Tag: ensembl

Microarray DEG scatterplot

Hi, I have found that my selected gene, probe I.D 201667_at is differentially expressed between WDLPS and DDLPS tumour tissue samples after performing microarray DEG analysis. Instead of just a p value in a table format: Probe I.D “201667_at” logFC 10.8205874181535 AveExpr 10.6925705768407 t 82.8808890739766 P.Value 3.10189446528995e-88 adj.P Val 3.10189446528995e-88…

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How can I convert Ensembl ID to gene symbol in R?

I tried several R packages (mygene, org.Hs.eg.db, biomaRt, EnsDb.Hsapiens.v79) to convert Ensembl.gene to gene.symbol, and found that the EnsDb.Hsapiens.v79 package / gene database provides the best conversion quality (in terms of being able to convert most of Ensembl.gene to gene.symbol). Install the package if you have not installed by running…

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Live-seq enables temporal transcriptomic recording of single cells

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

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Installing ensembl-vep

Installing ensembl-vep 1 Hello all , I tried installing ensembl-Vep on mu ubuntu using following commands git clone github.com/Ensembl/ensembl-vep cd ensembl-vep perl INSTALL.pl I got the error as :- ERROR: DBI module not found. VEP requires the DBI perl module to function I tried installing DBI etc but the error…

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Patrick Murphy Bulk RNA-Seq – HackMD

Patrick Murphy Bulk RNA-Seq – HackMD        owned this note   Published Linked with GitHub — title: ‘Patrick Murphy Bulk RNA-Seq’ disqus: hackmd — Patrick Murphy bulk RNA-Seq Analysis === ## Table of Contents [TOC] ## 1. Introduction This is a bulk RNA-Seq project, which includes human data….

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hgmd variants from Ensembl

hgmd variants from Ensembl 0 I know that Ensembl has hgmd variants amongst other annotations as given here: hgmd variants How can I download these variants from Ensembl? I downloaded VEP because it uses multiple tracks including HGMD: VEP Is it possible to use VEP to extract just the HGMD…

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Error in Create switchAnalyzeRlist

Error in Create switchAnalyzeRlist 0 Hello everyone., I am using isoformswitchinganalysisR to look at different transcript expression and quantification data generated using Kallisto. I have stuck in step of Create switchAnalyzeRlist. According to warning error it looks I have problem in gtf file. Really appreciate anybody can help me how…

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In vivo transomic analyses of glucose-responsive metabolism in skeletal muscle reveal core differences between the healthy and obese states

Animals and sample preparation Animal experiments were performed as previously described12. C57BL/6J WT mice or ob/ob mice at ten weeks of age were purchased from Japan SLC Inc. (Shizuoka, Japan). The phenotypic data of the mice are summarized in Table S1. Animal experiments were approved by the animal ethics committee…

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Genomic architecture of adaptive radiation and hybridization in Alpine whitefish

Sampling the radiation To understand the phylogenetic relationships between Alpine whitefish, we carried out whole-genome resequencing on 96 previously collected whitefish (with associated phenotypic measurements including standard length and gill-raker counts; collected in accordance with permits issued by the cantons of Zurich (ZH128/15), Bern (BE68/15), and Lucerne (LU04/14); these fish…

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Ensembl ID mapping GRCh37 vs GRCh38

Ensembl ID mapping GRCh37 vs GRCh38 0 I currently have a large list of Ensembl protein IDs (ENSP) that are from GRCh37. I need to map these IDs to the entry name listed on the UniProt website (e.g. ‘CASPE_HUMAN’ ). I am having trouble doing this using the UniProt dataset…

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EnWik > Expasy

Expasy is an online bioinformatics resource operated by the SIB Swiss Institute of Bioinformatics. It is an extensible and integrative portal which provides access to over 160 databases and software tools and supports a range of life science and clinical research areas, from genomics, proteomics and structural biology, to evolution…

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Get gene names from rs SNP ids for mmusculus_gene_ensembl

Get gene names from rs SNP ids for mmusculus_gene_ensembl 1 I have mouse data with an old mapping from rs SNP IDs to base pair position and chromosome. I would like to query Ensembl to get the genes and then the gene annotations for the rs SNP IDs in my…

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r – Alternative Biomart Hosts

I am trying to run the following Biomart script (params$species == “rabbit”){ ensembl = useMart(biomart=”ENSEMBL_MART_ENSEMBL”, dataset=”ocuniculus_gene_ensembl”, host=”uswest.ensembl.org“, ensemblRedirect = FALSE) orgSymbols <- unlist(getBM(attributes=”ensembl_gene_id”, mart=ensembl)) mart <- useMart(dataset = “ocuniculus_gene_ensembl”, biomart=”ensembl”, host=”uswest.ensembl.org“) The host keeps timing out – does anyone know another host URL I could use? Thank you Read more…

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Uncharted genetic territory offers insight into human-specific proteins

When researchers working on the Human Genome Project completely mapped the genetic blueprint of humans in 2001, they were surprised to find only around 20,000 genes that produce proteins. Could it be that humans have only about twice as many genes as a common fly? Scientists had expected considerably more….

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Scientist I, Bioinformatics job at Vir Biotechnology in United States – 53516780

Vir Biotechnology is a commercial-stage immunology company focused on combining immunologic insights with cutting-edge technologies to treat and prevent serious infectious diseases. Vir has assembled four technology platforms that are designed to stimulate and enhance the immune system by exploiting critical observations of natural immune processes. Its current development pipeline…

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Unexprected Ensembl-vep results

Unexprected Ensembl-vep results 0 Hi.I got a VCF from an individual that shows symptoms of a known disease with known mutations. I run it with Ensembl-vep, expecting to find some of those mutations in the results, yet, all the consequences in the results are “intergenic-variant”.The command I used was: –cache…

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Table 5 | Scripting Analyses of Genomes in Ensembl Plants

arabidopsis_thaliana The 1001 Genomes Project [18] arabidopsis_thaliana Nordborg [19] brachypodium_distachyon Jaiswal_lab_OSU [20] hordeum_vulgare International Barley Sequencing Consortium (IBSC) [21,22,23] hordeum_vulgare Ensembl Plants [24] hordeum_vulgare Illumina iSelect SNP chip [22] malus_domestica fruitbreedomics.com [25] oryza_glaberrima Glab (OGE) oryza_glaberrima Barthii (OGE) oryza_glumipatula Oryza Genome Evolution (OGE) oryza_indica dbSNP [26] oryza_sativa www.ebi.ac.uk/eva [27,28,29,30] oryza_sativa…

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Allelic expression imbalance of PIK3CA mutations is frequent in breast cancer and prognostically significant

Subjects Normal breast and tumor samples were obtained with the written informed consent from donors and appropriate approval from local ethical committees, with the detailed information described in the respective original publications: normal tissue9, METABRIC14, TCGA35. Differential allelic expression analysis DNA and total RNA from 64 samples of normal breast…

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Supporting African BioGenome Project to build bioinformatics capacity

The African BioGenome Project and EMBL have signed a Memorandum of Understanding to support each other in building genomics and bioinformatics capacity across Africa AfricaBP and EMBL MoU. Credit: Karen Arnott/EMBL-EBI The African BioGenome Project (AfricaBP) is an African-led effort to sequence the genomes of all species indigenous to the…

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Somatic point mutations are enriched in non-coding RNAs with possible regulatory function in breast cancer

Torre, L. A., Siegel, R. L., Ward, E. M. & Jemal, A. Global cancer incidence and mortality rates and trends—an update. Cancer Epidemiol. Prev. Biomark. 25, 16–27 (2016). Article  Google Scholar  Gerasimova, E. et al. Wavelet-based multifractal analysis of dynamic infrared thermograms to assist in early breast cancer diagnosis. Front….

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Combining SNP-to-gene linking strategies to identify disease genes and assess disease omnigenicity

Visscher, P. M. et al. 10 years of GWAS discovery: biology, function, and translation. Am. J. Hum. Genet. 101, 5–22 (2017). CAS  PubMed  PubMed Central  Google Scholar  Buniello, A. et al. The NHGRI-EBI GWAS Catalog of published genome-wide association studies, targeted arrays and summary statistics 2019. Nucleic Acids Res. 47,…

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RPKM threshold estimation – SEQanswers

Dear All, I have a doubt in the calculation of False postitive rate while checking for FPKM threshold in a RNAseq experiment. Following the method previously published (www.ploscompbiol.org/article/…l.pcbi.1000598). I am not getting desired results. I followed the method as mentioned the publication Reads were mapped to Ensembl genes (blue) and…

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xml – I am trying to importxml from ENSEMBL using xpath copied from Chrome, but it is not working

I want to use google sheet’s IMPORTXML to extract the gene name (SLC3A1) and ensembl ID (ENSG00000138079) from this URL: asia.ensembl.org/Multi/Search/Results?q=SLC3A1;site=ensembl I tried copying xpath from Chrome and also tried deriving it on my own step by step, but I am only getting a #NA. My xpath: /html/body/div[1]/div/div[2]/div[1]/div[1]/div[2]/div[2]/div[4]/div/div/div[2]/div/div/div[3]/div[2]/div[1]/div[2]/div/div/div/div[1]/div/div[2]/span From Chrome:…

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How to analyze the differential expression of a gene if it has several ensembl id

How to analyze the differential expression of a gene if it has several ensembl id 0 Hie, I have obtained the differential expressions of genes (from RNA-seq data) in an excel file. I can see one gene has several ensembl ids and I guess the gene is from the haplotype…

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Transcription Start Site

Transcription Start Site 2 What are the best databases to check out the transcription start sites of specific genes in human genome? TSS • 130 views wget -q -O – “http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/wgEncodeGencodeBasicV19.txt.gz” | gunzip -c | awk ‘(int($7)< int($8)) {if($4==”+”) {printf(“%s\t%d\t%d\t%s\t%s\n”,$3,$7,int($7)+1,$2,$4);}else {printf(“%s\t%d\t%d\t%s\t%s\n”,$3,int($8)-3,$8,$2,$4);}}’ chr1 69090 69091 ENST00000335137.3 + chr1 139306 139309 ENST00000423372.3…

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Bioconductor – AHEnsDbs

DOI: 10.18129/B9.bioc.AHEnsDbs     This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see AHEnsDbs. EnsDbs for AnnotationHub Bioconductor version: 3.10 Supplies AnnotationHub with EnsDb Ensembl-based annotation databases for all species. EnsDb SQLite databases are generated separately from Ensembl MySQL databases using functions from the…

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snp – Reference variant detected as altered one in bam file

I received (from manufacturer) several .bam files and I used four callers (samtools, freebayes, haplotypecaller, deepvariant) to find some sequence variants. In obtained .vcf files, I took a closer look to some calls. I found interesting, homozygous one rs477033 (C/G Ref/Alt) with flag ‘COMMON=0’ and very low MAF. I also…

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Antiplatelet response to clopidogrel is associated with a haplotype in CYP2C19 gene in Pakistani patients

Amsterdam, E. A. et al. 2014 AHA/ACC guideline for the management of patients with non-ST-elevation acute coronary syndromes: Executive summary: A report of the American College of Cardiology/American Heart Association Task Force on Practice Guidelines. Circulation 130, 2354–2394 (2014). Google Scholar  Kernan, W. N. et al. Guidelines for the prevention…

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How to trim a GFF3 file based on specific coordinates?

How to trim a GFF3 file based on specific coordinates? 0 Hi, I would like to create a GFF3 file containing information only for specific coordinates from the chromosome level GFF3 file. I know how to extract gene and CDS info separately but don’t know how to do trimming based…

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Inquiry related to vcf file and formatting

Hello everyone, I am trying to run predixcan software. But its showing error as segmentation fault implying that there is something wrong with my vcf files. I am sharing the header of vcf file. ##fileformat=VCFv4.1 ##INFO=<ID=LDAF,Number=1,Type=Float,Description=”MLE Allele Frequency Accounting for LD”> ##INFO=<ID=AVGPOST,Number=1,Type=Float,Description=”Average posterior probability from MaCH/Thunder”> ##INFO=<ID=RSQ,Number=1,Type=Float,Description=”Genotype imputation quality from…

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Antibody Matching Transcripts

Antibody Matching Transcripts 1 Hello everyone, I am interested to find the matching isoforms of a gene that my HPA antibody is able to hit. When I check the Human Atlas Protein website it gives me a list of 4 transcripts my antibody can recognize. However, when I open ensembl…

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Converting mouse Gene IDs to Human while keeping genes that don’t convert

Hi there, I am using bioMart to convert some gene IDs from mouse to human for some data I generated through RNA-seq. I am currently mapping using the following function: convertMouseGeneList <- function(x){ require(“biomaRt”) human = useMart(“ensembl”, dataset = “hsapiens_gene_ensembl”) mouse = useMart(“ensembl”, dataset = “mmusculus_gene_ensembl”) genesV2 = getLDS(attributes =…

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How to search dbSNP using a list of SNPs and retrieve Gene name (hgnc symbol if existing, otherwise just whatever is in there)

How to search dbSNP using a list of SNPs and retrieve Gene name (hgnc symbol if existing, otherwise just whatever is in there) 2 I have a list of 500.000 SNPs from which I want to obtain the gene name. I try to search with biomaRt library(data.table) library(biomaRt) rs <-…

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microarray miRNA expression data analysis

I wrote a script on how to analyze the microarray-based miRNA expression data. Here is my code: # general config baseDir <- ‘.’ annotfile <- ‘mirbase_genelist.tsv’ setwd(baseDir) options(scipen = 99) require(limma) # read in the data targets <- read.csv(“/media/mdrcubuntu/46B85615B8560439/microarray_text_files/targets.txt”, sep=””) # retain information about background via gIsWellAboveBG project <- read.maimages(targets,source=”agilent.median”,green.only…

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Answer: AnnotationHub::mapIds() cannot find existing ENSG (GEO supplemental data cross-r

Hi, a quick check on NCBI Gene reveals that the official symbol for this is *PRXL2C*, not *AAED1*. In this way, I would not have expected `org.Hs.eg.db` (using ‘recent’ annotation) to have it. However, I can see that `EnsDb.Hsapiens.v86` (older version) does [have it]. So, there must have been an…

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AnnotationHub::mapIds() cannot find existing ENSG (GEO supplemental data cross-referenced with ensembl.org)

Anyone know why I’m not getting ENSG ids for some of these symbols? The example below retrieves `NA` for multiple symbols, including AAED1 [whose ENSG is ENSG00000158122][1]. “` > library(AnnotationHub) > library(org.Hs.eg.db) > library(GEOquery) > temp download.file(getGEO(“GSM4430459″)@header$supplementary_file_1,temp) > genes unlink(temp) > ensids = mapIds(org.Hs.eg.db, keys=genes, column=”ENSEMBL”, keytype=”SYMBOL”, multiVals=”first”) > ensids[“AAED1”]…

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Why does Txdb transcript length not always match to transcript end-start position?

Why does Txdb transcript length not always match to transcript end-start position? 2 I have just found an example that biomart’s transcript_length is not identical with transcript_end – transcript_start. ensembl_gene_id mgi_symbol chromosome_name strand start_position end_position gene_biotype transcript_start transcript_end strand.1 transcript_length 128537 ENSMUSG00000037860 Aim2 1 1 173178445 173293606 protein_coding 173178445 173293606…

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install ensembl-vep

install ensembl-vep 0 Hello, I want to install ensembl-vep in my Ubuntu 18.04.2. I have already installed LWP::Simple. What can I do in the next step? Thanks in advance for great help! Best, Yue Inspiron-3670:~$ perl -MCPAN -e’install “LWP::Simple”‘ Reading ‘/home/jing/.cpan/Metadata’ Database was generated on Sat, 07 Aug 2021 06:55:53…

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Where To Find Annotation File For Agilent Microarray?

An easier way that has [probably] only come about since this question was posted is via biomaRt in R. You can build annotation tables for Agilent 4×44 arrays for mouse and human as follows: require(biomaRt) Homo sapiens # agilent_wholegenome_4x44k_v1 mart <- useMart(‘ENSEMBL_MART_ENSEMBL’) mart <- useDataset(‘hsapiens_gene_ensembl’, mart) annotLookup <- getBM( mart…

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