Trait Data and Analysis for 5612792

Glutamate receptor, ionotropic, NMDA2B (epsilon 2); intron 6

Details and Links

Group Mouse: BXD group
Tissue Hippocampus mRNA
Gene Symbol Grin2b
Aliases Wikidata: NR3; NMDAR2B; NR2B; DEE27; EIEE27; GluN2B; hNR3; MRD6; AW490526; Nmdar2b; GluRepsilon2
GeneNetwork: hNR3; NMDAR2B; NR2B; NMDAR2B; Nmdar2b; GluN2B; GluRepsilon2; AW490526; MRD6; hNR3
Location Chr 6 @ 135.798431 Mb on the minus strand
Summary Enables NMDA glutamate receptor activity; calcium channel activity; and neurotransmitter receptor activity involved in regulation of postsynaptic membrane potential. Involved in negative regulation of dendritic spine maintenance and positive regulation of neuron death. Acts upstream of or within several processes, including behavioral fear response; detection of mechanical stimulus involved in sensory perception of pain; and learning or memory. Located in several cellular components, including cytoplasmic vesicle; lysosome; and synaptic membrane. Part of NMDA selective glutamate receptor complex. Is active in glutamatergic synapse. Is integral component of postsynaptic density membrane. Is expressed in several structures, including adipose tissue; central nervous system; eye; gut; and reproductive system. Human ortholog(s) of this gene implicated in several diseases, including alcohol use disorder; autosomal dominant non-syndromic intellectual disability 6; bipolar disorder; developmental and epileptic encephalopathy 27; and neurodegenerative disease (multiple). Orthologous to human GRIN2B (glutamate ionotropic receptor NMDA type subunit 2B). [provided by Alliance of Genome Resources, Apr 2022]
Database UMUTAffy Hippocampus Exon (Feb09) RMA
GN2 Link: UMUTAffy Hippocampus Exon (Feb09) RMA
Target Score BLAT Specificity : 1.018    Score: 72.000
Resource Links Gene    OMIM    GeneMANIA    Protein Atlas    Rat Genome DB    GTEx Portal   
UCSC    BioGPS    STRING    PANTHER    Gemma    ABA    EBI GWAS   

Statistics

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Mapping Tools

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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

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  # read into R
  trait <- read.csv("5612792.csv", header = TRUE, comment.char = "#")

  # read into python
  import pandas as pd
  trait = pd.read_csv("5612792.csv", header = 0, comment = "#")

BXD Only


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  # read into R
  trait <- read.csv("5612792.csv", header = TRUE, comment.char = "#")

  # read into python
  import pandas as pd
  trait = pd.read_csv("5612792.csv", header = 0, comment = "#")

Other


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