UCLA AXB/BXA Liver Affy M430 2.0 (Jan16) RMA : 1452010

Trait Data and Analysis for Record ID 1452010_at

Details and Links

Gene Symbol: Chrna3
Aliases: (a)3; A730007P14Rik; Acra-3; Acra3; LNCR2; PAOD2; MGC104879; CHRNA3
Description: cholinergic receptor, nicotinic, alpha polypeptide 3; last two exons and proximal 3' UTR
Location: Chr 9 @ 55.012583 Mb on the minus strand
Target Score: BLAT specificity: 11.7   Score: 233
Species and Group: Mouse, AXBXA
Database 3: UCLA AXB/BXA Liver Affy M430 2.0 (Jan16) RMA
Resource Links: Gene  OMIM  UniGene  GenBank  HomoloGene
UCSC  BioGPS  STRING  PANTHER  Gemma  ABA  EBI GWAS  Wiki-Pi

Add Find Verify GeneWiki SNPs Probes

Basic Statistics

Include:

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

Statistic Value
N of Samples 21
Mean 6.673
Median 6.685
Standard Error (SE) 0.015
Standard Deviation (SD) 0.071
Minimum 6.533
Maximum 6.812
Range (log2) 0.279
Range (fold) 1.213
Interquartile Range 1.032

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 19
Mean 6.679
Median 6.689
Standard Error (SE) 0.016
Standard Deviation (SD) 0.069
Minimum 6.533
Maximum 6.812
Range (log2) 0.279
Range (fold) 1.213
Interquartile Range 1.032

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
Fewer than 4 non-AXBXA case data were entered. No statistical analysis has been attempted.

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 SE N
1 ABF1 ±
2 BAF1 ±
3 C57BL/6J ±
4 A/J ±
5 AXB1 ±
6 AXB2 ±
7 AXB3 ±
8 AXB4 ±
9 AXB5 ±
10 AXB6 ±
11 AXB7 ±
12 AXB8 ±
13 AXB9 ±
14 AXB10 ±
15 AXB11 ±
16 AXB12 ±
17 AXB13/14^# ±
18 AXB15 ±
19 AXB17 ±
20 AXB18/19/20^# ±
21 AXB21 ±
22 AXB23 ±
23 AXB24 ±
24 BXA1 ±
25 BXA2 ±
26 BXA4 ±
27 BXA7 ±
28 BXA8/17^# ±
29 BXA11 ±
30 BXA12 ±
31 BXA13 ±
32 BXA14 ±
33 BXA16 ±
34 BXA18 ±
35 BXA20 ±
36 BXA22 ±
37 BXA23 ±
38 BXA24 ±
39 BXA25 ±
40 BXA26 ±

Index Sample Value SE N
1 ABF1 ±
2 BAF1 ±
3 C57BL/6J ±
4 A/J ±
5 AXB13 ±
6 BXA8 ±