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Trait Data and Analysis for 1419709_at

Stefin A3

Details and Links

Group Mouse: BXD group
Tissue T Cell (helper) mRNA
Gene Symbol Stfa3
Aliases Wikidata: Not available
GeneNetwork: Stf3
Location Chr 16 @ 36.450554 Mb on the minus strand
Summary Predicted to enable cysteine-type endopeptidase inhibitor activity and protease binding activity. Predicted to be involved in several processes, including keratinocyte differentiation; negative regulation of proteolysis; and peptide cross-linking. Predicted to be located in several cellular components, including cornified envelope; extracellular space; and nucleoplasm. Predicted to be part of peptidase inhibitor complex. Predicted to be active in cytosol. Is expressed in femur; humerus; radius; tibia; and ulna. Human ortholog(s) of this gene implicated in peeling skin syndrome 4. Orthologous to human CSTA (cystatin A). [provided by Alliance of Genome Resources, Jul 2025]
Database HZI Thelp M430v2 (Feb11) RMA
Target Score BLAT Specificity : 3.273    Score: 180.000
Resource Links Gene    GeneMANIA    Protein Atlas    Rat Genome DB    GTEx Portal   
UCSC    BioGPS    STRING    PANTHER    Gemma    ABA    EBI GWAS   

Statistics


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

Transform and Filter Data

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Calculate Correlations

Chr:     Mb:  to 
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("1419709_at.csv", header = TRUE, comment.char = "#")

  # read into python
  import pandas as pd
  trait = pd.read_csv("1419709_at.csv", header = 0, comment = "#")
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Samples


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