Tag: gtex

Comprehensive Analysis of NPSR1-AS1 as a Novel Diagnostic and Prognostic Biomarker Involved in Immune Infiltrates in Lung Adenocarcinoma

The incidence of lung adenocarcinoma (LUAD), the most common subtype of lung cancer, continues to make lung cancer the largest cause of cancer-related deaths worldwide. Long noncoding RNAs (lncRNAs) have been shown to have a significant role in both the onset and progression of lung cancer. In this study, we…

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UCSC Genome Browser | Encyclopedia MDPI

1. History Initially built and still managed by Jim Kent, then a graduate student, and David Haussler, professor of Computer Science (now Biomolecular Engineering) at the University of California, Santa Cruz in 2000, the UCSC Genome Browser began as a resource for the distribution of the initial fruits of the…

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Long-range phasing of dynamic, tissue-specific and allele-specific regulatory elements

Baylin, S. B. & Jones, P. A. A decade of exploring the cancer epigenome – biological and translational implications. Nat. Rev. Cancer 11, 726–734 (2011). CAS  PubMed  PubMed Central  Article  Google Scholar  Greenberg, M. V. C. & Bourc’his, D. The diverse roles of DNA methylation in mammalian development and disease….

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Population-level variation in enhancer expression identifies disease mechanisms in the human brain

Schizophrenia Working Group of the Psychiatric Genomics Consortium. Biological insights from 108 schizophrenia-associated genetic loci. Nature 511, 421–427 (2014). PubMed Central  Article  CAS  Google Scholar  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 …

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Human hg38 chr7:73,678,750-73,740,129 UCSC Genome Browser v435

Use drop-down controls below and press refresh to alter tracks displayed.Tracks with lots of items will automatically be displayed in more compact modes.    Custom Tracks H3K27ac Meta NeuN SCZhidedensesquishpackfull H3K27ac NeuN SCZ del_CRDhidedensesquishpackfull H3K27ac NeuN SCZ del_CRD_del_peakshidedensesquishpackfull H3K27ac Tissuehidedensesquishpackfull H3K27ac Tissue BDhidedensesquishpackfull H3K27ac Tissue BD del_CRDhidedensesquishpackfull H3K27ac Tissue BD…

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Index of /gbdb/hg38/gtex/cov

Name Last modified Size Description Parent Directory – GTEX-1C475-0726-SM-73KVL.Esophagus_Muscularis.RNAseq.bw 2019-12-16 09:16 160M GTEX-1C475-1826-SM-73KWA.Skin_Sun_Exposed_Lower_leg.RNAseq.bw 2019-12-16 09:16 194M GTEX-1GMR3-0626-SM-9WYT3.Artery_Coronary.RNAseq.bw 2019-12-16 09:16 177M GTEX-1H1E6-0826-SM-9WG83.Pancreas.RNAseq.bw 2019-12-16 09:16 122M GTEX-1HFI6-0011-R7b-SM-CM2SS.Brain_Putamen_basal_ganglia.RNAseq.bw 2019-12-16 09:16 172M GTEX-1HGF4-0011-R5b-SM-CM2ST.Brain_Caudate_basal_ganglia.RNAseq.bw 2019-12-16 09:17 178M GTEX-1HSGN-0726-SM-A9G2F.Thyroid.RNAseq.bw 2019-12-16 09:17 194M GTEX-1HSKV-0011-R1b-SM-CMKH7.Brain_Hippocampus.RNAseq.bw 2019-12-16 09:17 149M GTEX-1I1GU-1226-SM-A9SKT.Esophagus_Gastroesophageal_Junction.RNAseq.bw 2019-12-16 09:17 186M GTEX-1IDJC-1326-SM-CL53H.Colon_Transverse.RNAseq.bw 2019-12-16 09:17 217M GTEX-1IDJU-1026-SM-AHZ2U.Vagina.RNAseq.bw 2019-12-16…

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New ‘Ramp Atlas’ Aims to Improve Understanding of Gene Expression

CHICAGO – A first-of-its-kind atlas of “ramp sequences” near the 5′ end of highly expressed genes promises to help researchers better understand gene expression and disease development. Bioinformaticians and computational biologists at the University of Kentucky and Brigham Young University recently released the Ramp Atlas, a compendium of 18,388 tissue-…

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Genome-wide association study of musical beat synchronization demonstrates high polygenicity

Savage, P. E., Brown, S., Sakai, E. & Currie, T. E. Statistical universals reveal the structures and functions of human music. Proc. Natl Acad. Sci. USA 112, 8987–8992 (2015). CAS  PubMed  PubMed Central  Article  Google Scholar  Ravignani, A., Delgado, T. & Kirby, S. Musical evolution in the lab exhibits rhythmic…

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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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Impact of sweet, umami, and bitter taste receptor (TAS1R and TAS2R) genomic and expression alterations in solid tumors on survival

Despite being best known for their role in taste sensing1, T2Rs and T1Rs have been identified in various extra-oral tissues where they serve diverse chemosensory roles17,18,19,20,21,22,48. Emerging data on the role of taste receptors in malignancy led us to explore the genetic and expression alterations for solid tumors and implications…

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Polygenic Risk Score Performance Improved With Expression-Related Rare Variant Insights

NEW YORK – A team from Stanford University and other centers in the US and China have demonstrated that polygenic risk scores (PRS) based on common variants can be bolstered by incorporating clues from rare variants linked to significant gene expression shifts, dubbed expression outliers. “As individual PRS estimates are…

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Single-cell eQTL models reveal dynamic T cell state dependence of disease loci – Nature – Alert Breaking News

Wei, K. et al. Notch signalling drives synovial fibroblast identity and arthritis pathology. Nature 582, 259–264 (2020). ADS CAS PubMed PubMed Central Article Google Scholar  Cembrowski, M. S. & Menon, V. Continuous variation within cell types of the nervous system. Trends Neurosci. 41, 337–348 (2018). CAS PubMed Article Google Scholar  Maurano, M. T. et al. Systematic localization of…

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Role of CD68 in tumor immunity and prognosis prediction in pan-cancer

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),…

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Frontiers | COMMD2 Upregulation Mediated by an ncRNA Axis Correlates With an Unfavorable Prognosis and Tumor Immune Infiltration in Liver Hepatocellular Carcinoma

Introduction Liver hepatocellular carcinoma (LIHC) is the most common type of primary cancer in the liver and third leading cause of cancer-related mortality worldwide (1). Although substantial improvements have been made in LIHC therapy, particularly in molecular targeted therapy and immunotherapy (2, 3), the 5-year survival rate of LIHC is…

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A genome-scale screen for synthetic drivers of T cell proliferation

Abramson, J. S. et al. Transcend NHL 001: immunotherapy with the CD19-directed CAR T-cell product JCAR017 results in high complete response rates in relapsed or refractory B-cell non-Hodgkin lymphoma. Blood 128, 4192–4192 (2016). Google Scholar  Shifrut, E. et al. Genome-wide CRISPR screens in primary human T cells reveal key regulators…

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eQTL mapping using allele-specific count data is computationally feasible, powerful, and provides individual-specific estimates of genetic effects

Using information from allele-specific gene expression (ASE) can improve the power to map gene expression quantitative trait loci (eQTLs). However, such practice has been limited, partly due to computational challenges and lack of clarification on the size of power gain or new findings besides improved power. We have developed geoP,…

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Genetic associations at regulatory phenotypes improve fine-mapping of causal variants for 12 immune-mediated diseases

Cooper, G. S., Bynum, M. L. K. & Somers, E. C. Recent insights in the epidemiology of autoimmune diseases: improved prevalence estimates and understanding of clustering of diseases. J. Autoimmun. 33, 197–207 (2009). PubMed  PubMed Central  Google Scholar  El-Gabalawy, H., Guenther, L. C. & Bernstein, C. N. Epidemiology of immune-mediated…

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Enrichment of eQTLs in functional categories using the eQTL results from 28 GTEx tissues.

In panel (a)-(c) and (e)-(f), a dot indicates point estimate, and a line indicates 95% confidence interval. (a) Enrichment evaluated using all the SNPs by torus [17] based on the eQTL results from MatrixEQTL, TReC or TReCASE. (b) Enrichment of the top eQTL per gene for the eGenes identified by…

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split gtex genotype data by chromosomes.

Hello, I used and edited the command line to use –vcf to import vcf file. I used these commands: for chr in $(seq 1 22); do      plink –vcf /dbGAP/GTEx_Analysis_2017-06-05_v8_WholeExomeSeq_979Indiv_VEP_annot.vcf.gz            –chr $chr            –recode            –out…

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Validation of hub genes in acute pancreatitis

Introduction Acute pancreatitis (AP) is a common disease found in clinics, and requires urgent Hospital admission. The incidence of AP is increasing in recent years worldwide.1 The patients with AP increased from 1,727,789.3 to 2,814,972.3 between 1990 and 2019 in 204 countries and territories.2 Meanwhile, nearly 20% of AP patients…

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Multi-ancestry eQTL meta-analysis of human brain identifies candidate causal variants for brain-related traits

1. Jansen, I. E. et al. Genome-wide meta-analysis identifies new loci and functional pathways influencing Alzheimer’s disease risk. Nat. Genet. 51, 404–413 (2019). CAS  PubMed  PubMed Central  Google Scholar  2. Schizophrenia Working Group of the Psychiatric Genomics Consortium. Biological insights from 108 schizophrenia-associated genetic loci. Nature 511, 421–427 (2014). PubMed…

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KINNEY_DNMT1_METHYLATION_TARGETS

Standard name KINNEY_DNMT1_METHYLATION_TARGETS Systematic name M2508 Brief description Hypomethylated genes in prostate tissue from mice carrying hypomorphic alleles of DNMT1 [GeneID=1786]. Full description or abstract Previous studies have shown that tumor progression in the transgenic adenocarcinoma of mouse prostate (TRAMP) model is characterized by global DNA hypomethylation initiated during early-stage…

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Postdoctoral Fellow job with Cleveland Clinic – Genomic Medicine Institute

We are seeking multiple Experimental and Bioinformatics research positions (including Postdoctoral Research Fellows and Research Associate) to join the Alzheimer’s Network Medicine and Artificial Intelligence (AI) research group (www.lerner.ccf.org/gmi/cheng/) led by Dr. Feixiong Cheng at the Genomic Medicine Institute, Cleveland Clinic Lerner Research Institute, and Department of Molecular Medicine at…

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Nucleic Acids Research Papers on OncoDB, mBodyMap, Genomicus

Researchers at the University of Illinois at Chicago and Washington University describe an online database called OncoDB, designed for analyzing large cancer datasets to detect gene expression shifts and viral infections with potential ties to cancer, such as human papillomavirus. The current version of the resource contains data for more…

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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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error while running predictdb tutorial

error while running predictdb tutorial 0 Hello, I am trying to use predictdb tutorial. The link is: github.com/hakyimlab/PredictDB-Tutorial When I run gtex_tiss_chrom.R script, it throws an error Error in file(file, “rt”) : cannot open the connection Calls: main …get_filtered_snp_annot -> %>% -> distinct -> filter -> read.table -> file In…

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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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(Senior) Bioinformatician job with AL2S3 LTD

(Senior) Bioinformatician            AL Solutions are searching for a Bioinformatician or Senior Bioinformatician to work within the Data Science team of an innovative start-up Biotechnology company in Cambridge. This company are developing innovative medicines within the Oncology & Immunology space. Your position will be to drive the development of computational tools…

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What exactly is RNA-seq probe?

What exactly is RNA-seq probe? 0 Hi all, I’m a long time lurker, but this is my first post here, so I’m sorry if I do something wrong or post something that is against the rule, I’m new to RNA-seq analysis. But I’ve downloaded a huge dataset with matched RNA-seq…

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how to upload more than one rsIDs to get gene expression or eQTL information

GTEX – how to upload more than one rsIDs to get gene expression or eQTL information 1 Hi everyone, I am trying to see how my variants affect the host gene -or other eQTLs- to see the direction of effect basically. I looked on GTEx but I only found the…

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GTEX eQTLs’ extraction

GTEX eQTLs’ extraction 0 Hello everyone, I am a still a student and I am new to this forum, but I would need help regarding GTEX and how to work with it. I was given a task, which includes finding and extracting eQTLs for specific genes from the GTEX portal…

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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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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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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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Counting the number of SNPs (VCF) for each genomic coordinates (BED)

Counting the number of SNPs (VCF) for each genomic coordinates (BED) 1 I want to count the number of recorded variations for each genomic coordinates of a .bed file from the corresponding .vcf file. I guess it should be solved by vcftools, but I could not find any suitable option…

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Bioinformatics Scientist job with Hyper Recruitment Solutions (HRS)

We are currently looking for a Bioinformatics Scientist to join a leading biotech company based in the Cambridge area. As the Bioinformatics Scientist you will drive the development of computational tools and perform omics data analysis to support target identification and therapeutics development platforms KEY DUTIES AND RESPONSIBILITIES: Your duties…

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Bioinformatics Research Associate II/III, Immuno-Oncology Job Opening in Mountain View, CA at IGM Biosciences

IGM Biosciences (Nasdaq: IGMS) is a clinical-stage biotechnology company focused on creating and developing engineered IgM antibodies. IgM antibodies have inherent properties that we believe may enable them to improve upon the efficacy and safety of IgG antibodies in multiple therapeutic applications. We have created a proprietary IgM antibody technology…

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Bioinformatics Biomedical Scientist – Bilsborough Lab

Bioinformatics Biomedical Scientist – Bilsborough Lab – Inflammatory Bowel Diseases Drug Discovery and Development Apply Now Share Requisition # HRC0697538 Join us in accelerating the pace of research and discovery within our unique IBD3 lab! Cedars-Sinai provides virtually every known gastroenterologic analytical procedure and treatment…

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Misuse of RPKM or TPM normalization when comparing across samples and sequencing protocols

Forum:Misuse of RPKM or TPM normalization when comparing across samples and sequencing protocols 2 Published in the RNA Journal in 2020 – this paper argues that if the original RNA amount in the different samples is different, TPM should not be used to find differentially expressed genes. www.ncbi.nlm.nih.gov/pmc/articles/PMC7373998/ Seems like…

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Aro Biotherapeutics hiring Investigator, Genetics & Bioinformatics in Philadelphia, Pennsylvania, United States

About Aro BioTx Join the team at Aro Biotherapeutics creating breakthrough biotherapeutics based on Centyrin oligonucleotide conjugates. Centyrins are small protein domains based on the fibronectin domains of human Tenascin C that combine the affinity and specificity properties of antibodies with the stability and tissue penetration properties of small molecules….

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Bioinformatics Scientist – reed.co.uk

We are currently looking for a Bioinformatics Scientist to join a leading biotech company based in the Cambridge area. As the Bioinformatics Scientist you will drive the development of computational tools and perform omics data analysis to support target identification and therapeutics development platforms KEY DUTIES AND RESPONSIBILITIES: Your duties…

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low / high grade ovarian cancer

TCGA data: low / high grade ovarian cancer 0 Dear All, I have downloaded ovarian cancer annotation data from the TCGA using the TCGAbiolinks package (recount2 data) as follows: ovary_rec2_gtex <- TCGAquery_recount2(project=”gtex”, tissue = “ovary”) tcga_sampleAnnot <- data.frame(ovary_rec2_tcga_scaled@colData) I can check the cancer type with command like this one unique(tcga_sampleAnnotgdc_cases.project.name)…

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TMM followed by inverse normal transform

TMM followed by inverse normal transform 0 Hey all, I am following a protocol from a paper that uses the following pre-processing procedure: a. Read counts were normalized between samples using TMM (Robinson, M. D. & Oshlack, A. A scaling normalization method for differential expression analysis of RNA-seq data. Genome…

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How to download GTEx figure from USCS genome browser

How to download GTEx figure from USCS genome browser 1 Hello, Unfortunately the GTEx images are generated on demand then erased later. In case it helps, these are dynamically generated by R from the track data. We can help with finding the exact parameters if you are interested. The temporary…

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Differential expression analysis between normal/cancer on recount2 data

Differential expression analysis between normal/cancer on recount2 data 0 Hi everyone, I have download GTEX data and TCGA data (only tumor samples available) for a given cancer type using the “recount” R package. After having filtered the genes that are in common between the 2 datasets, I would like to…

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Download TCGA and GTEX data from Xena toilHub for (full genome but for 1 cancer/tissue type)

Download TCGA and GTEX data from Xena toilHub for (full genome but for 1 cancer/tissue type) 0 Dear All, I would like to download TCGA and GTEX gene expression data for ovarian cancer and ovary respectively from the Xena toilHub platform (all genes; RSEM expected counts). However, I only found…

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Rancho BioSciences hiring RShiny Scientist/Bioinformatics in San Diego, California, United States

Rancho Biosciences is seeking a RShiny bioinformatics expert to provide support for a range of projects which include the development of R-Shiny applications, managing NGS data associated with clinical and metadata organization. Work from home while supporting high impact pharmaceutical, academic and institutional science programs. We are specifically looking for…

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normalization two different datasets tcga vs gtex

normalization two different datasets tcga vs gtex 0 using tcga and gtex to look for lncrna DE (using raw files) – what are the best ways to normalize? deseq2 and edger? also if i want to look at lncrnas of specific chromosomes, how should i approach normalization? tcga gtex normalization…

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