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Embryonic stage alignment_tool

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Shivang Singh

This document describes an embryo stage alignment tool that compares gene expression and morphological features across species to align embryonic development stages between vertebrates. The tool uses ontologies, databases, and user input to generate distance matrices and heat maps showing commonalities. It aims to standardize stage terminology and help comparative biology by identifying conserved developmental processes. Future improvements include using a more detailed anatomical ontology and clustering analyses.

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Embryo Stage Alignment Tool
Background • Multiple stage alignment papers (Comparative transcriptomics) • Ontology (tracks the hierarchy and progression of expression) • XenoBase, Zfa, Mouse Atlas Project • SES stages are supposed to be used to standardize nomenclature across vertebrate • Stage Alignment helps comparative biology – In hourglass project will help determine clusters of stages more defined than early, middle, late
Current Tool Pipeline Distance matrix Ontology Databases (Xenobase, Zfa) Manual Embryological Stages Entry Outside/User Input Secondary Gene Expression Data Stage Alignment Based on user inputted aspects Heat Maps Ontological Analysis Generates common features list using interspecific mappings , outputs absence presence matrix Distance Algorithm User Input Filtering algorithm, filters based on what user wants to be included in analysis
Using common OGGs (Euclidean correlation across stages) Using SES text mining matrices (Euclidean correlation across stages) Using common 144 features (Euclidean correlation across stages)
Future Directions • Uberon lacks a lot of mapping (for lower level characters) • Zfa: 345 listings • Mmus: 415 listings • Xenopus: 2245 listings – Bugs and assumptions made – Need to used anatomical reference ontology • Uberon not ideal for matching anatomical parts • K-means clustering • Like-wise comparisons reveals a lack of specific features – The ends are disrupted.

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Embryonic stage alignment_tool

  • 2. Background • Multiple stage alignment papers (Comparative transcriptomics) • Ontology (tracks the hierarchy and progression of expression) • XenoBase, Zfa, Mouse Atlas Project • SES stages are supposed to be used to standardize nomenclature across vertebrate • Stage Alignment helps comparative biology – In hourglass project will help determine clusters of stages more defined than early, middle, late
  • 3. Current Tool Pipeline Distance matrix Ontology Databases (Xenobase, Zfa) Manual Embryological Stages Entry Outside/User Input Secondary Gene Expression Data Stage Alignment Based on user inputted aspects Heat Maps Ontological Analysis Generates common features list using interspecific mappings , outputs absence presence matrix Distance Algorithm User Input Filtering algorithm, filters based on what user wants to be included in analysis
  • 4. Using common OGGs (Euclidean correlation across stages) Using SES text mining matrices (Euclidean correlation across stages) Using common 144 features (Euclidean correlation across stages)
  • 5. Future Directions • Uberon lacks a lot of mapping (for lower level characters) • Zfa: 345 listings • Mmus: 415 listings • Xenopus: 2245 listings – Bugs and assumptions made – Need to used anatomical reference ontology • Uberon not ideal for matching anatomical parts • K-means clustering • Like-wise comparisons reveals a lack of specific features – The ends are disrupted.