MA Expression_50759265

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title: "TheNessLab : MA Expression"

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TheNessLab : MA Expression

Created by Robert Ness, last modified on Apr 28, 2021

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MA Expression

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Authors:

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- Eni Balogun
- Peter/Nick??
- Rob Ness

Motivation

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- How does de novo mutation influence changes in gene expression

Research Questions

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1. What is the effect of de novo mutation in overall variation in gene expression?
    - Does expression diverge up and down at same rate
    - What is the per mutation change in gene expression

2. How do locations of mutations co-localize with expression changes
    - Is there evidence of cis- vs trans-regulatory changes? 

3. Does change in expression differ based on gene properties
    - Does expression change correlate with evolutionary constraint
    - Do expression changes correlate with expression level
    - Do expression changes differ by in network properties
    - Do expression changes cluster in network sections

Core Analysis

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1. What is the effect of de novo mutation in overall variation in gene expression?
    - Does expression diverge up and down at same rate
        Calculate fold-change of each gene in each line relative to ancestor
        Calculate mean/median/deviation of up-regulated and down-regulated genes
    - What is the per mutation change in gene expression
        calculate absolute fold change per line
        calculate fold change per mutation (abs(sum of fold_change_line)/number_mutations)
        calculate fold change per generation using per mutation and mutation rate

2. How do locations of mutations co-localize with expression changes
    - Is there evidence of cis- vs trans-regulatory changes? 
         - Calculate distance to nearest mutation for each gene that is differentially expressed
         - Compare fold change of genes with mutations within N-bp of gene to other genes

3. Does change in expression differ based on gene properties
    - Does expression change correlate with evolutionary constraint
        - for each gene calculate Dn:Ds (Rob has this)
        - correlate expression change with Dn:Ds (non-synonymous sub rates/synonymous sub rates)
* Learn more about Dn:Ds
    - Do expression changes correlate with expression level
        - Do high expression genes have their expression more constrained (Compare the Vm of high/low expressed genes)
        - Does the proportional expression change correlate with expression level
    - Do expression changes differ by in network properties (topGO)
       - Do hub or other central genes have different expression change patterns
       - Calculate various network properties for each gene across expression and metabolic networks
       - Calculate correlations of fold change with network properties
    - Do expression changes cluster in network sections
       - read about statistic clustering of genes in network

Task Status

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Does fitness change correlate with expression divergence? 

Document generated by Confluence on May 22, 2024 11:44

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