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Trait Data and Analysis for BXD_23777

Details and Links

Group Mouse: BXD group
Phenotype
Metagenome, microbiota, gastrointestinal system, metabolism: OTU11 (Firmicutes;Clostridiales;Peptostreptococcaceae) proportion assessed by 16S rRNA sequencing of cecum content from young adult males (3-6 months) on a standard chow diet (CD, EPFL LISP3 Cohort, 2014-2018) [normalised log fraction]
Authors
Perez-Munoz ME, McKnite AM, Williams EG, Auwerx J, Williams RW, Peterson DA, Ciobanu DC
Title
Diet Modulates Cecum Bacterial Diversity and Physiological Phenotypes across the BXD Mouse Genetic Reference Population
Journal PLoS One (2019)
Database BXD Published Phenotypes
Resource Links PubMed

Statistics


More about Normal Probability Plots and more about interpreting these plots from the glossary

Transform and Filter Data

Edit or delete values in the Trait Data boxes, and use the Reset option as needed.



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Samples with no value (x) can be hidden by clickingHide No Value button.

Calculate Correlations

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Sample Correlation
The Sample Correlation is computed between trait data and any other traits in the sample database selected above. Use Spearman Rank when the sample size is small (<20) or when there are influential outliers.
Literature Correlation
The Literature Correlation (Lit r) between this gene and all other genes is computed
using the Semantic Gene Organizer and human, rat, and mouse data from PubMed. Values are ranked by Lit r, but Sample r and Tissue r are also displayed.
More on using Lit r
Tissue Correlation
The Tissue Correlation (Tissue r) estimates the similarity of expression of two genes or transcripts across different cells, tissues, or organs (glossary). Tissue correlations are generated by analyzing expression in multiple samples usually taken from single cases.
Pearson and Spearman Rank correlations have been computed for all pairs of genes using data from mouse samples.

Mapping Tools

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GEMMA
GEMMA maps with correction for kinship using a linear mixed model and can include covariates such as sex and age. Defaults include a minor allele frequency of 0.05 and the leave-one-chromosome-out method (PMID: 2453419, and GitHub code).
Haley-Knott Regression
HK regression (QTL Reaper) is a fast mapping method with permutation that works well with F2 intercrosses and backcrosses (PMID: 16718932), but is not recommended for admixed populations, advanced intercrosses, or strain families such as the BXDs (QTL Reaper code).
R/qtl (version 1.44.9)
R/qtl maps using several models and uniquely support 4-way intercrosses such as the "Aging Mouse Lifespan Studies" (NIA UM-HET3). We will add support for R/qtl2 (PMID: 30591514) in the near future—a version that handles complex populations with admixture and many haplotypes.
R/qtl2 (version 0.36)
R/qtl2 (aka qtl2) is a reimplementation of the QTL analysis software R/qtl, to better handle high-dimensional data and complex cross designs.. R/QTL2 documentation
Pair Scan (R/qtl v 1.44.9)
The Pair Scan mapping tool performs a search for joint effects of two separate loci that may influence a trait. This search typically requires large sample sizes. Pair Scans can included covariates such as age and sex. For more on this function by K. Broman and colleagues see www.rdocumentation.org/packages/qtl/versions/1.60/topics/scantwo
More information on R/qtl mapping models and methods can be found here.

Review and Edit Data



Show/Hide Columns: 


            
  # read into R
  trait <- read.csv("BXD_23777.csv", header = TRUE, comment.char = "#")

  # read into python
  import pandas as pd
  trait = pd.read_csv("BXD_23777.csv", header = 0, comment = "#")

Samples


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