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Related Concept Videos

Base Excision Repair01:54

Base Excision Repair

One of the common DNA damages is the chemical alteration of single bases by alkylation, oxidation, or deamination. The altered bases cause mispairing and strand breakage during replication. This type of damage causes minimal change to the DNA double helix structure and can be repaired by the base excision repair (BER) pathways. BER corrects damaged DNA sequences by removing the damaged base and restoring the original base sequence using the complementary strand as a template.
The first step of...
Base Excision Repair01:54

Base Excision Repair

One of the common DNA damages is the chemical alteration of single bases by alkylation, oxidation, or deamination. The altered bases cause mispairing and strand breakage during replication. This type of damage causes minimal change to the DNA double helix structure and can be repaired by the base excision repair (BER) pathways. BER corrects damaged DNA sequences by removing the damaged base and restoring the original base sequence using the complementary strand as a template.
The first step of...
Cis-regulatory Sequences02:02

Cis-regulatory Sequences

Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
Cis-regulatory Sequences02:02

Cis-regulatory Sequences

Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
X-ray Imaging01:24

X-ray Imaging

German physicist Wilhelm Röntgen (1845–1923) was experimenting with electrical current when he discovered that a mysterious and invisible "ray" would pass through his flesh but leave an outline of his bones on a screen coated with a metal compound. In 1895, Röntgen made the first durable record of the internal parts of a living human: an "X-ray" image (as it came to be called) of his wife’s hand. Scientists worldwide quickly began their own experiments with X-rays, and by 1900, X-ray was widely...
X-ray Crystallography02:18

X-ray Crystallography

The size of the unit cell and the arrangement of atoms in a crystal may be determined from measurements of the diffraction of X-rays by the crystal, termed X-ray crystallography.
Diffraction
Diffraction is the change in the direction of travel experienced by an electromagnetic wave when it encounters a physical barrier whose dimensions are comparable to those of the wavelength of the light. X-rays are electromagnetic radiation with wavelengths about as long as the distance between neighboring...

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Updated: May 15, 2026

Genome-wide Snapshot of Chromatin Regulators and States in Xenopus Embryos by ChIP-Seq
10:23

Genome-wide Snapshot of Chromatin Regulators and States in Xenopus Embryos by ChIP-Seq

Published on: February 26, 2015

The Xenbase literature curation process.

Jeff B Bowes1, Kevin A Snyder, Christina James-Zorn

  • 1Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada T2N1N4. bowes@ucalgary.ca

Database : the Journal of Biological Databases and Curation
|January 11, 2013
PubMed
Summary
This summary is machine-generated.

Xenbase provides curated data for Xenopus tropicalis and Xenopus laevis, supporting developmental biology research. It integrates gene expression patterns and full-text mining for enhanced accessibility.

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Area of Science:

  • Developmental Biology
  • Comparative Genomics
  • Bioinformatics

Background:

  • Xenopus tropicalis and Xenopus laevis are crucial model organisms in developmental and cell biology research.
  • Efficient data management and accessibility are vital for advancing Xenopus research.

Purpose of the Study:

  • To describe the Xenbase model organism database and its curation processes.
  • To enhance data retrieval and analysis for Xenopus research.

Main Methods:

  • Importing PubMed papers with the keyword 'Xenopus'.
  • Two curation tracks: automated gene/anatomy association and manual gene expression annotation.
  • Full-text indexing and searching via the Textpresso tool.

Main Results:

  • Xenbase associates papers with genes and extracts gene expression patterns.
  • Semi-automated image import and manual annotation of gene expression.
  • Full-text indexing enables advanced search capabilities.

Conclusions:

  • Xenbase serves as a comprehensive resource for Xenopus research.
  • The database facilitates the study of developmental and cell biology in Xenopus.
  • Integrated data and text mining tools improve research efficiency.