Trait Data and Analysis for 1427571_at

Sonic hedgehog (hedgehog); last exon

Details and Links

Group Mouse: BXD group
Tissue Hippocampus mRNA
Gene Symbol Shh
Aliases Wikidata: TPT; HLP3; HHG1; HPE3; MCOPCB5; ShhNC; SMMCI; TPTPS; Hhg1; Hx; Hxl3; M100081; 9530036O11Rik; Dsh
GeneNetwork: HHG1; HLP3; HPE3; SMMCI; Dsh; Hhg1
Location Chr 5 @ 28.457886 Mb on the minus strand
Summary Enables glycosaminoglycan binding activity; laminin-1 binding activity; and patched binding activity. Involved in several processes, including hematopoietic or lymphoid organ development; positive regulation of T cell activation; and regulation of smooth muscle cell differentiation. Acts upstream of or within several processes, including animal organ development; limb morphogenesis; and neurogenesis. Located in several cellular components, including cell surface; extracellular space; and membrane raft. Is expressed in several structures, including alimentary system; central nervous system; genitourinary system; limb bud; and sensory organ. Used to study brachydactyly type A1 and holoprosencephaly 3. Human ortholog(s) of this gene implicated in several diseases, including Hirschsprung's disease; holoprosencephaly (multiple); hypoplastic or aplastic tibia with polydactyly; middle cerebral artery infarction; and polydactyly. Orthologous to human SHH (sonic hedgehog signaling molecule). [provided by Alliance of Genome Resources, Apr 2022]
Database Hippocampus Consortium M430v2 (Jun06) PDNN
Target Score BLAT Specificity : 11.000    Score: 220.000
Resource Links Gene    OMIM    GeneMANIA    Protein Atlas    Rat Genome DB    GTEx Portal   
UCSC    BioGPS    STRING    PANTHER    Gemma    ABA    EBI GWAS   

Statistics

Select Group:

Select Group:
Select Group:


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.



Outliers highlighted in orange can be hidden using the Hide Outliers button.

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

Calculate Correlations

Chr:     Mb:  to 
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.

Mapping Tools

No collections available. Please add traits to a collection to use them as covariates.

No collections available. Please add traits to a collection to use them as covariates.
No collections available. Please add traits to a collection to use them as covariates.
GEMMA
Maps traits with correction for kinship among samples using a linear mixed model method, and also allows users to fit multiple covariates such as sex, age, treatment, and genetic markers (PMID: 2453419, and GitHub code). GEMMA incorporates the Leave One Chromosome Out (LOCO) method to ensure that the correction for kinship does not remove useful genetic variance near each marker. Markers can be filtered to include only those with minor allele frequencies (MAF) above a threshold. The default MAF is 0.05.
Haley-Knott Regression
Fast linear mapping method (PMID 16718932) works well with F2 intercrosses and backcrosses, but that is not recommended for complex or admixed populations (e.g., GWAS or heterogeneous stock studies) or for advanced intercrosses, recombinant inbred families, or diallel crosses. Interactive plots in GeneNetwork have relied on the fast HK mapping for two decades and we still use this method for mapping omics data sets and computing genome-wide permutation threshold (QTL Reaper code).
R/qtl (version 1.44.9)
The original R/qtl mapping package that supports classic experimental crosses including 4-parent F2 intercrosses (e.g., NIA ITP UM-HET3). R/qtl is ideal for populations that do not have complex kinship or admixture (PMID: 12724300). Both R/qtl as implemented here, and R/qtl2 (PMID: 30591514) are available as R suites.
Pair Scan
Pair Scan using the R/qtl scantwo function.
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("1427571_at.csv", header = TRUE, comment.char = "#")

  # read into python
  import pandas as pd
  trait = pd.read_csv("1427571_at.csv", header = 0, comment = "#")

BXD Only


Loading...
 

            
  # read into R
  trait <- read.csv("1427571_at.csv", header = TRUE, comment.char = "#")

  # read into python
  import pandas as pd
  trait = pd.read_csv("1427571_at.csv", header = 0, comment = "#")

Other


Loading...