UCLA BXH and BXD Cartilage : ILM6760100: Display Trait

Trait Data and Analysis for Record ID ILM6760100

Details and Links

Gene Symbol: Chrna3
Aliases: (a)3; A730007P14Rik; Acra-3; Acra3; MGC104879
Description: cholinergic receptor, nicotinic, alpha polypeptide 3; 3' UTR
Location: Chr 9 @ 55.012711 Mb on the minus strand
Target Score: BLAT specificity: 5.0   Score: 50
Species and Group: Mouse, BXH
Database 3: UCLA BXH and BXD Cartilage
Resource Links: Gene  OMIM  UniGene  GenBank  HomoloGene
UCSC  BioGPS  STRING  PANTHER  Gemma  ABA  EBI GWAS  Wiki-Pi

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Basic Statistics

Include:

Basic Table
Probability Plot
Bar Graph (by name)
Bar Graph (by rank)
Box Plot

Statistic Value
N of Samples 25
Mean 7.930
Median 7.930
Standard Error (SE) 0.005
Standard Deviation (SD) 0.026
Minimum 7.884
Maximum 7.998
Range (log2) 0.114
Range (fold) 1.082
Interquartile Range 1.026

This plot evaluates whether data are normally distributed. Different symbols represent different groups.

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

More about Box Plots

Basic Table
Probability Plot
Bar Graph (by name)
Bar Graph (by rank)
Box Plot

Statistic Value
N of Samples 10
Mean 7.939
Median 7.933
Standard Error (SE) 0.008
Standard Deviation (SD) 0.027
Minimum 7.912
Maximum 7.998
Range (log2) 0.086
Range (fold) 1.061
Interquartile Range 1.018

This plot evaluates whether data are normally distributed. Different symbols represent different groups.

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

More about Box Plots

Basic Table
Probability Plot
Bar Graph (by name)
Bar Graph (by rank)
Box Plot

Statistic Value
N of Samples 17
Mean 7.925
Median 7.926
Standard Error (SE) 0.006
Standard Deviation (SD) 0.025
Minimum 7.884
Maximum 7.963
Range (log2) 0.079
Range (fold) 1.056
Interquartile Range 1.030

This plot evaluates whether data are normally distributed. Different symbols represent different groups.

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

More about Box Plots

Calculate Correlations

Sample r
Literature r
Tissue r

Database:
Return:
Samples:

Pearson Spearman Rank

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.
Database:
Return:
Samples:

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
Database:
Return:
Samples:

Pearson Spearman Rank

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

Interval
Marker Regression
Composite
Pair-Scan

Chromosome:
Mapping Scale:
Permutations:

Bootstrap Test (n=2000)
Use Parents
Use Weighted

Interval Mapping computes linkage maps for the entire genome or single
chromosomes. The Permutation Test estimates suggestive and significant
linkage scores. The Bootstrap Test estimates the precision of the QTL location.
Display LRS above:
Permutations:

Display all LRS
Use Parents
Use Weighted

Marker regression computes and displays LRS values for individual markers.
This function also lists additive effects (phenotype units per allele) and
dominance deviations for some datasets.

Chromosome:
Mapping Scale:
Control Locus:
Permutations:

Bootstrap Test (n=2000)
Use Parents

Composite Interval Mapping allows you to control for a single marker as
a cofactor. To find a control marker, run the Marker Regression function.
Sort by:
Return:

Permutation Test (n=500)

Pair-Scan searches for pairs of chromosomal regions that are
involved in two-locus epistatic interactions.

Review and Edit Data

Edit or delete values in the Trait Data boxes, and use the Reset option as needed.
  Block samples by index:
  Options:

  Outliers highlighted in yellow can be hidden using the Hide Outliers button,
  and samples with no value (x) can be hidden by clicking Hide No Value .

Index Sample Value
1 BHF1
2 HBF1
3 C57BL/6J
4 C3H/HeJ
5 BXH2
6 BXH3
7 BXH4
8 BXH6
9 BXH7
10 BXH8
11 BXH9
12 BXH10
13 BXH11
14 BXH12
15 BXH14
16 BXH19
17 BXH20
18 BXH21
19 BXH22
20 B6cC3-1

Index Sample Value
1 BHF1
2 HBF1
3 C57BL/6J
4 C3H/HeJ
5 B6cC3-1
6 BXD1
7 BXD12
8 BXD16
9 BXD19
10 BXD2
11 BXD24
12 BXD27
13 BXD28
14 BXD32
15 BXD39
16 BXD40
17 BXD42
18 BXD6
19 DBA/2J