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Phenotype from Genotype

Front Matter

  • Declaration
  • Abstract
  • Acknowledgements
  • Table of Contents

Background

  • 1. Thesis style and philosophy
  • 2. How phenotype arises from genotype
    • 2.1. Big questions: What is genetically determined, and how?
    • 2.2. Biological molecules: DNA, RNA, Proteins and the central dogma of molecular biology.
    • 2.3. A closer look at DNA: Genomes, Genes, and Genetic Variation
    • 2.4. Looking more closely at proteins: function, structure and classification
    • 2.5. Phenotype
    • 2.6. Summary: how genotype and phenotype are linked
  • 3. How genotype and phenotype are measured and researched
    • 3.1. Sequencing and microarrays
    • 3.2. From genotype to phenotype: what is measured
    • 3.3. Ontologies
    • 3.4. Predictive computational methods
    • 3.5. Sources of bias in computational biology
    • 3.6. Proteome Quality Index
    • 3.7. Summary

Phenotype prediction

  • 4. Phenotype prediction with Snowflake
    • 4.1. Introduction
    • 4.2. Snowflake Algorithm
    • 4.3. Creating Snowflake inputs
    • 4.4. Preprocessing
    • 4.5. Considerations for Clustering SNPs
    • 4.6. Discussion
  • 5. Predicting phenotypes of the ALSPAC cohort using Snowflake
    • 5.1. Introduction
    • 5.2. Discussion

Tissue-specific gene expression

  • 6. Filtering computational predictions with tissue-specific expression information
    • 6.1. Introduction
    • 6.2. Algorithm
    • 6.3. Data
    • 6.4. Validation method
    • 6.5. Filip results
    • 6.6. Discussion and Future work
  • 7. Ontolopy
    • 7.1. Introduction
    • 7.2. Functionality
    • 7.3. Ontolopy tools and practices
    • 7.4. Example uses: mapping samples to diseases or phenotypes
    • 7.5. Example use: mapping samples to tissue-related phenotypes
    • 7.6. Discussion
    • 7.7. Future Work
  • 8. Combining RNA-seq datasets
    • 8.1. Introduction
    • 8.2. Data Acquisition
    • 8.3. Data Wrangling
    • 8.4. Results and discussion

Concluding remarks

  • 9. Concluding remarks

End Matter

  • Appendix
  • Bibliography
Theme by the Executable Book Project

Index

_ | D | G | L | M | O | R | S | U

_

  • __init__() (ontolopy.obo.Obo method)
    • (ontolopy.relations.Relations method)
    • (ontolopy.uberon.Uberon method)

D

  • download_obo() (in module ontolopy.obo)

G

  • get_overall_tissue_mappings() (ontolopy.uberon.Uberon method)

L

  • load_obo() (in module ontolopy.obo)

M

  • merge() (ontolopy.obo.Obo method)

O

  • Obo (class in ontolopy.obo)

R

  • relation_path_to_text() (in module ontolopy.relations)
  • Relations (class in ontolopy.relations)

S

  • sample_map_by_name() (ontolopy.uberon.Uberon method)
  • sample_map_by_ont() (ontolopy.uberon.Uberon method)

U

  • Uberon (class in ontolopy.uberon)

By Natalie Zelenka
© Copyright 2020.