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Intro to transcriptomics - from counts to functional analysis. Session 4: Gene annotation with biomaRt R package In-Person

Registration Required

The Bioinformatics Support Hub has designed this teaching series for researchers interested in learning the basics steps for re-analysis of publicly available bulk-RNAseq data. We will introduce you to basic genomic data annotation concepts, including where to find data to re-analyze, how to perform differential gene analysis, how to add gene annotations, and how to visualize your results. Finally, we'll demonstrate different approaches to gene perform gene pathway analysis. Importantly, we have introduced interspersed coached-practice sessions to which attendees will be invited to participate. In these sessions, you will be able to try things for yourself and get immediate support if needed. (Please see below for overall schedule).   

  • Session 1 - Intro to annotation of gene expression data (Tue, August 2nd)
  • Session 2 - Where in the World is the Data You Need? How to Find and Reuse Data (e.g. GREIN) – (Thurs, August 4th)
  • Coached-practice 1 - Exercise sources and genomic information format (annotations and gene ID) of datasets (Tue, August 9th)

  • Session 3 - Re-analyze public dataset with DESeq2 package (Thurs, August 11th)
  • Session 4 - Gene annotation with biomaRt R package (Tue, August 16th)
  • Coached-practice 2 - Differential Gene expression, annotation (Thurs, August 18th)

  • Session 5 - Visualization with Qlucore (Tue, August 23rd)
  • Coached-practice 3 - Visualization with Qlucore (Thurs, August 25th)

  • Session 6 – Functional analysis of omics data: Overrepresentation Analysis ORA (Tue, August 30th)
  • Session 7 – Gene Set Enrichment Analysis GSEA (Thurs, September 1st)
  • Coached-practice 4 – Functional Pathway Analysis (Tue, August 6th)

Intro to annotation of gene expression data

Attendance in person

Genome annotation is the process of identifying functional and structural elements along the sequence of a genome. Attendees to this introductory session will learn— by using an example— how to find the right reference genome for their analysis and online annotation tools and available annotations (e.g., exons, introns, SNPs, database identifiers, orthologs, ontologies). The online version of Biomart (table browser of Ensembl), NCBI datasets, and other online tools will be used with an example dataset.

Attendees to this session will learn:

-Basic concepts/vocabulary for transcriptomics analysis.

-Where to find the right assembly or reference genome to use in their analysis

-What are the different types of genomic annotations and what tools using to annotate datasets

- How to use Enbsembl Biomart and NCBI datasets, and other tools to batch annotate lists

Tuesday, August 16, 2022
10:00am - 12:00pm
Time Zone:
Eastern Time - US & Canada (change)
SHM L 111, Cushing/Whitney Medical Library, 333 Cedar Street
Medical School

Registration is required. There are no seats available but a waiting list is available.

Event Organizer

Profile photo of Sofia Fertuzinhos
Sofia Fertuzinhos