Related Experiment Video
Updated: Jun 19, 2026
08:32
Neurovascular Network Explorer 2.0: A Simple Tool for Exploring and Sharing a Database of Optogenetically-evoked Vasomotion in Mouse Cortex In Vivo
Published on: May 4, 2018
The Human EST Ontology Explorer: a tissue-oriented visualization system for ontologies distribution in human EST
Ivan Merelli1, Andrea Caprera, Alessandra Stella
1Istituto Tecnologie Biomediche-Consiglio Nazionale delle Ricerche, Via Fratelli Cervi 93, Segrate (MI), Italy. ivan.merelli@itb.cnr.it
BMC Bioinformatics
|October 16, 2009
Summary
The Human EST Ontology Explorer (HEOE) tool analyzes over eight million human Expressed Sequenced Tags (ESTs) to compare gene expression across healthy and diseased tissues. It provides novel insights into Gene Ontology (GO) category and metabolic pathway involvement for ESTs.
Area of Science:
- Bioinformatics
- Genomics
- Molecular Biology
Background:
- NCBI dbEST contains over 8 million human Expressed Sequenced Tags (ESTs), a valuable resource for gene expression studies.
- Existing web resources allow browsing EST data and comparing gene expression levels across libraries.
- A gap exists in tools for analyzing quantitative EST distributions within Gene Ontology (GO) categories and metabolic pathways.
Purpose of the Study:
- To present the Human EST Ontology Explorer (HEOE), a web facility for comparing gene expression levels among diverse human tissue libraries.
- To enable examination of EST distributions in GO categories and their involvement in metabolic pathways.
Main Methods:
- Large-scale BLAST annotation of EST sequences utilizing grid computing.
- Inference of library-specific EST distributions within the GO Graph.
- Implementation of a pathway-based search interface for metabolic pathway representation.
- Integration of EST processing using Perl scripts and storage in a MySQL database.
- Development of a PHP-based web interface for data visualization and comparison.
Main Results:
- The HEOE provides library-dependent statistics on GO Direct Acyclic Graph (DAG) distributions at each GO hierarchical level.
- It allows simultaneous visualization, retrieval, and comparison of data from different libraries.
- Statistically significant differences in GO categories among selected libraries can be computed.
- The tool was tested for grid scalability using a large-scale human EST dataset.
Conclusions:
- HEOE offers a complementary approach to existing resources for inspecting EST expression levels.
- The analysis procedure is adaptable for inclusion of additional libraries, expanding tissue representation.
- The HEOE currently includes analysis from 70 non-normalized libraries, covering healthy and unhealthy tissues.
Related Concept Videos
01:20Anatomical Terminology
Knowledge of anatomy is essential to understand human biology and medicine. Anatomists and health care professionals use standard terminology to describe the human body with more precision and no ambiguity. Anatomical terms have mostly Greek and Latin-derived roots. Because these languages are rarely used in conversation, the meaning of words remains the same. Each term is made up of a root in between the prefixes and suffixes. The root of a term often refers to an organ, tissue, or condition,...
01:18Structural Organization of the Human Body: An Overview
It is convenient to consider the body's structures in terms of fundamental levels of organization that increase in complexity: subatomic particles, atoms, molecules, organelles, cells, tissues, organs, organ systems, and organisms.
To study the chemical level of organization, scientists consider the simplest building blocks of matter: subatomic particles, atoms, and molecules. All matter in the universe is composed of one or more unique pure substances called elements, familiar examples of...
To study the chemical level of organization, scientists consider the simplest building blocks of matter: subatomic particles, atoms, and molecules. All matter in the universe is composed of one or more unique pure substances called elements, familiar examples of...
01:25Tissues
Tissues are a group of cells that share a common embryonic origin. Microscopic observation reveals that the cells in a tissue share morphological features and are arranged in an orderly pattern to perform specific functions. From an evolutionary perspective, tissues appear in more complex organisms. Although there are many types of cells in the human body, they are organized into four broad categories of tissues: epithelial, connective, muscle, and nervous. Each of these categories is...
01:18Tissues
Cells with similar structure and function are grouped into tissues. A group of tissues with a specialized function is called an organ. There are four main types of tissue in vertebrates: epithelial, connective, muscle, and nervous.
01:22Classification of Epithelial Tissues: Overview
Epithelial tissues are classified according to the shape of the cells and the number of cell layers formed. Cell shapes can be squamous (flattened and thin), cuboidal (square-like, as wide as it is tall), or columnar (rectangular, taller than it is wide). Additionally, the nucleus shape helps identify the type of epithelial cells. Squamous cells have flattened disc-shaped nuclei, cuboidal cells have spherical nuclei, and columnar cells have elongated nuclei.
Based on the number of cell layers,...
Based on the number of cell layers,...
01:24Overview of Anatomy and Physiology
Human anatomy is the scientific study of the body's structures. Some of these structures are very small and can only be observed and analyzed with the assistance of a microscope. Other larger structures can readily be seen, manipulated, measured, and weighed. The word "anatomy" comes from a Greek root that means "to cut apart." Human anatomy was first studied by observing the body's exterior and the wounds of soldiers and other injuries. Later, physicians were allowed to dissect the bodies of...