UCLA BXH and BXD Cartilage v2 : 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 v2
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 27
Mean 6.496
Median 6.579
Standard Error (SE) 0.079
Standard Deviation (SD) 0.409
Minimum 5.438
Maximum 7.260
Range (log2) 1.822
Range (fold) 3.535
Interquartile Range 1.336

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 11
Mean 6.541
Median 6.526
Standard Error (SE) 0.109
Standard Deviation (SD) 0.361
Minimum 5.878
Maximum 7.260
Range (log2) 1.381
Range (fold) 2.605
Interquartile Range 1.304

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 18
Mean 6.468
Median 6.617
Standard Error (SE) 0.100
Standard Deviation (SD) 0.426
Minimum 5.438
Maximum 7.104
Range (log2) 1.666
Range (fold) 3.174
Interquartile Range 1.336

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 BXD21
12 BXD24
13 BXD27
14 BXD28
15 BXD32
16 BXD39
17 BXD40
18 BXD42
19 BXD6
20 DBA/2J