OHSU/VA B6D2F2 03/04 RMA : 1452010_at

Trait Data and Analysis for Record ID 1452010_at_A

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, B6D2F2
Database 3: OHSU/VA B6D2F2 Brain mRNA M430A (Mar04) 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 56
Mean 7.763
Median 7.771
Standard Error (SE) 0.015
Standard Deviation (SD) 0.114
Minimum 7.458
Maximum 8.101
Range (log2) 0.643
Range (fold) 1.562
Interquartile Range 1.095

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 55
Mean 7.763
Median 7.771
Standard Error (SE) 0.015
Standard Deviation (SD) 0.115
Minimum 7.458
Maximum 8.101
Range (log2) 0.643
Range (fold) 1.562
Interquartile Range 1.095

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-B6D2F2 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
1 B6D2F1
2 D2B6F1
3 C57BL/6J
4 DBA/2J
5 CASE001
6 CASE002
7 CASE003
8 CASE004
9 CASE005
10 CASE006
11 CASE007
12 CASE008
13 CASE009
14 CASE010
15 CASE011
16 CASE012
17 CASE013
18 CASE014
19 CASE015
20 CASE016
21 CASE019
22 CASE020
23 CASE021
24 CASE022
25 CASE023
26 CASE024
27 CASE025
28 CASE027
29 CASE028
30 CASE030
31 CASE031
32 CASE032
33 CASE033
34 CASE034
35 CASE035
36 CASE036
37 CASE037
38 CASE038
39 CASE039
40 CASE040
41 CASE041
42 CASE042
43 CASE043
44 CASE044
45 CASE046
46 CASE047
47 CASE048
48 CASE050
49 CASE051
50 CASE052
51 CASE053
52 CASE054
53 CASE055
54 CASE056
55 CASE057
56 CASE058
57 CASE059
58 CASE060
59 CASE062
60 CASE063

Index Sample Value
1 B6D2F1
2 D2B6F1
3 C57BL/6J
4 DBA/2J
5 CASE063