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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.