Tag: tcga

A novel STR panel for human protein-coding genes To explore STR mutations in CRC, we first annotated STRs in the introns, exons, and promoter sequence of all protein-coding genes in the GRCh38 reference genome (“Methods”). We discarded STR loci for which genotyping was expected to be inaccurate due to genomic…

“[…] mutational signatures are not only genomic noise of passenger mutations, but they provide etiological and biological information on carcinogenesis.” BUFFALO, NY- January 19, 2024 – A new editorial paper was recently published in Oncoscience (Volume 10), by researcher Peeter Karihtala from the University of Helsinki and University Hospital Comprehensive…

Are you passionate about significantly improving the future of medicine? Do you believe that people are the most important asset of any company? If so, join AmplifyBio! AmplifyBio is a company dedicated to building an integrated environment where clients can access technologies, platforms, capabilities and safety testing for the scale…

Team Leader Bioinformatics – Ryvu Therapeutics, Krakow Team Leader Bioinformatics Ryvu Therapeutics Krakow, Poland As Bioinformatics Team Leader you will be responsible for development of this area within Data Science department which includes managing and growing the team, setting and executing short and long term plans, propagating collaboration with other…

Position Summary: Stealth NewCo is a discovery-stage biotechnology company leveraging insights in RNA biology to discover and develop new therapeutics for indications across multiple disease areas including oncology and neuromuscular disorders. We are seeking a talented Bioinformatics and Data Science Senior/Principal Scientist with experience analyzing multidimensional chemical, biological, and sequencing…

Cancer is measured in stages and grades. The stage describes the size of the tumor and how far it has spread. Meanwhile, grade describes the appearance of the cancerous cells compared to normal cells. The stage and grade help doctors determine the best course of treatment and predict the risks…

Introduction Skin cutaneous melanoma (SKCM), as one of the most aggressive types of cancer due to its elevated degree of heterogeneity, has gained increasing attention during the past few decades.1 Also known as “the cancer that rises with the sun”,2 melanoma originates from cancerous melanocytes due to molecular or genetic…

DOI: 10.18129/B9.bioc.clusterProfiler     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see clusterProfiler. statistical analysis and visualization of functional profiles for genes and gene clusters Bioconductor version: 3.12 This package implements methods to analyze and visualize functional profiles (GO and KEGG) of gene…

Identification of DRGs in PCa Figure 1a showed the flow chart of this study. To explore the role of DRGs in PCa, we analyzed the gene expression profiles of these 15 DRGs in PCa patients. As shown in Fig. 1b, for ACTN4, TLN1, IQGAP1, CD2AP, FLNA, MYH9, MYL6, and ACTB genes, the…

What you will do Work with other engineers and scientists to build Isos platform, applying AI to biological systems. Design, develop and maintain bioinformatics pipelines for the ingestion, management and analysis of biological datasets, especially -omics, imaging, and clinical data. Perform data analysis and data quality assurance according to best…

My goal is to produce an OncoPlot with somatic mutation, copy number, and clinical information. I’m able to produce a MAF file with clinical info: maf.plus.clin <- read.maf( maf = maf, clinicalData = clinical.all, ) and also a MAF file with GISTIC info: maf.plus.gistic <- read.maf( maf = maf, gisticAllLesionsFile…

mTORC1 signaling in bladder cancer Initially, we assessed the mTORC1 signaling scores of both normal and bladder cancer samples. We analyzed the TCGA dataset and observed that the mTORC1 signaling score in normal tissues was considerably lower than that in breast cancer tissue samples (Fig. 2A). We analyzed the expression of…

The code and approaches that I share here are those I am using to analyze TCGA methylation data. At the bottom of the page, you can find references used to make this tutorial. If you are coming from a computer background, please bear with a geneticist who tried to code…

CHEK2 expression increased in cancer tissues First, the expression levels of CHEK2 in different tumor types in the TIMER database were evaluated. All tumors except for chromophobe renal cell carcinoma (KICH) showed elevated levels of CHEK2 expression compared to normal cells (Fig. 1A). Similarly, CHEK2 protein expression was upregulated in all…

ProCogia is a data consulting firm headquartered in Vancouver, BC with employees and clients across the United States and Canada. We specialize in Data Operations, Data Engineering, BI & Analytics, Data Science & Bioinformatics across a broad range of industries including Telecom, Pharma, Biotechnology, Retail, Logistics, Technology, Financial Services, Media…

     Custom Tracks ac4C-RIP-seq peaks, hESC CTL-1hidedensesquishpackfull ac4C-RIP-seq peaks, hESC CTL-2hidedensesquishpackfull ac4C-RIP-seq peaks, hESC NAT10-KD-1hidedensesquishpackfull ac4C-RIP-seq peaks, hESC NAT10-KD-2hidedensesquishpackfull    Mapping and Sequencing Base Positionhidedensefull p14 Fix Patcheshidedensesquishpackfull p14 Alt Haplotypeshidedensesquishpackfull Assemblyhidedensesquishpackfull Centromereshidedensesquishpackfull Chromosome Bandhidedensesquishpackfull Clone Endshidedensesquishpackfull Exome Probesetshidedensesquishpackfull FISH Cloneshidedensesquishpackfull Gaphidedensesquishpackfull GC Percenthidedensefull GRC Contigshidedensefull GRC Incidenthidedensesquishpackfull Hg19…

Company Summary: Each day, the lives of more than 2 billion people across the globe are impacted by chronic diseases. Moreover, the economic burden on society of treating chronic disease is spinning out of control. Today, this dire situation appears unlikely to change as >95% of global healthcare costs are…

Yang J, Liu X, Cao S, Dong X, Rao S, Cai K. Understanding esophageal cancer: the challenges and opportunities for the next decade. Front Oncol. 2020;10:1727. Article  PubMed  PubMed Central  Google Scholar  Li J, Xu J, Zheng Y, Gao Y, He S, Li H, et al. Esophageal cancer: epidemiology, risk…

doi: 10.1002/jex2.108. Epub 2023 Sep 25. Vera Mugoni  1 , Yari Ciani  1 , Orsetta Quaini  1 , Simone Tomasini  1 , Michela Notarangelo  1 , Federico Vannuccini  1 , Alessia Marinelli  1 , Elena Leonardi  2 , Stefano Pontalti  3 , Angela Martinelli  1 , Daniele Rossetto  1 , Isabella Pesce  1 , Sheref S Mansy  1 , Mattia Barbareschi  2 , Antonella…

Introduction Lung cancer remains the leading cause of cancer-related mortality worldwide, and the majority are non-small-cell lung cancer (NSCLC).1,2 Genetic variation is a typical feature of NSCLC that drives cancer initiation and progression.3 Understanding the role of mutated genes in NSCLC is the basis of the development of novel treatment…

Hi all. Thanks in advance for helping me out. I’m trying to analyze copy number data from TCGA (using TCGAbiolinks), and trying to define genes that are either amplified or deleted. To download gene level copy number alteration, I used the code below: query <- GDCquery(project=”TCGA-BRCA”, data.category = ‘Copy Number…

Identification of the SKCM necroptosis cluster The comprehensive analysis encompassed a total of 803 patients drawn from five distinct melanoma cohorts, namely, TCGA-SKCM, GSE65094, GSE53118, GSE54467, and GSE19234. Employing an unsupervised clustering algorithm, we stratified melanoma patients based on their NRG expression profiles. This facilitated a deeper exploration of the…

Can I use TCGA-LUAD RNAseq count that had already normalized by RSEM in Limma-voom 0 Hi everyone, first of all, I’m new for bioinformatics. I have downloaded RNAseq data of TCGA-LUAD from UCSC that had already normalized RSEM normalized count and log2 transformed (log2 normcount+1). i wonder if i can…

ProCogia is a data consulting firm headquartered in Vancouver, BC with employees and clients across the United States and Canada. We specialize in Data Operations, Data Engineering, BI & Analytics, Data Science & Bioinformatics across a broad range of industries including Telecom, Pharma, Biotechnology, Retail, Logistics, Technology, Financial Services, Media…

missing region in the process of annotation 0 Hi. I am analyzing TCGA methylation data from TCGAbiolinks and I faced one problem during annotation process with annotatr. This TCGA data has covered a gene in the chromosome 19, but annotated result did not contain one region in chromosome 19. I…

TCGA/Broad Institute CNV Files Segment Mean 3 Hello everybody, I am trying to analyse CNV data from TCGA to get a measure of overall CNV per patient. When I download the Level 3 files taken from the SNP6 array, there is a column in the file called Segment_Mean. (Example at…

Failla, G. The aging process and cancerogenesis. Ann. N. Y. Acad. Sci. 71, 1124–1140 (1958). Article  CAS  PubMed  Google Scholar  Szilard, L. On the nature of the aging process. Proc. Natl Acad. Sci. USA 45, 30–45 (1959). Article  CAS  PubMed  PubMed Central  Google Scholar  Vijg, J. & Dong, X. Pathogenic…

Hi, Im exploring and integrating the LUAD TGCA transcriptomic and genomic data. Im trying to do so both with TCGAbiolinks in R and cBioportal. With TCGAbiolinks I acces the data this way (bioconductor.org/packages/devel/bioc/vignettes/TCGAbiolinks/inst/doc/analysis.html#TCGAvisualize:_Visualize_results_from_analysis_functions_with_TCGA%E2%80%99s_data) query <- GDCquery(#legacy = T, project = “TCGA-LUAD”, data.category = “Transcriptome Profiling”, data.type = “Gene Expression Quantification”,…

Doxo and Abe promote cellular senescence accompanied by an altered profile of senescence-related genes in breast cancer cells Doxo and Abe were used to treat breast cancer cells (human triple-negative breast cancer cell line MDA-MB-231 and human luminal A subtype breast cancer cell line MCF-7) for 24 h, without a robust…

Per user feedback, we are hosting a comprehensive training on how to effectively use sample level public data and metadata from sources like GEO, SRA, TCGA, GTEx, Blueprint, CCLE and other sources through Ingenuity Pathway Analysis (IPA) and IPA Analysis Match Explorer feature. The trainer will walk through usecases in…

Help doing differential expression analysis -experimental design and gProfiler TF interpretation- 0 Hi! I’m trying to do a differential expression analysis using breast cancer TCGA data. Firstly, I split the breast cancer cohort into two groups based on the expression level in z-score of a particular gene I’m interested in,…

how to get ER, PR and HER2 data from TCGA BRCA 2 Hi I have dowloaded the BRCA data from TCGA using TCGABiolinks I have done this: BRCARnaseqSE <- GDCprepare(query.a, directory = “BRCA_all”) sample.info <- SummarizedExperiment::colData(BRCARnaseqSE) Now I want to get data on ER, PR and HER2 – positive, negative…

Personalized medicine aims to revolutionize healthcare by providing tailored treatments based on an individual’s unique characteristics. Genetic information of the host and target plays a crucial role in determining disease susceptibility and treatment response [1, 2]. By utilizing genomic analysis, biomarker identification, risk assessment, tailored treatment strategies, and continuous monitoring,…

Bioinformatics analysis The GEO database (www.ncbi.nlm.nih.gov/geo/) provided detailed gene expression information for the GSE62165 microarray. Differentially expressed genes were identified using the online tool Morpheus (software.broadinstitute.org/morpheus/) (fold change = normal pancreatic tissue gene expression/PDAC tissue gene expression, P value < 0.05 and |log2(fold change)|>1). The downstream analysis was based on the genes with the…

Hi, I am trying to A/B compartment analysis with minfi, but I got following error. “`r Error in { : task 1 failed – “is(object, “SummarizedExperiment”) is not TRUE” “` Since I want to use data with hg38 annotation but `makeGenomicRatioSetFromMatrix` function has only `ilmn12.hg19`, I did `makeGenomicRatioSetFromMatrix` function with…

Senior Bioinformatician – Centogene, Berlin or Remote Senior Bioinformatician Centogene Berlin or Remote, Germany Your tasks and responsibilities: We are looking for senior Bioinformatician to join in the R&D bioinformatics team in either Berlin or remotely from all over the world. You will be responsible for developing new bioinformatics pipelines…

1. Introduction Pancreatic ductal adenocarcinoma (PDAC) has one of the highest case-specific mortality rates of all cancers [1]. Although resection remains the only curative therapy for PDAC, improvements in long-term survival are attributable to advances in systemic treatment [2,3,4,5]. Currently, 5-fluorouracil-based (i.e., with irinotecan and oxaliplatin as FOLFIRINOX) or gemcitabine-based…

Appropriate genome reference for converting TCGA VCF files to MAF 0 I have a directory of MAF files obtained from TCGA and I want to convert it to VCF format. Reference: GRCh38.d1.vd1 Reference Sequence Source: gdc.cancer.gov/about-data/gdc-data-processing/gdc-reference-files maf2vcf.pl –input-maf maf/* –output-dir VCF -ref-fasta /home/melchua/.vep/homo_sapiens/GRCh38/GRCh38.d1.vd1.fa.tar.gz Traceback: Use of uninitialized value $lines in…

In a recent study published in Nature Communications, researchers from the United States of America (USA) investigated the potential of the transcriptome of tumor-adjacent normal lung tissue in predicting the prognosis of lung cancer. They found that molecular profiling of the tumor-adjacent normal (TAN) lung tissue, rather than the tumor…

DOI: 10.18129/B9.bioc.TCGAbiolinks     TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data Bioconductor version: Release (3.5) The aim of TCGAbiolinks is : i) facilitate the GDC open-access data retrieval, ii) prepare the data using the appropriate pre-processing strategies, iii) provide the means to carry out different standard analyses…

Why are there several gene expression files (for example, miRNA) in TCGA for one case? 0 Hello I am working on gene expression data at TCGA Now I realized that for a case and a miRNA-Seq, for example, mirna-isoform, there is more than one gene expression file and the counts…

mRNA expressions of DDR-related genes are upregulated in CRPC compared to those in Pca To identify a cluster of upregulated genes in CRPC, we previously conducted directional RNA-seq analysis using clinical samples obtained from localized Pca and CRPC patients21. We used RNA samples obtained from prostate cancer patients by radical…

DOI: 10.18129/B9.bioc.maftools     Summarize, Analyze and Visualize MAF Files Bioconductor version: Release (3.6) Analyze and visualize Mutation Annotation Format (MAF) files from large scale sequencing studies. This package provides various functions to perform most commonly used analyses in cancer genomics and to create feature rich customizable visualzations with minimal…

Help locating TCGA data from cbioportal 0 Hi, I am a newbie, I want to locate the following files: data_RNA_Seq_v2_expression_median.txt data_linear_CNA.txt From what I read from other threads/google search, these data are supposed to come from cbioportal? But I can’t seem to locate these files in the cbioportal website! Any…

JaBbA v1 outperforms previous CN algorithms We enhanced our previous JaBbA (v0.1; ref. 4) model with several methodological innovations to increase robustness to read depth waviness, improve algorithm convergence and enforce junction balance for allele-specific as well as total CN (Extended Data Fig. 1a–d and Methods). We also rigorously defined…

Abstract Acute myeloid leukaemia (AML) is a heterogeneous disease with complex pathogenesis that affects hematopoietic stem cells. Ethnic and racial disparities have been reported to affect treatment and survival outcomes in AML patients. Here, we analysed clinical and transcriptomic data from The Cancer Genome Atlas (TCGA) to investigate potential differences…

Two days_to_last_followups encountered when conducting Survival Analysis with TCGA Clinical Data 0 I was conducting Survival Analysis to TCGA-LIHC project, and when I look through the clinical data I found that there are two days_to_last_followups tags. One of it belongs clin_shared:race_list,and the other lihc:follow_ups one that belongs to clin_shared:race_list <clin_shared:days_to_last_followup…

Expression of PPIA in pan-cancer and prognostic value of PPIA in GC To assess the effects of PPIA on the genesis of human tumor, TCGA database was utilized to detect the mRNA levels of PPIA in 33 types of cancer. The findings demonstrated that the levels of PPIA were upregulated…

Genmab A/S Media Release COPENHAGEN, Denmark; November 2, 2023 Eighteen total abstracts accepted for presentation and publication, including results from four clinical trials evaluating epcoritamab in multiple treatment settings and patient populations Oral presentations highlighting new findings from a clinical trial of epcoritamab in patients with relapsed/refractory (R/R) diffuse large…

Fasting-mimicking diet (FMD) is emerging as an effective dietary intervention with the potential to prolong life span in healthy people and boost antitumor immunity in patients with cancer. FMD refers to a medically designed fasting-like state that allows periodic consumption of a very-low-calorie and low-protein diet (1, 2). Compared with…

Hello! I’m working on comparing tumor and healthy samples with DESeq2. My analysis only cares about the adjusted Fold Change values that DESeq2 computes. The input data encompasses a huge number of samples (I’m working with TCGA and GTEX data), and I need to run the calculation a bunch of…

A postdoctoral position with competitive salaries is immediately available in the laboratory of Dr. Yi Li, Professor in the Lester and Sue Smith Breast Center, Baylor College of Medicine.  Baylor College of Medicine is a prestigious biomedical research institute in the U.S. and is a founding component of the world’s…

It is located in Houston, one of the four largest metropolitan cities in the U.S. The Li laboratory primarily investigates the molecular and cellular mechanisms of breast cancer initiation, progression, and therapeutic resistance. The Li lab has just developed new rat models of breast cancer that are uniquely suited to…

Background: Head neck squamous cell carcinoma (HNSCC) is globally prevalent cancer attributed to tobacco habit. Despite the significant advances in early diagnosis and treatment of HNSCC chemo-radio resistance are routinely observed in patients. Aberrant DNA repair mechanisms mainly microhomology mediated DNA end joining (MMEJ) pathway causing deleterious mutations and is…

circRNADisease v2.0 is an enhanced and reliable database that offers experimentally verified relationships between circular RNAs (circRNAs) and various diseases. It is accessible at cgga.org.cn/circRNADisease/ or cgga.org.cn:9091/circRNADisease/. The database currently includes 6998 circRNA-disease entries across multiple species, representing a remarkable 19.77-fold increase compared to the previous version. This expansion consists…

FPKM values for DE analysis – Why? 1 Hello everyone! I believe my questions are quite naive, but I am super new to RNA-seq data analysis, so forgive me! I already saw some questions regarding this subject, but I still do not understand it well. I am currently performing (trying…

About Elucidata Delivering ML-ready biomedical molecular data. Job Description Elucidata’s mission is to power drug discovery by harnessing the power of structured and unstructured biomedical data. Our state-of-the-art technology transforms data so that it is analysis-ready. Biomedical data is vast but unstandardized, hence it remains underutilized. Or as we say…

Need Control Gene Count Files 0 I am doing differential expression analysis of isoform quantification data in R studio. I am looking at the floor of mouth, tongue, and tonsil subsites of HNSCC and I am using TCGA for my data. The issue with this is that there is not…

Problems when running GDC_prepare in R 0 @2158037f Last seen 3 hours ago Macao Enter the body of text here Code should be placed in three backticks as shown below library(TCGAbiolinks) query <- GDCquery( project = “TCGA-LIHC”, data.category = “Transcriptome Profiling”, data.type = “Gene Expression Quantification”, workflow.type = “STAR -…

What are some alternatives? When comparing dada2 and TCGAbiolinks you can also consider the following projects: kraken-biom – Create BIOM-format tables (biom-format.org) from Kraken output (ccb.jhu.edu/software/kraken/, github.com/DerrickWood/kraken). MicrobiomeStat – Supporting Longitudinal Microbiome Analysis in R GTDBTk – GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes….

(UroToday.com) The 2023 ESMO annual meeting included a session on urothelial carcinoma, featuring a discussant presentation by Dr. Michiel Van der Heijden. For this presentation, Dr. Van der Heijden discussed the abstract “Phase 3 THOR Study: Results of Erdafitinib vs Pembrolizumab in Pretreated Patients with Advanced or Metastatic Urothelial Cancer…

Parent directory/ – – r-bioc-tcgabiolinks_2.22.4+dfsg-1.debian.tar.xz 4.9 KiB 2022-Jan-30 23:29 r-bioc-tcgabiolinks_2.22.4+dfsg-1.dsc 2.5 KiB 2022-Jan-30 23:29 r-bioc-tcgabiolinks_2.22.4+dfsg-1_all.deb 5.2 MiB 2022-Jan-30 23:29 r-bioc-tcgabiolinks_2.22.4+dfsg.orig.tar.xz 6.2 MiB 2022-Jan-30 23:29 r-bioc-tcgabiolinks_2.25.3+dfsg-1.debian.tar.xz 5.0 KiB 2022-Nov-21 23:24 r-bioc-tcgabiolinks_2.25.3+dfsg-1.dsc 2.5 KiB 2022-Nov-21 23:24 r-bioc-tcgabiolinks_2.25.3+dfsg-1_all.deb 6.2 MiB 2022-Nov-22 12:10 r-bioc-tcgabiolinks_2.25.3+dfsg.orig.tar.xz 7.3 MiB 2022-Nov-21…

PHF5A expression analysis Figure 1A demonstrated that PHF5A expression level was compared between tumor and corresponding normal tissues using TIMER2 tool. As compared to normal tissues, PHF5A expression was considerably elevated in Bladder urothelial carcinoma (BLCA), Breast invasive carcinoma (BRCA), Cholangiocarcinoma (CHOL), Colon adenocarcinoma (COAD), Esophageal carcinoma (ESCA), Head and neck…

SilicoScientia Pvt Ltd is looking for a freelance scientific writer with extensive experience in Bioinformatics – Genomics as the core area of scientific research.  Responsibilities § Should be able to write scientific manuscript independently for publishing the same in peer review journal. § Should have sound knowledge for providing query based Bioinformatics…

Bray, F., Laversanne, M., Weiderpass, E. & Soerjomataram, I. The ever-increasing importance of cancer as a leading cause of premature death worldwide. Cancer 127, 3029–3030. doi.org/10.1002/cncr.33587 (2021). Article  PubMed  Google Scholar  Xia, C. et al. Cancer statistics in China and United States, 2022: Profiles, trends, and determinants. Chin. Med. J….

Background: In select patients, pancreatic adenocarcinoma remains a local disease, yet there are no validated biomarkers to predict this behavior and who may benefit from aggressive local treatments. This study sought to determine if SMAD4 (mothers against decapentaplegic homolog 4) messenger RNA-sequencing (RNA-seq) expression is a robust method for predicting…

—–BEGIN PGP SIGNED MESSAGE—– Hash: SHA512 Format: 1.8 Date: Thu, 12 Oct 2023 10:59:27 +0200 Source: r-bioc-tcgabiolinks Architecture: source Version: 2.28.4+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian R Packages Maintainers <r-pkg-t…@alioth-lists.debian.net> Changed-By: Andreas Tille <ti…@debian.org> Changes: r-bioc-tcgabiolinks (2.28.4+dfsg-1) unstable; urgency=medium . * New upstream version Checksums-Sha1: 57218af05f8bbbb7f01df36ad3451abf038279c7 2553 r-bioc-tcgabiolinks_2.28.4+dfsg-1.dsc 456c110e8f7b41ac18beb4ff696d8f7e17721702…

different sample size between TCGA portal and TCGAbiolinks package 0 I was looking for the mutation data through TCGA portal using TCGAbiolinks and I have realized that sample size are not the same. for instance TCGA-OV case TCGA data portal shows 419 cases, however TCGAbiolinks shows 462 samples. File counts…

Are you passionate about significantly improving the future of medicine? Do you believe that people are the most important asset of any company? If so, join AmplifyBio! AmplifyBio is a company dedicated to building an integrated environment where clients can access technologies, platforms, capabilities and safety testing for the scale…

How does one access TCGA controlled data in AWS S3? 0 AWS Data Exchange for TCGA pages points to the existence of the S3 bucket tcga-2-controlled. Does anyone know how to download data from the bucket using the GDC Data access token that one needs to access the controlled data?…

. 2023 Sep 18:14:1197418. doi: 10.3389/fphar.2023.1197418. eCollection 2023. Affiliations Expand Affiliation 1 Chongqing Three Gorges Medical College, Chongqing Key Laboratory of Development and Utilization of Genuine Medicinal Materials in Three Gorges Reservoir Area, Chongqing, China. Free PMC article Item in Clipboard Wei Xiong et al. Front Pharmacol. 2023. Free PMC article…

Diffuse large B-cell lymphoma (DLBCL) and follicular lymphoma (FL) are two of the most prevalent non-Hodgkin’s lymphoma subtypes. Despite advances, treatment resistance and patient relapse remain challenging issues. Our study aimed to scrutinize gene expression distinctions between DLBCL and FL, employing a cohort of 53 DLBCL and 104 FL samples…

The exploration of methylated biomarkers in plasma for pancreatic cancer is still in its early stages, and the number of studies conducted to date for this purpose is limited. Analysis of cfDNA methylation patterns in pancreatic cancer has been approached both at the whole genome level and by identifying and…

Introduction Breast cancer (BC) is a malignant tumor originating from the epithelial tissue of the breast and is the most common malignancy in women.1 It is estimated that by 2040, there will be 3,000,000 new cases of BC and 100,000 deaths worldwide. Triple-negative breast cancer (TNBC), which accounts for 15–20%…

Figure 1 SAMHD1 expression is up-regulated in… Figure 1 SAMHD1 expression is up-regulated in DLBCL and related to tumor growth. A, B.… Figure 1 SAMHD1 expression is up-regulated in DLBCL and related to tumor growth. A, B. The mRNA levels of SAMHD1 in DLBCL samples from the Oncomine (A) and…

Hello Everyone, recently I have been conducting the survival analysis of liver cancer patients expressing CD47, using the TCGA data. The project in this case is “TCGA-LIHC”. After downloading the gene expression data of 20 primary tumor sample, I tried to get the counts from the downloaded data. However I…

TPM RNA-seq data for differential expression analysis 1 Hello. I have a project where I need to identify differences in gene expression between two categories of cancer patients: low and high survival rate. I am retrieving RNA seq data from the Cancer Genome Atlas TCGA, but I can only find…

Open Access ARTICLE MENGQIN ZHU1,2,3,4,#, TIANYI XU5,#, HAN ZHANG3,4, XIN FAN3,4, YULAN WANG6, JIAJIA ZHANG3,4, FEI YU1,2,3,4,* 1 Shanghai Clinical College, Anhui Medical University, Shanghai, 200040, China2 The Fifth Clinical Medical College, Anhui Medical University, Hefei, 230032, China3 Department of Nuclear Medicine, Shanghai Tenth People’s Hospital, Tongji University School of…

Background: The presence of genetic variations in mitochondrial DNA (mtDNA) has been associated with a diverse array of diseases. The objective of this study was to examine the correlations between mtDNA D-loop, its haplotypes, and polycystic ovary syndrome (PCOS) in the Chinese population, and the associations between mtDNA D-loop and…

Hi I am trying to understand the fields in a TCGA barcode which is separated by decimal points/dots For example portal.gdc.cancer.gov/files/00117a5c-d9eb-4081-be23-35eb193949fc The filename for the pathology report is TCGA-AK-3460.95FC84F5-4FB3-4CE7-ACD0-C7E0D8F03DD7.PDF I do not understand what the field 95FC84F5 means which is separated by a dot from the patient ID. The wiki…

CRC Upregulated 153-5p HIF-1 activates LINC00511, targeting HIF-1’s 3-UTR and +ve feedback loop [78] Oncogene Human CRC tissues vs. paired adjacent non-tumor and CRC cell lines HT29, LOVO, SW620, SW480 vs. normal colon epithelial FHC cell line and athymic BALB/c nude mice for implantation – HNF4 promotes LINC00511 transcription, interaction…

– In TCGA BRCA data (Legacy data),  dataset: gene expression RNAseq – IlluminaHiSeq from tcga.xenahubs.net have  20,531 identifiers corresponding to about 20000 genes. However,  in GDC TCGA BRCA data ( Harmonized Data),  dataset: gene expression RNAseq – HTSeq – Counts from hub: gdc.xenahubs.net, there are  60,489 identifiers. What is the difference between them?…

Calculation of TMB on gene level 1 Hi all, I have TCGA cancer data and i want to calculate TMB on gene level. Can anyone please tell me how to do that? TCGA has TMB score based on patient level. I need on gene level. Thanks! genomics • 30 views…

Datasets The gene expression data, mutation data, CRISPR, and drug perturbation data sets used in this study were obtained from the Depmap project depmap.org/portal/download/all/. The gene expression data set consists of the log2 transformed transcript per million (TPM) values of 19,221 protein-coding genes from 1406 cell lines across 33 cancer…

About the team/job EMBL-EBI and AstraZeneca are located nearby in Cambridge which will allow fellows to spend time at both sites and take advantage of the complementary expertise and opportunities this offers. Fellows will have easy access to scientific expertise, well-equipped computational facilities and an active seminar programme. Your role…

How to DESeq2 using miRNA data obtained using TCGAbiolinks 0 Hi, I’m sorry if this is a bit of a stupid question, I am currently trying to obtain miRNA expression data from TCGA-COAD using TCGAbiolinks to carry out miRNA differential expression analysis between normal and tumour samples using DESeq2. I…

maftools – median survival time doesn’t match plot 0 Hello all, I’m using maftools in R to plot some basic survival curves based on gene mutation, for example: mafSurvival(maf = TCGA_maf, genes = “TP53”, time = “overall_survival”, Status = “deceased”) I get the following output plot: The output text from…

Genomic analysis and cohort description We generated whole-exome sequencing (WES) and RNA sequencing (RNA-Seq) data from tumors and blood samples from 27 advanced urothelial cancer patients treated with anti-PD-1/PD-L1 ICIs at Hospital del Mar (Fig. 1a). WES data was obtained from the tumors before treatment as well as from blood samples,…

  Abstract: According to the Global Cancer Statistics 2020, prostate cancer (PCa) is the second most commonly diagnosed male cancer and second leading cause of cancer death among men globally. Prostate cancer is known to be more aggressive among men of African origin with reasons not fully known. Previous studies…

Sung, H. et al. Global Cancer Statistics 2020: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries. CA Cancer J. Clin. 71, 209–249. doi.org/10.3322/caac.21660 (2021). Article  PubMed  Google Scholar  Siegel, R. L., Miller, K. D., Fuchs, H. E. & Jemal, A. Cancer statistics, 2022. CA A…

Job Title: Sr. Bioinformatics Scientist Location: Hybrid (Bangalore/Delhi) About Elucidata: www.elucidata.io Elucidata’s mission is to power data-centric discovery by harnessing the power of ML and cloud computing to find answers to biological questions. Our state-of-the-art technology transforms semi-structured data so that it is analysis-ready. Polly has been used to discover…

TCGAbiolinks MSI data 0 Hi! I am trying to use this code to access Microsatellita data: query <- GDCquery(project = “TCGA-COAD”, data.category = “Other”, legacy = TRUE, access = “open”, data.type = “Auxiliary test”, barcode = c(“TCGA-AD-A5EJ”,”TCGA-DM-A0X9″)) from TCGAbiolinks help documents, but I have this error message: “Error in checkDataCategoriesInput(project,…

Data collection and bioinformatic analysis GSE10846, GSE19246, GSE32918, GSE50721, GSE64820, and GSE94669, were downloaded from the Gene Expression Omnibus database (www.ncbi.nlm.nih.gov/geo/). DLBCL datasets from the GEPIA (Gene Expression Profiling Interactive Analysis) (gepia.cancer-pku.cn) and the TCGA (The Cancer Genome Atlas) (xenabrowser.net/datapages/) were also used in this study. A total of 284…

What gene annotation was used for PanCanAtlas EBPlusPlus-corrected RNA-seq TCGA dataset? 0 Is there any info about what gene annotation (eg. genecode v26, ensembl 75, etc.) has been used to generate the PanCanAtlas EBpluPlus-corrected RNA-seq TCGA dataset (that is ebplusplusadjustpancan_illuminahiseq_rnaseqv2.geneexp.tsv from www.synapse.org/#!Synapse:syn4976363 )? RNAseq RSEM TCGA • 16 views Read…

TCGAbiolinks not working anymore 0 The script in this tutorial does not work anymore bioconductor.org/packages/devel/bioc/vignettes/TCGAbiolinks/inst/doc/analysis.html I get to GDCprepare stage and get error: Starting to add information to samples => Add clinical information to samples => Adding TCGA molecular information from marker papers => Information will have prefix paper_ brca…

Research Scientist – Bioinformatics Job highlightsExperience in molecular biology and associated sequencing platforms,technologies,and standards.Computing Languages: Python (NumPy,SciPy,Pandas,Sklearn,Keras),R (Bioconductor),Perl. Molecular / Clinical Sources: RNA-SEQ,NGS,TCGA,CCLE,dbGaP. Well versed with utilisation and of omics data Job description Identify new targets and potential pipeline molecules for Immuno-oncology by working closely with Artificial Intelligence and drug…

PanCanAtlas EBPlusPlus-corrected RNA-seq TCGA dataset 4 Hi, I am wondering in which normalisation format (RPKM, FPKM, TPM,… etc) the PanCanAtlas EBPlusPlus-corrected RNA-seq TCGA dataset (the EBPlusPlusAdjustPANCAN_IlluminaHiSeq_RNASeqV2.geneExp.tsv file available here) is in? I know it is batch-corrected, but I don’t know in which normalisation format the original data was in. Thanks…

DOI: 10.18129/B9.bioc.RTCGA.miRNASeq     This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see RTCGA.miRNASeq. miRNASeq datasets from The Cancer Genome Atlas Project Bioconductor version: 3.10 Package provides miRNASeq datasets from The Cancer Genome Atlas Project for all available cohorts types from gdac.broadinstitute.org/. Data format…

Converting the TCGA ID to the Cohort ID 0 Hello everyone, I am basically trying to map between DepMap lineage and TCGA cohorts. In the depmap annotation file there is lineage column which contains disease names. There is a page in the DepMap called depmap.org/portal/celligner/ which I can download alignment…

New Delhi, India Elucidata Full time Job Title: Sr.Bioinformatics Scientist Location: Hybrid (Bangalore/Delhi) About Elucidata: www.elucidata.io Elucidata’s mission is to power data-centric discovery by harnessing the power of ML and cloud computing to find answers to biological questions.Our state-of-the-art technology transforms semi-structured data…