The in-silico zebrafish matrisome: A new tool to study extracellular matrix gene and protein functions

Matrix Biol. 2018 Jan;65:5-13. doi: 10.1016/j.matbio.2017.07.001. Epub 2017 Jul 21.


Extracellular matrix (ECM) proteins are major components of most tissues and organs. In addition to their crucial role in tissue cohesion and biomechanics, they chiefly regulate various important biological processes during embryonic development, tissue homeostasis and repair. In essence, ECM proteins were defined as secreted proteins that localized in the extracellular space. The characterization of the human and mouse matrisomes provided the first definition of ECM actors by comprehensively listing ECM proteins and classified them into categories. Because zebrafish is becoming a popular model to study ECM biology, we sought to characterize the zebrafish matrisome using an in-silico gene-orthology-based approach. We report the identification of 1002 genes encoding the in-silico zebrafish matrisome. Using independent validations, we provide evidence for the robustness of the orthology-based approach. Moreover, we evaluated the orthology relationships between human and zebrafish genes at the whole-genome and matrisome levels and showed that the different categories of ECM genes are differentially subjected to evolutionary pressure. Last, we illustrate how the zebrafish matrisome list can be employed to annotate big data using the example of a previously published proteomic study of the skeletal ECM. The establishment of the zebrafish matrisome will undoubtedly facilitate the analysis of ECM components in "-omic" data sets.

Keywords: Extracellular matrix; Gene orthology; Genome; In-silico matrisome; Zebrafish.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Collagen / genetics
  • Computational Biology / methods*
  • Computer Simulation
  • Databases, Genetic
  • Extracellular Matrix / genetics*
  • Extracellular Matrix Proteins / genetics
  • Humans
  • Mice
  • Molecular Sequence Annotation
  • Proteoglycans / genetics
  • Whole Genome Sequencing
  • Zebrafish / genetics*
  • Zebrafish Proteins / genetics*


  • Extracellular Matrix Proteins
  • Proteoglycans
  • Zebrafish Proteins
  • Collagen