Search Results for: environmental enrichment

Radiation Oncology Branch is part of CCR. Bioinformatics core is a collaborative resource to support ROB branch and provide service to ROB investigators from NCI and other Institutes access to new technologies, bioinformatics, statistical analysis Read More...

CREx News & Updates October 2021 Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More NIH Collaborative Research Exchange (CREx) News Site Spotlight FACILITY HIGLIGHTS Learn more about services from the CPTR Read More...

Protein and Metabolite Characterization Core (PMCC), formerly known as the Protein Characterization Lab (PCL),  offers various technologies to CCR investigators to characterize proteins and metabolites. The core develops and applies state-of-the-art analytical technologies, primarily mass Read More...

01/07/2022 - Environmental exposures such as smoking are widely recognized risk factors in the emergence of lung diseases including lung cancer and acute respiratory distress syndrome (ARDS). However, the strength of environmental exposures is difficult to Read More...

Because we are now creating different folders that stores results from various stages in our data analysis, we could set up some environmental variables for these so we can more easily reference these folders while Read More...

06/18/2025 - Gene et enrichment analy i (G EA) i a popular tool for evaluating functional enrichment, e pecially following differential expre ion analy i . Thi e ion of the BTEP Coding Club will how attendee Read More...

“Gene set enrichment analysis” refers to the process of discovering the common characteristics potentially present in a list of genes. When these characteristics are GO terms, the process is called “functional enrichment.” Warning Overall GO Read More...

“Gene set enrichment analysis” refers to the process of discovering the common characteristics potentially present in a list of genes. When these characteristics are GO terms, the process is called “functional enrichment.” Warning Overall GO Read More...

06/15/2023 - Since its release in September 2005, the Gene Set Enrichment Analysis (GSEA) software and its companion gene set collections, the Molecular Signatures Database (MSigDB), have been invaluable resources for interpreting the biological significance of expression Read More...

05/17/2023 - Functional enrichment analysis is used to understand the biological context of gene lists or differential expression results. There are a multitude of tools available for this purpose. clusterProfiler is a popular R / Bioconductor package Read More...

This page contains content taken directly from the Biostar Handbook by Istvan Albert. Always remember to start the bioinformatics environment. conda activate bioinfo We will be analyzing differential expression of genes on Chr22 from the Read More...

This page contains content taken directly from the Biostar Handbook by Istvan Albert. Always remember to start the bioinformatics environment. conda activate bioinfo We will be analyzing differential expression of genes on Chr22 from the Read More...

Whether you are measuring mRNA expression, protein expression, DNA methylation, expressed miRNAs, protein binding to DNA or RNA, etc., you will likely end up with a list of genes or gene products from which you Read More...

06/02/2021 - Register Description: Over the last 15 years the Gene Set Enrichment Analysis (GSEA) software and its companion gene set collections, the Molecular Signatures Database (MSigDB) have served as key resources for interpreting the biological significance Read More...

“Gene set enrichment analysis” refers to the process of discovering the common characteristics potentially present in a list of genes. When these characteristics are GO terms, the process is called “functional enrichment.” Warning Overall GO Read More...

04/06/2022 - Gene set enrichment analysis (GSEA) is a statistical method that can be used to determine if gene sets are differentially expressed in different phenotypes. Qlucore Omics Explorer has implemented the GSEA method in a Read More...

09/24/2020 - Over the last 15 years, since its release in September 2005, the Gene Set Enrichment Analysis (GSEA) software and its companion gene set collections, the Molecular Signatures Database (MSigDB) have served as key resources for interpreting Read More...

04/03/2025 - DAVID (the Database for Annotation, Visualization and Integrated Discovery) provides a comprehensive set of functional annotation tools for investigators to understand the biological meaning behind large lists of genes acquired from high-throughput assays such Read More...

03/27/2024 - DAVID (the Database for Annotation, Visualization and Integrated Discovery) provides a comprehensive set of functional annotation tools for investigators to understand the biological meaning behind large lists of genes acquired from high-throughput assays such Read More...

Functional enrichment and comparison with R . ClusterProfiler, pathview, and good introductory information Article on the impact of the evolving GO Ten Years of Pathway Analysis: Current Approaches and Outstanding Challenges, PLOS Computation Biology, 2012 Pathway enrichment Read More...

Pathway Analysis IPA (Qiagen - CCR License) Future talk Functional Analysis Gene Set Enrichment Analysis (GSEA) https://www.gsea-msigdb.org/gsea/index.jsp DAVID https://david.ncifcrf.gov/ Enrichr https://maayanlab.cloud/Enrichr/ Other Types Read More...

Determine potential next steps following differential expression analysis. Tour geneontology.org and understand the three main ontologies. Learn about different methods and tools related to functional enrichment and pathway analysis. Get familiar with databases commonly Read More...

06/24/2025 - Tran late gene li t into biological in ight u ing pathway enrichment tool . Thi training will provide an overview the current tatu of pathway tool , with focu on oftware available to NIH community.  Read More...

04/01/2025 - Whether you are measuring mRNA expression, protein expression, DNA methylation, expressed miRNAs, protein binding to DNA or RNA, etc., you will likely end up with a list of genes or gene products from which Read More...

Understand the difference between alpha and beta diversity Introduce several alpha diversity metrics Understand what rarefaction is and why it is important Introduce the debate regarding rarefaction and other methods of normalization Often many questions Read More...

As mentioned above, instructions for using the Biostar module on Biowulf can be found in the course documents . The Biostars module loads the software used in this course series. A list of the software included Read More...

Recall that the scripts used for differential expression analysis are in the folder /usr/local/code. We can also access this folder using the environmental variable CODE. How many scripts are in this folder (find Read More...

Many of the tools used to understand functional enrichment will use sets of GO terms, examining GO enrichment. What do we mean by GO? The Gene Ontology (GO) provides a framework and set of concepts Read More...

10/20/2022 - An overview of the geospatial tools that are useful for characterizing areas of the country in terms of cancer incidence, mortality, screening frequency, risk factors, socio-demographic and environmental variables relevant to cancer. The presentation Read More...

Course Wrap-up This lesson concludes the Bioinformatics for Beginners course series. Please email us any time at ncibtep@nih.gov for help with your bioinformatics questions or concerns. Lesson Objectives Short course overview. Review BTEP Read More...

02/18/2026 - Partek Flow is a point-and-click platform for building analysis workflows for Next Generation Sequences (NGS), including DNA, bulk and single-cell RNA, spatial transcriptomics, ATAC, and ChIP, helping scientists avoid the steep learning curve of Read More...

{{Sdet}} Answer{{Esum}} Tools that we will be using for RNA sequencing analysis in this course series include command line applications for raw data quality assessment, data cleanup, trimming, alignment, etc. We will also be Read More...

Gene Set Enrichment Analysis (GSEA) EnrichmentMap REVIGO (reducing and visualizing gene ontology) Pathview iPathwayGuide (proprietary) Qiagen IPA (proprietary, CCR license) Qlucore (proprietary, CCR license) GeneMANIA CellNetAnalyzer PARADIGM

Functional enrichment and pathway analysis have broad and varying definitions. For our purposes, there are three general approaches: 1. Over-Representation Analysis (ORA), 2. Functional Class Scoring (FCS), and 3. Pathway Topology (PT) ( Khatri et al. 2012 ). Examining genes in Read More...

statistically evaluates the fraction of genes in a particular pathway found among the set of genes showing changes in expression --- Khatri et al. 2012 From this, ORA determines which pathways are over or under represented Read More...

Lessons focus on gene ontology and pathway analysis. Lesson 17: Introduction to gene ontology and pathway analysis ( Recording ) Lesson 18: Functional enrichment with DAVID ( Recording ) Lesson 19: Pathway analysis with Qiagen IPA ( Recording ) Lesson 20: Review and Course Wrap-up ( Read More...

Resources Tertiary Analysis - Biological Meaning Pathway Analysis IPA (Qiagen - CCR License) Future talk Functional Analysis Gene Set Enrichment Analysis (GSEA) https://www.gsea-msigdb.org/gsea/index.jsp DAVID https://david.ncifcrf.gov/ Enrichr Read More...

Access the NIH network; this will require you to VPN if off campus. Connect to Biowulf ssh user_name@biowulf.nih.gov where user_name is your NIH username. Use sinteractive to work on an Read More...

GO terms provide information about a gene product GO terms as a vocabulary are species agnostic, but there are species constraints ontology and annotations are updated regularly computer readable - suitable for bioinformatics GO integrates Read More...

Thus far we have: Learned how to interact with our computer via command line. Downloaded raw RNA-Seq data (.fastq files). Examined raw data quality using fastqc and multiqc . Performed adapter and quality trimming using Trimmomatic . Read More...

Mostly Computational intensive task requiring signigicant computer hardware. Quality Control Sample quality and consistency Is Trimming appropriate - quality/adaptors Alignment/Mapping Reference Target (Sequence and annotation) Alignment Program Alignment Parameters Mark Duplicates Post-Alignment Quality Read More...

11/16/2022 - Attend this webinar to hear a moderated, five-person panel expand on the presentation, “Perspectives on CMS Linkage for Cancer Research in Cohort Studies.” This presentation is from the recent 2022 Annual Meeting of the NCI Read More...

09/07/2022 - In this session of the University of Alabama at Birmingham’s O’Neal Research Seminar Series, CBIIT’s Dr. Jill Barnholtz-Sloan will share how  big data  has provided insight on brain and central nervous Read More...

05/17/2022 - Metabolomic and multi-omic data are increasingly being collected in basic, preclinical, and clinical research studies. Interpretation of these data though remains challenging.  Common challenges include the difficulty in identifying metabolites and assigning unique identifiers, Read More...

12/14/2021 - Speaker: Alisa Goldstein, Ph.D. Senior Investigator NCI, Division of Cancer Epidemiology and Genetics, Clinical Genetics Branch Dr. Alisa Goldstein is a Senior Investigator in NIH’s Division of Cancer Epidemiology and Genetics (DCEG), Read More...

10/12/2021 - Speaker :  Tali Mazor, Ph.D., Scientist, Knowledge Systems Group, Dana-Farber Cancer Institute Tali Mazor, Ph.D., of the Dana-Farber Cancer Institute will discuss the functions and features of the cBioPortal for Cancer Genomics. This Read More...

06/16/2020 - The capability to unambiguously and comprehensively identify thousands of metabolites and other chemicals in clinical samples, including the microbiome, will revolutionize the search for environmental, dietary, and metabolic determinants of health and disease. By Read More...

11/06/2025 - Qlucore Omics Explorer is a point-and-click software that enables analysis of RNA sequencing (bulk and single cell), proteomics and metabolomics data. It’s machine learning capabilities allow for cell type classification. This Read More...

03/13/2025 - UCSC Xena showcases seminal cancer genomics datasets from The Cancer Genome Atlas (TCGA) and the Pan-Cancer Atlas, as well as the Genomic Data Commons, Pan-cancer Atlas of Whole Genomes, and the International Cancer Genome Read More...

11/12/2024 - Join us at the upcoming hybrid NIH BRAIN NeuroAI Workshop on November 12 and 13, with virtual access to in-person panels and discussions at the NIH Campus in Bethesda, MD. Artificial intelligence (AI) is reshaping technology Read More...

10/24/2024 - NIH Text Mining and Natural Language Processing SIG is pleased to welcome you to this special event featuring two extraordinary speakers focused on the applications of Deep Learning in Computational Biology.  & Read More...

06/27/2024 - During this presentation, you will learn about the GenePattern ecosystem, an environment for accessible, reproducible research that has been serving the needs of the cancer genomics community since 2004. GenePattern hosts hundreds of genomics analysis Read More...

05/08/2024 - Qlucore Omics Explorer is a point-and-click software that enables analysis of RNA sequencing (bulk and single cell), proteomics and metabolomics data. It’s machine learning capabilities also allow for classification of cell types. This Read More...

03/29/2024 - This first of five webinars will introduce NIH’s All of Us Research Program, including the program’s mission and core values. Learn about the current size and diversity of Read More...

Throughout this module, we will be running various tools, including helper R scripts on the Unix command line to analyze the HBR and UHR RNA sequencing dataset. The helper R scripts were developed by the Read More...

Throughout this module, we will be running various tools, including helper R scripts on the Unix command line to analyze the HBR and UHR RNA sequencing dataset. The helper R scripts were developed by the Read More...

Notes: PANTHER DAVID Qiagen IPA - more detailed R Bioconductor clusterProfiler GSVA goseq GOexpress (for GO annotation) pathview EGSEA seqGSEA CRAN GANPA GOxploreR geneset GSEA, GSVA, ORA https://www.rna-seqblog.com/blitzgsea-efficient-computation-of-gene-set-enrichment-analysis-in-python/ https://github.com/ Read More...

ORA and FCS discard a large amount of information. These methods use gene sets, and even if the gene sets represent specific pathways, structural information such as gene product interactions, positions of genes, and types Read More...

Provides a gene-centric view which lists the genes and their associated annotation terms... -- DAVID help documents See https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4717906/ for difference between pathway and network analysis DAVID Read More...

Biostars on Biowulf To complement this course, there is a module available on Biowulf with installed programs associated with the Biostar Handbook. During class, we will work on the command line on the GOLD system Read More...

Gene ontology and pathway analysis Objectives Determine potential next steps following differential expression analysis. Tour geneontology.org and understand the three main ontologies. Learn about different methods and tools related to functional enrichment and pathway Read More...

This page uses content directly from the Biostar Handbook by Istvan Albert. Learn: FASTQC for assaying quality of sequence reads MultiQC for combining multiple FASTQC reports into one report Trimmomatic for removing sequence data based Read More...

This page uses content directly from the Biostar Handbook by Istvan Albert. Learn: FASTQC for assaying quality of sequence reads MultiQC for combining multiple FASTQC reports into one report Trimmomatic for removing sequence data based Read More...

Here, let's change back in the ~/biostar_class/hbr_uhr/hbr_uhr_hisat2 folder. cd $hbr_uhr_hisat2 To align FASTQ files for one sample, we construct the HISAT2 command with the following options Read More...

Module 3: Pathway Analysis Lesson #: Intro to Gene ontology and pathway analysis Discuss what this is Where can we find descriptors geneontology.org organism specific databases What is KEGG? Lesson #: More on ORA, GSEA, GSVA pros Read More...

Lesson 13: Aligning raw sequences to reference genome Before getting started, remember to be signed on to the DNAnexus GOLD environment. Lesson 11 Review In Lesson 11 we learned to aggregate multiple FASTQC reports into one using MultiQC, Read More...

Thus far we have: Downloaded raw RNA-Seq data (.fastq files). Examined raw data quality using fastqc and multiqc . Performed adapter and quality trimming using Trimmomatic . Aligned the raw sequences to a reference genome (human chromosome 22 Read More...

Lesson 15 Practice Objectives Previously, we performed QC on the Golden Snidget RNA sequencing data, aligned the sequencing reads to its genome, and obtained expression counts. We can now finally perform differential expression analysis, to find Read More...

Fisher Exact Test DAVID performs over representation analysis (ORA) at its core, which aims to find enriched molecular functions, pathways, or other annotations represented by the input gene list. In other words, many genes in Read More...

Fisher Exact Test DAVID performs over representation analysis (ORA) at its core, which aims to find enriched molecular functions, pathways, or other annotations represented by the input gene list. In other words, many genes in Read More...

Data Analysis Overview RNASEQ - Data Analysis WorkFlow Mostly Computational intensive task requiring signigicant computer hardware. Quality Control Sample quality and consistency Is Trimming appropriate - quality/adaptors Alignment/Mapping Reference Target (Sequence and annotation) Read More...

Database for Annotation, Visualization and Integrated Discovery (DAVID) - an overview Before getting started, remember to be signed on to the DNAnexus GOLD environment. Lesson 17 review In the previous class, we got an overview of Read More...

07/27/2023 - This new webinar will be covering and discussing the host responses to vaccines with invited speakers Dr. Oliver He and Dr. Guanming Wu. During the hour long webinar, Vaccine Induced Gene Expression Analysis Tool ( Read More...

11/09/2022 - Since its release in September 2005, the Gene Set Enrichment Analysis (GSEA) software and its companion gene set collections, the Molecular Signatures Database (MSigDB) have served as key resources for interpreting the biological significance of Read More...

06/29/2022 - THIS EVENT HAS BEEN RESCHEDULED FROM 6/22 TO 6/29 AT 11:00 AM USING THE SAME MEETING LINK. We will go over RNA-seq from experimental design,  data import options, data normalization options, to to statistical tests and biological Read More...

03/10/2022 - Attendees will learn how to use Partek Flow to identify cell subtypes using both gene and protein expression in a peripheral blood mononuclear cell (PBMC) sample using Cellular Indexing of Transcriptomes and Epitopes by Read More...

02/11/2022 - The seminar is open to the public and registration is required each month. Dr. Hunter Mosely plans to discuss the richness of open data resources in biology and how they can support machine learning Read More...

07/14/2021 - Attendees will learn how to use Partek Flow to identify cell subtypes using both gene and protein expression in a peripheral blood mononuclear cell (PBMC) sample using Cellular Indexing of Transcriptomes and Epitopes by Read More...

04/21/2021 - Register Here Inherited and environmental influences can put people at greater risk of cancer and impact their response/resistance to treatment. In this presentation, Dr. Eliezer Van Allen will describe how a patient’s Read More...

02/09/2021 - Sarah Teichmann Head of the Cellular Genetics Programme - Wellcome Sanger Institute - Cambridge UK Lab homepage: https://www.sanger.ac.uk/group/teichmann-group/ Venue: zoom conference https://nih.zoomgov.com/j/1619988709?pwd=dEIwM0 Read More...

11/06/2020 - Register Abstract: The need to integrate knowledge types into big data analytics, generally referred to as explanatory-artificial-intelligence (x-AI), is growing. This talk will describe progress with three approaches to such knowledge enrichment: 1) the use Read More...

11/02/2020 - Attendees will learn how to use Partek Flow to identify cell subtypes using both gene and protein expression in a peripheral blood mononuclear cell (PBMC) sample using Cellular Indexing of Transcriptomes and Epitopes by Read More...

07/07/2020 - In systems biology, inference of functional associations among genes is compelling because the construction of functional association networks facilitates biomarker discovery. Specifically, such gene associations in human can help identify putative biomarkers that can Read More...

07/07/2020 - In systems biology, inference of functional associations among genes is compelling because the construction of functional association networks facilitates biomarker discovery. Specifically, such gene associations in human can help identify putative biomarkers that can Read More...

06/24/2020 - Traditional methods of epidemic modeling continue to be used fruitfully for characterizing outbreaks and predicting the spread of disease in populations. However, these methods, typically rely on what are known as “compartment models”, requiring Read More...

Most BTEP courses include detailed course materials including lesson content, additional resources, and lesson associated data. These course materials are listed here so that learners can easily return to and review concepts taught in class Read More...

This archive contains past and present issues of the  BTEP BioInformatics Bulletin. The BTEP Bioinformatics Bulletin features select upcoming bioinformatics events offered across NIH and is distributed monthly via email to the Center Read More...

Listed below are the video recordings of past BTEP events (classes, seminars, workshops). Videos are hosted on various servers and may play slightly differently. Some videos may be downloaded for local viewing. Recorded Videos of Read More...

What is bioinformatics? Bioinformatics integrates biology, statistics, and computer science to develop and apply theory, methods, and tools for the collection, storage, and analysis of biological and related data. Bioinformatics plays a critical role in Read More...

Lesson 5: Microbial diversity, alpha rarefaction, alpha diversity Learning Objectives Understand the difference between alpha and beta diversity Introduce several alpha diversity metrics Understand what rarefaction is and why it is important Introduce the debate regarding Read More...

NCI scientists have many choices available to them for bioinformatic analyses of Next Generation Sequencing (NGS) data. While some require expertise in programming, others provide a more user-friendly, point-and-click interface. These options include programs for Read More...

Bioinformatics for Beginners: RNA-Seq Course Description: This course was designed to teach the basic skills needed for bioinformatics, including working on the Unix command line. This course primarily focuses on RNA-Seq analysis. All steps of Read More...

Lesson 17: RNA sequencing review 2 Learning objectives This lesson will serve as comprehensive review of Module 2. We will spend roughly the first hour reviewing the Module 2 material the second hour answering specific questions from the poll Read More...

Retrieve R "helper" scripts developed for Biostars environment. curl -O http://data.biostarhandbook.com/rnaseq/code/deseq1.r curl -O http://data.biostarhandbook.com/rnaseq/code/deseq2.r curl -O http://data.biostarhandbook. Read More...

We previously stored FASTQC results for the HBR and UHR raw sequencing data in the ~/biostar_class/hbr_uhr/QC directory (recall that ~ denotes home directory). So before getting started, change into this folder. cd ~/ Read More...

In lesson 9, we learned that reference genomes came in the form of FASTA files, which essentially store nucleotide sequences. In this lesson, we will learn about the FASTQ file, which is the file format that Read More...

Lesson 10: Introducing the FASTQ file and assessing sequencing data quality Before getting started, remember to be signed on to the DNAnexus GOLD environment. Lesson 9 Review In the previous lesson, we explored the reference genomes and Read More...

This page uses content directly from the Biostar Handbook by Istvan Albert. Obtain RNA-seq test data. The test data consists of two commercially available RNA samples: Universal Human Reference (UHR) and Human Brain Reference (HBR) . Read More...

Lesson 9: Reference genomes and genome annotations used in RNA sequencing Before getting started, remember to be signed on to the DNAnexus GOLD environment. Lesson 8 Review In Lesson 8, we learned about the basics of RNA sequencing, Read More...

Lesson 9: Reference genomes and genome annotations used in RNA sequencing Before getting started, remember to be signed on to the DNAnexus GOLD environment. Lesson 8 Review In Lesson 8, we learned about the basics of RNA sequencing, Read More...

Database for Annotation, Visualization and Integrated Discovery (DAVID) - an overview Lesson 17 review In the previous class, we got an overview of functional and pathway analysis, which help to put RNA sequencing results into biological Read More...

Lesson 11: Merging FASTQ quality reports and data cleanup Before getting started, remember to be signed on to the DNAnexus GOLD environment. Lesson 10 Review In the previous lesson, we learned about the structure of the FASTQ Read More...

10/05/2022 - For our next CDSL webinar we will have presentations by two CDSL fellows:  Ekaterina Kazantseva  and Sanna Madan.  Ekaterina is a master’s student in Dr. Mikhail Kolmogorov's group and the title of Read More...