: 10.1016/j.compbiomed.2021.105043. Online ahead of print. ABSTRACT BACKGROUND: Clear cell renal cell carcinoma (ccRCC) is one of the common subtypes of kidney cancer. Circular RNAs (circRNAs) act as competing endogenous RNAs (ceRNAs) to affect the expression of microRNAs (miRNAs), and hence the expression of…

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Collabera Inc. hiring Bioinformatics Analyst in North Chicago, Illinois, United States

Job Description We have an exciting contract opportunity for a Bioinformatics Analyst to perform bulk differential gene. Ideally microarray and RNA-seq and enrichment analysis in the R programing language, leveraging public domain datasets from NCBI GEO/SRA and/or EBI ArrayExpress/ENA repositories. This includes performing quality control, normalization, differential gene limma/variance Parition…

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Importing GEO dataset

I need to import data GSE76124 in R studio the command I used is library(GEOquery) my_id <- "GSE76124" gse <- getGEO(my_id) the output and warning I'm getting is : Found 1 file(s) GSE76124_series_matrix.txt.gz trying URL 'ftp.ncbi.nlm.nih.gov/geo/series/GSE76nnn/GSE76124/matrix/GSE76124_series_matrix.txt.gz&#039; Content type 'application/x-gzip' length 58695125 bytes (56.0 MB) ================================================== downloaded 56.0 MB Error: The…

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Bioinformatics Scientist at Infectious Disease Institute

IDI seeks to hire a Bioinformatics Scientist (BS) for the centre. The BS will be a fulltime staff who is familiar with the application of computational and biotechnology capabilities to biomedical and public health problems like genetics, clinical and medical research, as well as other data intensive analyses. By coordinating…

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Index of /~psgendb/doc/local/biopython-1.64.old/Tests/output

Name Last modified Size Description Parent Directory   –   test_AlignIO 2014-05-29 05:23 31K   test_AlignIO_FastaIO 2014-05-29 05:23 60K   test_ClustalOmega_tool 2014-05-29 05:23 1.2K   test_Clustalw 2014-05-29 05:23 5.8K   test_Clustalw_tool 2014-05-29 05:23 1.3K   test_CodonTable 2014-05-29 05:23 21   test_CodonUsage 2014-05-29 05:23 784   test_DocSQL 2014-05-29 05:23 42  …

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Most useful public genomic/genetic databases/tools/applications

Forum:Most useful public genomic/genetic databases/tools/applications 1 Hi guys, I am looking for suggestions/recommendations from the research community regarding public databases that are most commonly used by researchers in their analysis. These could be the open access data or controlled access. Also, what are some of the applications used most commonly…

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Bioconductor – GSE159526

DOI: 10.18129/B9.bioc.GSE159526     Placental cell DNA methylation data from GEO accession GSE159526 Bioconductor version: Release (3.14) 19 term and 9 first trimester placental chorionic villi and matched cell-sorted samples ran on Illumina HumanMethylationEPIC DNA methylation microarrays. This data was made available on GEO accession [GSE159526](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE159526). Both the raw and…

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Bioinformatics analysis pinpoints the pathways involved in intestinal SARS/CoV-2 infection

Severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) is a positive-strand RNA virus, which appears spherical under a transmission electron microscope. Many studies have shown that SARS-CoV-2 infects host cells via the interaction between the viral spike protein and the host receptor, angiotensin-converting enzyme II (ACE2). SARS-CoV-2 can spread through…

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WGCNA Analysis Identifies Polycystic Ovary Syndrome-Associated Circula

Introduction Polycystic ovary syndrome (PCOS) is a common endocrine metabolic disorder in women of childbearing age.1 PCOS patients are typically characterized by androgen excess, polycystic ovaries and anovulation, and are often accompanied by insulin resistance and obesity.2 Consequently, patients with this syndrome not only suffer from infertility,3 but also have…

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Bioconductor – tuberculosis

DOI: 10.18129/B9.bioc.tuberculosis     Tuberculosis Gene Expression Data for Machine Learning Bioconductor version: Release (3.14) The tuberculosis R/Bioconductor package features tuberculosis gene expression data for machine learning. All human samples from GEO that did not come from cell lines, were not taken postmortem, and did not feature recombination have been…

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PyTorch implementation of our ICCV 2021 paper Intrinsic-Extrinsic Preserved GANs for Unsupervised 3D Pose Transfer.

This is the PyTorch implementation of our ICCV 2021 paper Intrinsic-Extrinsic Preserved GANs for Unsupervised 3D Pose Transfer. Haoyu Chen, Hao Tang, Henglin Shi, Wei Peng, Nicu Sebe, Guoying Zhao. Citation If you use our code or paper, please consider citing: @inproceedings{chen2021IEPGAN, title={Intrinsic-Extrinsic Preserved GANs for Unsupervised 3D Pose Transfer}, …

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Index of /~psgendb/local/biopython-1.64.old/Bio

Name Last modified Size Description Parent Directory   –   Affy/ 2014-05-29 05:25 –   Align/ 2014-06-11 10:27 –   AlignIO/ 2014-06-11 10:27 –   Alphabet/ 2014-06-11 10:27 –   Application/ 2014-05-29 05:25 –   Blast/ 2014-05-29 05:25 –   CAPS/ 2014-05-29 05:25 –   Cluster/ 2014-05-29 05:25 –  …

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circRNA-miRNA-mRNA regulatory network in atrial fibrillation

Introduction Atrial fibrillation (AF) is the most common type of arrhythmia in clinical practice, with global prevalence continuing to increase primarily with age.1 In China, 6.5 persons out of every thousand suffer from AF, and there are about 3.9 million patients with AF who are over 60 years old, but…

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Differential gene expression analysis on microarray dataset with files from two chips

Hello all, I’m used to analyzing mostly RNAseq data, microarray is a bit new to me. I’m trying to analyze data from www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE47183 in R. When I try to read in the .CEL files using read.celfiles() from the oligo package, it informs me that the CEL files are not of…

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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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Multiple stages of evolutionary change in anthrax toxin receptor expression in humans

Human research participants We have complied with all relevant ethical regulations and informed consent was obtained from all participants. This work was approved by the Cornell University IRB under protocol 1506005662. Animal research This work was approved by the Cornell University IACUC under protocol 2009-0044. Welfare and handling of all…

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Not able to show data on choropleth map with ggplot2 – R Markdown

Hi everyone, I am working on some data visualisations for a project. I have very limited experience with R so any help will be greatly appreciated. I have run the code below. I have gotten a map but no colours and Co2 Emission data for the countries. Co2_Country_Graph4=plot_geo(Co2Country3,locationmode =”country”,frame= ~Year)%>%add_trace(location…

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sequencing – Plotting QC output for scRNA data analysis using Seurat R and accessing Seurat object data

I am new to R, and want to analyse some public scRNA seq data published in Sade-Feldman M, Yizhak K, Bjorgaard SL, Ray JP et al. Defining T Cell States Associated with Response to Checkpoint Immunotherapy in Melanoma. Cell 2018 Nov 1;175 (www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE120575). I have tried to follow the online…

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Sending Fasta files : bioinformatics

What is the source of your fasta file? If it’s your personal data from sequencing I would not give it out without ensuring they are keeping anonymity and proper ethical considerations, like who else will this file be shared with and how. Many publications have Geo datasets or SRA archives…

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How to load GEO datasets for analysis using Scvi tools/Scanpy? : bioinformatics

I am super new to bioinformatics and omics studies. I am currently trying to analyse single cell RNA seq data using Scanpy and Scvi, and I am trying it out with datasets on GEO. They look a little different than the ones that were used in the tutorials. It seems…

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Error using getGEO – error reading from the connection

Error using getGEO – error reading from the connection 0 Hi, I’ve been trying to open GEO data in R studio. So far I have the following code, copied from a tutorial: #tutorial for analysing data from GEO library(GEOquery) my_id <- “GSE33126” gse <- getGEO(my_id) However, I get the following…

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Error using getGEO

Hi, I’ve been trying to open GEO data in R studio. So far I have the following code, copied from a tutorial: library(GEOquery) my_id <- “GSE33126” gse <- getGEO(my_id) However, I get the following error when running this code: Found 1 file(s) GSE33126_series_matrix.txt.gz trying URL ‘ftp.ncbi.nlm.nih.gov/geo/series/GSE33nnn/GSE33126/matrix/GSE33126_series_matrix.txt.gz‘ Content type ‘application/x-gzip’ length…

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How to calculate fold change values from GSM data

How to calculate fold change values from GSM data 0 I want to calculate fold change values from the GSM data. For example, under GSE8158 there are many samples available like the image below: The only file that is available under each GSM sample is a .gpr file as well…

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r – Including Subscript/Greek Letter/Symbols to ggplot x-axis text

I have a following code that generates a ggplot: ggplot(data = t, aes(x = grp, y = b.hat, group = geo.l)) + geom_hline(yintercept = unique(temp$b), lty=’dotted’, color=”gray20″) + geom_point(aes(color = geo.l), position = position_dodge(width = 1)) + geom_errorbar(aes(ymin = b.hat – 2 * b.hat.se, ymax = b.hat + 2 *…

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GEOquery with R

GEOquery with R 0 I am trying to start some analysis of RNA seq data with R. However, I am having some trouble with downloading the data. I have downloaded the following libraries: install.packages(“BiocManager”) install.packages(“forcats”) install.packages(“stringr”) install.packages(“ggplot2”) install.packages(“ggrepel”) install.packages(“readr”) install.packages(“tidyr”) install.packages(“survminer”) BiocManager::install(“GEOquery”) BiocManager::install(“limma”) BiocManager::install(“pheatmap”) BiocManager::install(“org.Hs.eg.db”) Ran this code: library(GEOquery) gse…

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Help with accessing GEO dataset

Help with accessing GEO dataset 0 Hi. I am trying to access a GEO dataset by following the instructions in a tutorial. However, I am unable to. I keep on getting this message. Found 1 file(s) GSE33126_series_matrix.txt.gz Using locally cached version: C:UsersSharonAppDataLocalTempRtmpmaCHbX/GSE33126_series_matrix.txt.gz Using a locally cached version of GPL6947 found…

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Job Opening – Bioinformatics Analyst

job summary: As the world’s largest staffing and recruitment agency in the world, we can commit to find you the perfect role that gives you the opportunity to learn and grow in the life sciences arena. Utilizing a recruiter for your job search gives you access to a large network…

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Synectics Inc. hiring Bioinformatics Analyst in North Chicago, Illinois, United States

Contract: 3 months Pay: $22.91/hr ONSITE Description Perform bulk differential gene (ideally microarray and RNA-seq) and enrichment analysis in the R programming language, leveraging public domain datasets from NCBI GEO/SRA and/or EBI ArrayExpress/ENA repositories. This includes performing quality control, normalization, differential gene (limma/varianceParition dream or other R method) and single-sample…

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Spectraforce Technologies hiring Bioinformatics analyst in Waukegan, Illinois, United States

Job Title: Bioinformatics analystLocation: Lake County, IL; 100% remoteDuration: 6 months Payrate: $24/hr on W2 DescriptionWe have an exciting contract opportunity for a Bioinformatics Analyst to perform bulk differential gene ideally microarray and RNA-seq) and enrichment analysis in the R programing language, leveraging public domain datasets from NCBI GEO/SRA and/or…

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Biomea Fusion Publishes Abstract on BMF-219 at ASH Annual Meeting

Figure 1 Menin and various co-factors Menin and various co-factors Figure 2 Transcription factor (TF) activity inference using ChIP-seq of differentially expressed genes in MOLM-13 cells incubated with 500 nM BMF-219 at 24 hours. Each bar represents a study in the GEO repository using the specified TF antibody. TFs with…

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ARGs as potential biomarkers & therapeutic targets in AF

Introduction Atrial fibrillation (AF) is the most common clinically sustained cardiac rhythm disorder. There is a high prevalence of AF all over the world, the highest in North America, Europe, China, and Southeast Asia, with approximately 270–360 cases per 100,000 people.1 Due to the lack of understanding of the pathogenesis…

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Candidate genes associated with synovial macrophages

Jia Xu,1 Ming-Ying Zhang,2 Wei Jiao,1 Cong-Qi Hu,1 Dan-Bin Wu,2 Jia-Hui Yu,1 Guang-Xing Chen2,3 1First Clinical Medical School, Guangzhou University of Chinese Medicine, Guangzhou, 510405, Guangdong, People’s Republic of China; 2Department of Rheumatology, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, 510405, Guangdong, People’s Republic of China;…

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Exploration of Prognostic Biomarkers of Muscle-Invasive Bladder Cancer (MIBC) by Bioinformatics

This article was originally published here Evol Bioinform Online. 2021 Oct 28;17:11769343211049270. doi: 10.1177/11769343211049270. eCollection 2021. ABSTRACT We aimed to discover prognostic factors of muscle-invasive bladder cancer (MIBC) and investigate their relationship with immune therapies. Online data of MIBC were obtained from The Cancer Genome Atlas (TCGA) and Gene Expression…

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Bioconductor – leukemiasEset

DOI: 10.18129/B9.bioc.leukemiasEset     This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see leukemiasEset. Leukemia’s microarray gene expression data (expressionSet). Bioconductor version: 3.8 Expressionset containing gene expresion data from 60 bone marrow samples of patients with one of the four main types of leukemia…

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Bioinformatics Analyst position in North Chicago, Illinois

Open for discussion of Remote  We have an exciting contract opportunity for a Bioinformatics Analyst to perform bulk differential gene?ideally microarray and RNA-seq) and enrichment analysis in the R programing language, leveraging public domain datasets from NCBI GEO/SRA and/or EBI ArrayExpress/ENA repositories. This includes performing quality control, normalization, differential…

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CONVERT PSF to TOP grimaces

namd-l: Re: CONVERT PSF to TOP grimaces I might be a little biased since I wrote TopoGromacs for my own needs, but I think it’s a fine way to generate the .top file GROMACS expects. This defines the system topology and parameters, which are combined with a .mdp file into…

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The Biostar Herald for Monday, November 01, 2021

The Biostar Herald publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed. You too can submit links here. This edition of the Herald was brought to you by contribution from Mensur Dlakic, Istvan Albert, GenoMax, and was…

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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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GO analyses background genes

GO analyses background genes 0 I analysed three microarrays includes lncRNAs from GEO. These are same platforms. After I found differentially expressed lncRNAs, I performed lncRNA:miRNA analyses using DIANA web tool. Then, I found mRNAs related to miRNAs using mirDB, miRTarBase and TargetScan tools. I found to be 354 overlapped…

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Assign experimental groups and replicates within a GSE properly

Assign experimental groups and replicates within a GSE properly 0 Hello everyone! Is there a way to assign experimental groups and replicates within a GSE properly? Metadata does not follow a standard, so it is not possible to automatically distinguish groups and replicates with the information contained (no luck in…

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Cell Type Marker Databases?

Cell Type Marker Databases? 6 Hi, I’ve been looking to see if there is any kind of public database or resource for cell type-specific markers. These would include genes for proteins that can uniquely identify a cell population using techniques such as FACS. I’ve tried a variety of different search…

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How to annotate GPL for GEO data byhand?

How to annotate GPL for GEO data byhand? 1 Hello, getGEO() function always fail to AnnoGPL for GSE69644. Error because 1: In download.file(myurl, destfile, mode = mode, quiet = TRUE, method = getOption(“download.file.method.GEOquery”)) : cannot open URL ‘https://ftp.ncbi.nlm.nih.gov/geo/platforms/GPL13nnn/GPL13667/annot/GPL13667.annot.gz’: HTTP status was ‘404 Not Found’ I want to know how can…

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PER1 as a Tumor Suppressor Attenuates Breast Cancer

Introduction Breast cancer is one of the most common malignancies in women, with a high mortality rate around the world.1,2 Although multidisciplinary therapeutic strategies, including surgical resection, chemoradiotherapy, endocrine and anti-HER2 therapy, have made substantial progress over the past decade, there are still a considerable proportion of breast cancer patients…

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Identification of Significant Genes in Lung Cancer of Nonsmoking Women via Bioinformatics Analysis

This article was originally published here Biomed Res Int. 2021 Oct 11;2021:5516218. doi: 10.1155/2021/5516218. eCollection 2021. ABSTRACT BACKGROUND: The aim of this study was to identify potential key genes, proteins, and associated interaction networks for the development of lung cancer in nonsmoking women through a bioinformatics approach. METHODS: We used…

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LncRNA MIAT services as a noninvasive biomarker

Introduction BC is the most common cancer among women that is responsible for the most of the cancer-related death in worldwide.1 The occurrence of BC accounts for 7–8% of the entire number of malignant tumors.2 Accumulating evidence have shown that immunoreaction plays an important role in oncogenesis and progression.3,4 However,…

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Are there any studies that have computed the distribution on number of samples vs. number of features in Omics datasets?

Are there any studies that have computed the distribution on number of samples vs. number of features in Omics datasets? 0 I’m working on my PhD dissertation and making a statement about how Omics datasets tend to have more features than samples. I feel this fact is well known but…

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Bioinformatics Prediction and Analysis of MicroRNAs and Their Targets as Biomarkers for Prostate Cancer: A Preliminary Study

This article was originally published here Mol Biotechnol. 2021 Oct 19. doi: 10.1007/s12033-021-00414-8. Online ahead of print. ABSTRACT Prostate cancer (PCa) is the second most common form of cancer in men around the world. Due to its heterogeneity, presentations range from aggressive lethal disease to indolent disease. There is a…

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Severe trauma and burns accompanied by sepsis

Introduction Trauma accounts for approximately 10% of deaths and 16% of disabilities worldwide.1 Billions of dollars have been spent on research into new biological therapeutics for severe injuries, as well as post-traumatic sepsis and septic shock.2 Burn injuries cause unpredictable trauma and sepsis is a complication associated with high morbidity…

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H/ACA snoRNP gene family as diagnostic/prognostic biomarkers

Introduction Primary liver cancer, including hepatocellular carcinoma (HCC) and intrahepatic cholangiocarcinoma, is the sixth most commonly diagnosed cancer and the fourth leading cause of cancer-related deaths worldwide.1 High metastasis and recurrence rates, as well as limited treatment options, lead to the poor prognosis of advanced HCC.2 Among patients diagnosed with…

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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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GEO scRNA-seq entry with cell type information?

GEO scRNA-seq entry with cell type information? 1 Hello, I am trying to look for a scRNA-seq dataset hosted in GEO that, apart of the common files genes.tsv, barcodes.tsv and matrix.mtx, also has a file mapping barcode to cell types (as annotated by the paper). I have been trying to…

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How best to handle multiple probes for single genes in survival analysis of Geo data

How best to handle multiple probes for single genes in survival analysis of Geo data 0 I imported some microarray data from Geo and was able to write a for loop that plots survival curves for high/low expression of each probe corresponding to a specific gene. Now I am interested…

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How can I extract data from the expression matrix txt extension?

How can I extract data from the expression matrix txt extension? 1 I want to analyze this data (GSE60361) with the seurat package and also extract the gene expression matrix (including cells in rows and genes in columns). Is it possible? What other tools are there to obtain the expression…

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How can I be sure that raw read counts are well processed from fastq files?

How can I be sure that raw read counts are well processed from fastq files? 0 Hi. I’m new in bioinformatics and try to process fastq files for getting raw read count matrix. I downloaded fastq files from www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE63452 I used fasterq -dump to download fastq files from SRR Aligned…

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GEOexplorer: an R/Bioconductor package for gene expression analysis and visualisation

Abstract Background: Over the past three decades there have been numerous molecular biology developments that have led to an explosion in the number of gene expression studies being performed. Many of these gene expression studies publish their data to the public database GEO, making them freely available. By analysing gene…

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How can I find disease related RNA-seq data, where my gene of interest is differentially expressed?

How can I find disease related RNA-seq data, where my gene of interest is differentially expressed? 0 Hi, For our project, we would like to see if there is any disease relevance. For this, I would like to find publicly available RNA-seq data (preferably limited to RNA-seq in disease context)…

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Bioconductor – JctSeqData

DOI: 10.18129/B9.bioc.JctSeqData     This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see JctSeqData. Example Junction Count data for use with JunctionSeq Bioconductor version: 3.9 Junction count data from an example dataset taken from a subset of the RNA-seq reads from six samples. Data…

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Identification of immunization-related new prognostic biomarkers for papillary renal cell carcinoma by integrated bioinformatics analysis

This article was originally published here BMC Med Genomics. 2021 Oct 7;14(1):241. doi: 10.1186/s12920-021-01092-w. ABSTRACT BACKGROUND: Despite papillary renal cell carcinoma (pRCC) being the second most common type of kidney cancer, the underlying molecular mechanism remains unclear. Targeted therapies in the past have not been successful because of the lack…

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Livingston Co. Sheriff’s Office investigating theft from county road department garage

LIVINGSTON COUNTY, Ky. (KFVS) – The sheriff’s office is investigating a theft from the county road department garage. According to deputies, between 7:30 p.m. on October 4 and 5:30 a.m. on Oct. 5, someone broke into the storage yard at the Livingston County Road Department garage. They said a white…

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Colossal Begins Ambitious De-Extinction Plan With Elephant Sequencing Project, Despite Critics

NEW YORK – Bioscience and genetics startup Colossal made headlines around the world last month when it revealed its intentions to bring the woolly mammoth back from extinction. But underneath that sensational plan lies a mission that’s slightly more nuanced, beginning with the goal of genetically preserving endangered species for the benefit of…

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Analyzing gene expression in different RNAseq datasets

Analyzing gene expression in different RNAseq datasets 0 Hello! I really need some assistance here, I came up with an analysis of my own that makes sense to me but I really new in this (started studying bioinformatics on my own with the pandemics) and I’m not sure if I…

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Batch effect removal

Batch effect removal 1 Hi! I’m new to bioinformatics and I’m working with 6 different RNA-seq(high throughput) studies from GEO, 3 of the GSEs contain gene expression for tumors and the other 3 contains healthy tissue. I’m going to do batch correction, and I’m wondering do I merge all datasets…

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Govt experiment ends, Khallikote merges with Berhampur varsity- The New Indian Express

Express News Service BHUBANESWAR/BERHAMPUR: Berhampur University is considering creation of a PG department in Library Science to accommodate students of the Khallikote Research Intensive University after the latter merged with it on Friday, October 1, 2021. The Khallikote University had six PG departments offering MSc in Biosciences and Bioinformatics; Masters…

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khallikote university: Khallikote varsity merges with BU, staff transferred | Bhubaneswar News

BERHAMPUR: The existence of six-year-old Khallikote University (KU), whose merger with Berhampur University (BU) is set to be complete on Friday, will soon become a thing of the past. Officials said while the regular employees of the Khallikote University will become the staff of Berhampur University, its students will also…

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Regulation of prefrontal patterning and connectivity by retinoic acid

Data reporting No statistical methods were used to predetermine sample size.  Data collection was performed by independent investigators. Prior to data analysis, all experiments were randomized and analysed by independent blinded observers. Analysis of human and macaque transcriptomic data Developing human and macaque brain RNA-seq data (counts file) with the…

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Beginner in bioinformatics needs some help

Beginner in bioinformatics needs some help 0 Hi, I am new in Bioinformatics, trying to analyze two colour agilent microarray. I have decided to follow this protocol build the expression matrix step by step from GEO raw data I have created a folder that i have named “Targets.txt”. Inside I…

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visualisation of proteomics data using r and bioconductor

R package version 0.99.7, 2014. [9] have developed an approach to estimate peptide isoelectric point values using a Support Vector Machine classifier from the caret package [10]. [73] De Duve, C., Beaufay, H., A Short History of Tissue Fractionation. The readers are referred to the respective documentation and vignettes for…

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end to end workflow to import the download GEO data into tranSMART

end to end workflow to import the download GEO data into tranSMART 0 Dear all, Thanks for your always kindly help. I am playing with the GEO download set. I would like to import the downloaded data into tranSMART, I noticed I could import with some ETL tools like tMDATAloader…

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Survival analysis with gene expression

[*] For this example, we will load GEO breast cancer gene expression data with recurrence free survival (RFS) from Gene Expression Profiling in Breast Cancer: Understanding the Molecular Basis of Histologic Grade To Improve Prognosis. Specifically, we will encode each gene’s expression into Low | Mid | High based on…

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RNAseq count which strand to use

RNAseq count which strand to use 0 naive question, but do not find a clear answer to solve this, downloaded a raw count file from geo, which looks like this, gene unstranded fwd rev ENSMUSG00000102693 0 0 0 ENSMUSG00000064842 0 0 0 ENSMUSG00000051951 63 38 25 How could I use…

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Convert FPKM and RPKM to TPM values

Convert FPKM and RPKM to TPM values 0 Hi all, I’m trying to collect the datasets from public datasets from GEO. I found some data in fpkm and some in rpkm,tpm. My goal is to feed these data into a machine learning model, but my question is “ALL THESE DATA…

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how to process the raw data of illumina Arrays( Illumina HumanHT-12 V4.0 expression beadchip)

how to process the raw data of illumina Arrays( Illumina HumanHT-12 V4.0 expression beadchip) 2 For getting reliable expression matrices, I wanna know how to process the two non-normalized data from GEO database(GSE98278 & GSE47472). Here are the colnames of the two non-normalized data.Could someone share the codes?This will be…

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rs2507799 was found to be linked with increased risk for IS

Introduction Ischemic stroke (IS) is caused by the sudden loss of blood circulation to an area of the brain that causes injury to neurological function and represents a major cause of global disability and mortality.1 IS is known to be a heterogeneous and multifactorial disease. Genetic factors, particularly those involving…

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In what way should cellranger count be performed , when there are multiple runs for each of the samples ?

I am trying to analyze single-cell RNA-seq data using cellranger, from publicly available datasets/ studies which have been published. I am getting SRA files from NCBI GEO – the data set currently under consideration is GSE168388 . When I look into this data, I can see that this dataset consists…

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Batch effects

Batch effects 0 Hi! I’m new at bioinformatics and I’m working with a project where I combine several datasets from GEO. I retrieve the data from GREIN(GEO RNA-seq Experiment Interactive Navigator) which has processed all the datasets in the same way. They provide raw and normalised data. My question is…

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Difference between dataset analysis

Difference between dataset analysis 1 Hi! I’m going to merge several datasets from different studies from GEO, and I was wondering how I can check how different the datasets are compared to each other? Do I merge the datasets to one big set first, or do I do the analysis…

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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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