Embryonic stage alignment_tool

1. Embryo 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.