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Related Concept Videos

Genome Annotation and Assembly

Genome Annotation and Assembly

The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.

Gene Families

Gene Families

Gene families consist of groups of genes proposed to have originated from a common ancestor. Typically these arise through events in which a gene or genes are mistakenly duplicated during cell division. Unlike their parent genes (which are subject to selection pressure to maintain function), these gene copies do not need to preserve their sequences and may evolve at a relatively faster rate.
Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...

Gene Families

Gene Families

Gene families consist of groups of genes proposed to have originated from a common ancestor. Typically these arise through events in which a gene or genes are mistakenly duplicated during cell division. Unlike their parent genes (which are subject to selection pressure to maintain function), these gene copies do not need to preserve their sequences and may evolve at a relatively faster rate.
Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...

Genomics

Genomics

Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...

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Related Experiment Video

Updated: Jun 15, 2026

Transcriptomic Analysis of C. elegans RNA Sequencing Data Through the Tuxedo Suite on the Galaxy Project

Transcriptomic Analysis of C. elegans RNA Sequencing Data Through the Tuxedo Suite on the Galaxy Project

Published on: April 8, 2017

A collection of bioconductor methods to visualize gene-list annotations.

Gang Feng¹, Pan Du, Nancy L Krett

¹Northwestern University Biomedical Informatics Center (NUBIC, part of the Northwestern CTSA) and The Robert H, Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA.

BMC Research Notes

|February 26, 2010

Summary

New visualization methods reveal complex gene-annotation relationships. The "GeneAnswers" package offers novel ways to explore gene-concept connections, improving biological data interpretation.

Related Experiment Videos

Last Updated: Jun 15, 2026

Transcriptomic Analysis of C. elegans RNA Sequencing Data Through the Tuxedo Suite on the Galaxy Project

Transcriptomic Analysis of C. elegans RNA Sequencing Data Through the Tuxedo Suite on the Galaxy Project

Published on: April 8, 2017

Area of Science:

Bioinformatics
Computational Biology
Genomics

Background:

Gene-list annotations are crucial for understanding gene functions.
Current visualization methods (tables, barplots) obscure complex gene-category relationships.
Difficulty in extracting information on genes belonging to multiple annotation categories.

Purpose of the Study:

To develop explicit and efficient visualization methods for exploring gene-annotation connections.
To provide intuitive tools for interrogating relationships between biological categories and genes.
To address limitations of existing gene-list annotation summaries.

Main Methods:

Construction of a novel data model for gene-annotation relationships.
Development of two visualization methods: Concept-and-Gene Network and Concept-and-Gene Cross Tabulation.
Implementation within a Bioconductor package named "GeneAnswers".

Main Results:

Successful implementation of the "GeneAnswers" Bioconductor package.
Demonstration of simultaneous visualization of genes, concepts (annotation categories), and their connections.
Validation of the methods using microarray-derived gene lists.

Conclusions:

The "GeneAnswers" package effectively visualizes annotations from sources like Gene Ontology and Disease Ontology.
Supports user-defined gene annotations linked to an organism's genome.
Provides a valuable tool for researchers analyzing complex gene-annotation data.