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Related Concept Videos

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...
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Related Experiment Video

Updated: May 24, 2026

Quantitative Analysis of Protein Expression to Study Lineage Specification in Mouse Preimplantation Embryos
11:25

Quantitative Analysis of Protein Expression to Study Lineage Specification in Mouse Preimplantation Embryos

Published on: February 22, 2016

Preimplantation development regulatory pathway construction through a text-mining approach.

Elisa Donnard1, Adriano Barbosa-Silva, Rafael L M Guedes

  • 1Laboratório Biodados, Dept. de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, 31270-901, Belo Horizonte - MG, Brazil.

BMC Genomics
|February 29, 2012
PubMed
Summary

This study constructs a regulatory pathway for preimplantation development using text-mining. The pathway reveals a conserved gene core, aiding cross-species comparisons and evolutionary insights.

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Published on: June 6, 2016

Area of Science:

  • Genomics
  • Systems Biology
  • Developmental Biology

Background:

  • Biological pathway databases like KEGG are crucial for understanding complex processes.
  • Preimplantation development lacks a comprehensive pathway, hindering research and cross-species application.
  • Key genes in preimplantation development are not fully represented in existing orthology databases.

Purpose of the Study:

  • To develop a regulatory pathway for preimplantation development.
  • To identify gene interactions and evolutionary origins within this pathway.
  • To enable cross-species application of preimplantation development knowledge.

Main Methods:

  • Utilized text-mining tools (Medline Ranker, PESCADOR) to identify gene biointeractions.
  • Employed SeedServer software to cluster homologous genes.
  • Determined the last common ancestor for genes in the pathway.

Main Results:

  • A novel regulatory pathway for preimplantation development was generated.
  • The pathway comprises a conserved ancient core with added modern gene elements.
  • Homologous gene clusters facilitated visualization across different organisms.

Conclusions:

  • Text-mining effectively integrates data for comprehensive biological pathway visualization.
  • Homologous gene clustering and ancestry determination enhance understanding of evolutionary processes.
  • The developed pathway serves as a foundation for comparative genomics in preimplantation development.