Search Results for: Pathway

DAVID includes several pathway databases, and also includes a Pathway Viewer for annotations from KEGG, BioCarta, and WikiPathways. This viewer displays the user's genes on pathway maps. BioCarta Pathway information generated by BioCarta is 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...

04/08/2025 - Reactome is a free, open-source, curated and peer-reviewed pathway database that includes bioinformatics tools for the visualization, interpretation and analysis of pathway knowledge. This lesson will showcase the capabilities of Reactome in garnering biological 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...

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...

Lessons focus on gene ontology and pathway analysis. Lesson 15: Introduction to gene ontology and pathway analysis Lesson 16: Functional enrichment with DAVID Lesson 17: Pathway Analysis with Reactome

Lessons focus on gene ontology and pathway analysis. Lesson 15: Introduction to gene ontology and pathway analysis Lesson 16: Functional enrichment with DAVID Lesson 17: Pathway Analysis with Reactome

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...

10/23/2024 - Please send any questions and/or specific topic areas that you’re interested in hearing about for this presentation by Friday, 10/18 to Kayla Strauss . QIAGEN Ingenuity Pathway Analysis (IPA) is the leading Read More...

10/23/2023 - QIAGEN Ingenuity Pathway Analysis (IPA) is the leading pathway analysis application among the life science research community and is cited in tens of thousands of articles for the analysis, integration and interpretation of data 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...

Introduction to Qiagen Ingenuity Pathway Analysis Lesson objective In this lesson, we will continue to le arn about pathway analysis using the Qiagen Ingenuity Pathway Analysis(IPA) package. This class will be taught by Qiagen Read More...

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...

Gene ontology and pathway analysis: PowerPoint slides

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...

11/05/2020 - Register Learn how to get started on using QIAGEN’s Ingenuity Pathway Analysis (IPA) to quickly identify biological relationships, mechanisms, pathways, functions and diseases most relevant to experimental datasets. IPA is cited in tens Read More...

11/13/2017 - MetaCore™ is an integrated curated knowledge database and software suite for pathway analysis of experimental data and gene lists. The scope of data types includes microarray and sequence-based gene expression, SNPs and CGH arrays, Read More...

10/13/2015 - Ingenuity IPA® is the industry leading software solution to model, analyze, and understand complex biological and chemical systems foundational to human health and disease. Quickly identify biological relationships, mechanisms, pathways, functions and diseases most Read More...

11/14/2012 -   This is a repeat class for those who couldn't make it into the class on October 9th   Learn the basics of microarray gene expression analysis using Partek Genomics Suite and Partek Pathway. As Read More...

10/09/2012 - Learn the basics of microarray gene expression analysis using Partek Genomics Suite and Partek Pathway. As we walk though hands-on analysis of a cancer dataset, you will learn the principles of experimental design, batch Read More...

Presenter - Nancy Li, Ph.D. (Outreach Coordinator, Reactome) Reactome is a free, open-source, curated and peer-reviewed pathway database that includes bioinformatics tools for the visualization, interpretation and analysis of pathway knowledge. This lesson showcased Read More...

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...

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...

01/08/2025 - This three hour online training will focus on getting started on using QIAGEN’s  Ingenuity Pathway Analysis (IPA) . IPA enables you to quickly identify biological relationships, mechanisms, pathways, functions and Read More...

06/26/2024 - This in-person hands-on workshop will introduce the Ingenuity Pathway Analysis (IPA), which is  available to access from the NIH Library . IPA can be used identify biological relationships, mechanisms, pathways, functions, and diseases Read More...

Differential expression and interpretation of results Brief introduction to gene ontology and pathway analysis

11/01/2022 - Learn how to get started on using QIAGEN’s Ingenuity Pathway Analysis (IPA) to quickly identify biological relationships, mechanisms, pathways, functions and diseases most relevant to experimental datasets. IPA is cited in tens of Read More...

10/25/2022 - Qiagen Ingenuity Pathway Analysis (IPA) For modeling, analyzing, and understanding complex 'omics data. During this workshop you will learn how to: • Upload data, run an IPA core analysis and interpret the results • Use IPA Read More...

09/15/2022 - Learn how to get started on using QIAGEN’s Ingenuity Pathway Analysis (IPA) to quickly identify biological relationships, mechanisms, pathways, functions and diseases most relevant to experimental datasets. IPA is cited in tens of Read More...

09/01/2022 - Learn how to get started on using QIAGEN’s Ingenuity Pathway Analysis (IPA) to quickly identify biological relationships, mechanisms, pathways, functions and diseases most relevant to experimental datasets. IPA is cited in tens of Read More...

08/31/2022 - Users will learn how to: • Upload their dataset (RNA-seq, scRNA-seq, proteomics, metabolomics and more) and perform interactive core/pathway analysis in IPA • Understand the different result types produced (pathways, key regulators, impact on biological Read More...

06/15/2022 - Learn how to get started on using QIAGEN’s Ingenuity Pathway Analysis (IPA) to quickly identify biological relationships, mechanisms, pathways, functions and diseases most relevant to experimental datasets. IPA is cited in tens of Read More...

02/07/2022 - Learn how to get started on using QIAGEN’s Ingenuity Pathway Analysis (IPA) to quickly identify biological relationships, mechanisms, pathways, functions and diseases most relevant to experimental datasets. IPA is cited in tens of Read More...

09/01/2021 - Learn how to get started on using QIAGEN’s Ingenuity Pathway Analysis (IPA) to quickly identify biological relationships, mechanisms, pathways, functions and diseases most relevant to experimental datasets. IPA is cited in tens of Read More...

04/14/2021 - Register Session Description Learn how to get started on using QIAGEN’s Ingenuity Pathway Analysis (IPA) to quickly identify biological relationships, mechanisms, pathways, functions and diseases most relevant to experimental datasets. IPA is cited Read More...

05/28/2020 - Learn how to get started on using QIAGEN’s Ingenuity Pathway Analysis (IPA) to quickly identify biological relationships, mechanisms, pathways, functions and diseases most relevant to experimental datasets. IPA is cited in tens of Read More...

08/28/2019 - Please bring your computer with Partek Genomics Suite to this hands-on workshop. You'll need to submit a request through “NCI at Your Service” to obtain the access to this software. Partek will demonstrate Read More...

07/17/2019 - Learn how to get started on using QIAGEN’s Ingenuity Pathway Analysis (IPA) to quickly identify biological relationships, mechanisms, pathways, functions and diseases most relevant to experimental datasets. IPA is cited in >16,000 Read More...

11/05/2018 - RNA-seq, expression microarrays, and other omics profiling platforms are powerful tools for discovery, and analytical pipelines often return large numbers of significant genes or other markers.  This presents a challenge when trying to understand Read More...

02/09/2016 - BTEP Workshop on Pathway Analysis with MetaCore NOTE: This is a Bring Your Own Computer (BYOC) class, and will be simultaneously shared via GoToMeeting with attendees at the Advanced Technology Research Facility (ATRF) in Read More...

12/17/2014 - Day 1 - AM (9:30 AM – 12:30 PM)  Ingenuity IPA -   Basic Training  ( Kate Wendelsdorf, Ph.D. -  Ingenuity Pathway Analysis)   Ingenuity IPA® is the industry leading software solution to model, analyze, and understand complex biological and Read More...

QIAGEN  Ingenuity Pathway Analysis (IPA) works with differential expression data (NGS, microarray, proteomics, and others) or genetic variant data to extract various biological insights. QIAGEN Ingenuity Pathway Analysis (IPA) High Impact Features and Functionality in Read More...

09/19/2024 - Qiagen Ingenuity Pathway Analysis (IPA) is a point-and-click software that enables scientists to discern how genomic, transcriptomic, proteomic, and metabolomic changes influence molecular biology pathways and networks. This software is available to NCI investigators, Read More...

12/07/2023 - This hands-on workshop will introduce the Ingenuity Pathway Analysis (IPA) and CLC Genomics Workbench tools, which are available to access from the NIH Library. IPA can be used identify biological relationships, mechanisms, pathways, functions, 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...

02/28/2023 - This class, hosted by the Center for Biomedical Informatics & Information Technology  (CBIIT) will provide refresher training for the Qiagen Ingenuity Pathway Analysis (IPA) package. The class is two hours long 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...

11/19/2020 - Recording Link QIAGEN’s Ingenuity Pathway Analysis (IPA) allows for quick and easy biological interpretation using the results of your RNA-Seq differential expression analyses. IPA’s functionality is tied to an extensive, rich set Read More...

Discuss what this is Where can we find descriptors geneontology.org organism specific databases What is KEGG?

12/08/2022 - Learn how to leverage Activity Plot, Pattern Search, Comparison Analysis, Analysis Match and Land Explorer. Speaker: Shawn Prince Field Application Scientist

04/16/2019 - https://cbiit.webex.com/recordingservice/sites/cbiit/recording/68a77da9faa247b691939fdf7dba6899/playback

03/26/2019 - https://cbiit.webex.com/recordingservice/sites/cbiit/recording/f012b1e97835486fa8f62efa535aaf66/playback

2025 Sebastian R, Sun EG, Fedkenheuer M, Fu H, Jung S, Thakur BL, Redon CE, Pegoraro G, Tran AD, Gross JM, Mosavarpour S, Kusi NA, Ray A, Dhall A, Pongor LS, Casellas R, Aladjem MI. Mechanism Read More...

We see similar organization of information for other annotations. For instance, DAVID pulls biomolecular pathway information from several sources such as KEGG. Clicking on the chart view for KEGG pathways we can see what pathways Read More...

In this lesson, we will continue to le arn about pathway analysis using the Qiagen Ingenuity Pathway Analysis(IPA) package. This class will be taught by Qiagen field application scientist.

2024 Senatorov IS, Bowman J, Jansson KJ, Alilin AN, Capaldo BJ, Lake R, Riba M, Abbey YC, Mcknight C, Zhang X, Raj S, Beshiri ML, Shinn P, Ngyuyen H, Thomas CJ, Corey E, Kelly K. Castrate Read More...

In the previous class, we got an overview of functional and pathway analysis, which help to put RNA sequencing results into biological context by informing us of things like biomolecular pathway, biological function, cellular localization, 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...

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...

OSTR provides CCR investigators with access to a variety of software licenses for genomic, proteomic, pathway analysis and data visualization tools. These software are funded by OSTR and made available at no cost to CCR Read More...

No summary available.

The CCR Collaborative Bioinformatics Resource (CCBR) is a centrally funded resource group which provides a mechanism for CCR researchers to obtain many different types of bioinformatics assistance to further their research goals. The group has Read More...

The Functional Genomics Laboratory (formerly, the RNAi Screening Facility) of the National Center for Advancing Translational Sciences (NCATS) assist investigators with all stages of project planning and execution, beginning with assay development through genome-wide siRNA Read More...

Discover expert help with analysis, processing applications, and licensed software packages.

2024 Coutinho, L. L., Femino, E. L., Gonzalez, A. L., Moffat, R. L., Heinz, W. F., Cheng, R. Y. S., Lockett, S. J., Rangel, M. C., Ridnour, L. A. & Wink, D. A. NOS2 and Read More...

06/13/2025 - Dr. Fuhai Li,&nb p;A ociate Profe or at the chool of Medicine and Computer cience & Engineering, Wa hington Univer ity, will pre ent novel approache that combine large language 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...

01/27/2025 - NCI CCR Liver Cancer Program Seminar Series Dr. Sethupathy is professor of physiological genomics and chair of the Department of Biomedical Sciences at Cornell University. He leads a research lab focused on genome-scale and Read More...

01/22/2025 - This three hour online training covers QIAGEN’s CLC Genomics Workbench enables researchers to analyze NGS data without the use of command line and is a powerful tool for determining differential expression. Read More...

12/12/2024 - This class will introduce bulk RNA sequencing analysis using Qiagen software. Participants will learn how to process FASTQ files and obtain differential expression using CLC Genomics Workbench as well as extract biological insight using Read More...

12/03/2024 - This one and a half hour online training  will provide a demonstration of how to build a Bulk RNA-Seq data analysis pipeline using a fastq file. Partek  Flow   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...

10/23/2024 - CellMinerCDB is an interactive public web application ( https://discover.nci.nih.gov/cellminercdb/ ) that simplifies access and exploration of cancer cell line pharmacogenomic data across different sources such as the National Cancer Institute (NCI), Read More...

The NIH Library provides expert guidance on bioinformatics, biostatistics, data visualization, and data curation throughout the research process. Explore a variety of classes, on-demand trainings, resources, and services related to data science and bioinformatics available 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...

03/05/2024 - This in-person workshop will show participants how to identify cell types based on statistics, visualization, and canonical markers. One Peripheral blood mononuclear cells (PBMCs) sample will be used to illustrate a basic Single Cell Read More...

After this class, participants will Become familiar analyzing single cell RNA sequencing data using Partek Flow including Importing of data into a Partek Flow project QA/QC, filtering, and normalizing of single cell RNA data Read More...

Course Overview Partek Flow is a start-to-finish solution for analyzing high dimensional multi-omics sequencing data. It is a point-and-click software and is suitable for those who wish to avoid the steep learning curve associated with Read More...

Bioconductor packages are divided into four types: software annotation data experiment data workflows. Software packages themselves can be subdivided into packages that provide infrastructure (i.e., classes) to store and access data, and packages that Read More...

Love Data Week 2024 is quickly approaching! What is Love Data Week?  Love Data Week is an international week of celebrating all things data related, with an emphasis on data management, sharing, and security. 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...

11/16/2023 - This class will provide a demonstration of how to identify cell types based on statistics, visualization, and canonical markers. One Peripheral blood mononuclear cells (PBMCs) sample will be used to illustrate a basic Single Read More...

09/29/2023 - Dr. Peng Jiang started his research program at NCI in July 2019. His lab focuses on developing big data and artificial intelligence frameworks to identify biomarkers and new therapeutic approaches for cancer immunotherapies in solid Read More...

09/13/2023 - Partek Flow is your start-to-finish solution for analyzing high dimensional multi-omics sequencing data. It is a point-and-click software and is suitable for those who wish to avoid the steep learning curve associated with analyzing Read More...

No summary available.

We are a bioinformatics team within the Center for Biomedical Informatics and Information Technology’s (CBIIT’s) Cancer Informatics Branch (CIB)—soon to be referred to as the Informatics and Data Science (IDS) Program. Headed Read More...

CREx Monthly Newsletter Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More NIH Research Festival The NIH Research Festival highlights the groundbreaking science and the vibrant NIH community driving our 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...

CREx Monthly Newsletter Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More New CREx User Survey The CREx Team is carrying out a CREx User Survey. If you haven’t Read More...

Protein Characterization Laboratory (PCL) offers various technologies to CCR investigators to characterize proteins and metabolites. The laboratory develops and applies state-of-the-art analytical technologies, primarily mass spectrometry, liquid chromatography, and Surface Plasmon Resonance (SPR), to advance Read More...

Large STARS can be used to request supplemental funding exceeding $8,000 to offset experimental costs (e.g., core or vendor services or specialized reagents).  Applications require detailed scientific and budgetary justification and must be proposed in Read More...

Cores & Facilities From centralized laboratories to collaborative resources and technologies available to CCR Investigators. NCI Cores Centralized laboratories providing broad access to cutting-edge technologies and specialized expertise. Browse NCI Cores Collaborative Resources are technologies and Read More...

The Mouse Metabolic Phenotyping Center (MMPC)Live Program provides standardized, high quality, unique, and hard to find phenotyping services for mouse models of diabetes, obesity, and related metabolic disorders. Emerging as the next iteration of Read More...

CREx Monthly Newsletter Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More New NIH Resource Resources Advance your research with the NIH Mouse Imaging Facility (MIF) The NIH Mouse Imaging Read More...

The NIH Center for Human Immunology, Inflammation, and Autoimmunity (CHI) is a trans-NIH resource whose mission is to provide a collaborative hub of advanced translational immunology for NIH clinical and pre-clinical studies. This uniquely structured Read More...

The CCR Genomics Core is located in Building 41 on the NIH Bethesda campus. The primary goal of the Core is to provide investigators from CCR/NCI and other NIH Institutes access to genomic technologies and Read More...

Protein Characterization Laboratory (PCL) offers various technologies to CCR investigators to characterize proteins and metabolites. The laboratory develops and applies state-of-the-art analytical technologies, primarily mass spectrometry, liquid chromatography, and Surface Plasmon Resonance (SPR), to advance Read More...

Our Team Tatiana S. Karpova Ph.D.Core Headkarpovat@nih.govBuilding 41, Room C615240-760-6637 David A. Ball Ph.D.Core Biologistballa@nih.govBuilding 41, Room B114D240-760-6577 Mohamadreza Fazel, Ph.D.Core Biologistmohamadreza. Read More...

2016-2024 Publications using images obtained in OMC

Stephen Lockett, Ph.D. Director, OMAL locketts@nih.gov 301-846-5515 Valentin Magidson, Ph.D. Scientist magidsonv@mail.nih.gov 301-846-6092 Will Heinz, Ph.D. Scientist heinzwf@nih.gov 301-846-1239 David Read More...

Research Mission The goal of OMAL’s research is to understand molecular mechanisms driving carcinogenesis and the reversal of this process through treatment, by utilization and advancement of optical microscopy techniques. These techniques include multiplex Read More...

2024 Date: Tuesday, October 15, 2024 Time and Location: 11 am EST, ZOOM (INVITATION BY LMIG LIST SERVER) Speaker: Dr. Diego Presman (U Buenos Aires) Title: “Insights on Glucocorticoid Receptor Activity Through Live Cell Imaging” Summary: Eucaryotic transcription factors ( 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...

Register now for an upcoming seminar on January 22, 2025 , “Revealing Tumor-Promoting Signals in Breast Cancer Subtypes: A NIDAP Analysis of Single-Cell Data” . This one-hour talk will feature guest speaker and NIDAP developer, Josh Meyer, who will Read More...

09/23/2024 - Come to the Fair!  In the morning session, several different groups will speak about their training and education programs. The afternoon session will be devoted to learning about research using AI across Read More...

02/21/2024 - Dear colleagues, The Bioinformatics and Computational Biosciences Branch (BCBB) at NIAID invites you to join us for in-person hands-on workshops that will explore biovisualization techniques. Developers of UCSF ChimeraX and Cytoscape will be on Read More...

Objectives To explore Bioconductor, a repository for R packages related to biological data analysis. To learn about options for report generation with R: RMarkdown and Quarto. Introducing Bioconductor Bioconductor is both an open source project Read More...