MDC/CAS/UCL Liver 230v2 (Dec08) RMA : 1369001

Trait Data and Analysis for Record ID 1369001_at

Details and Links

Gene Symbol: Chrna3
Description: cholinergic receptor, nicotinic, alpha 3
Location: Chr 8 @ 55.401778 Mb on the minus strand
Target Score: BLAT specificity: 20.0   Score: 232
Species and Group: Rat, HXBBXH
Database 3: MDC/CAS/UCL Liver 230v2 (Dec08) RMA
Resource Links: Gene  OMIM  UniGene  GenBank  HomoloGene
UCSC  BioGPS  STRING  PANTHER  Gemma  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 31
Mean 5.988
Median 5.947
Standard Error (SE) 0.048
Standard Deviation (SD) 0.267
Minimum 5.784
Maximum 7.377
Range (log2) 1.593
Range (fold) 3.017
Interquartile Range 1.078

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 30
Mean 5.989
Median 5.949
Standard Error (SE) 0.050
Standard Deviation (SD) 0.272
Minimum 5.784
Maximum 7.377
Range (log2) 1.593
Range (fold) 3.017
Interquartile Range 1.078

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-HXBBXH 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:
  Block samples by group:


  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 RRID
1 SHR_BNF1 (HSRBNF1) ±
2 BN_SHRF1 (BNHSRF1) ±
3 BN-Lx/Cub (BN) ± RGD_61117
4 SHR/OlaIpcv (SHR) ± RGD_631848
5 SHR/OlaIpcv (SHR) ± RGD_631848
6 BN-Lx/Cub (BN) ± RGD_61117
7 BXH2 ± RGD_2307121
8 BXH3 ± RGD_2307134
9 BXH5 ± RGD_2307115
10 BXH6 ± RGD_2307136
11 BXH8 ± RGD_2307126
12 BXH9 ± RGD_2307129
13 BXH10 ± RGD_2307124
14 BXH11 ± RGD_2307127
15 BXH12 ± RGD_2307139
16 BXH12a ±
17 BXH13 ± RGD_2307123
18 HXB1 ± RGD_2307094
19 HXB2 ± RGD_2307096
20 HXB3 ± RGD_2307079
21 HXB4 ± RGD_2307077
22 HXB5 ± RGD_2307099
23 HXB7 ± RGD_2307086
24 HXB9 ±
25 HXB10 ± RGD_2307083
26 HXB13 ± RGD_2307091
27 HXB14 ± RGD_2307092
28 HXB15 ± RGD_2307095
29 HXB16 ±
30 HXB17 ± RGD_2307085
31 HXB18 ± RGD_2307082
32 HXB19 ±
33 HXB20 ± RGD_2307080
34 HXB21 ± RGD_2307097
35 HXB22 ± RGD_2307088
36 HXB23 ± RGD_2307093
37 HXB24 ± RGD_2307084
38 HXB25 ± RGD_2307098
39 HXB26 ±
40 HXB27 ± RGD_2307078
41 HXB29 ± RGD_2307089
42 HXB30 ±

Index Sample Value SE N RRID
1 SHR_BNF1 (HSRBNF1) ±
2 BN_SHRF1 (BNHSRF1) ±
3 BN-Lx/Cub (BN) ± RGD_61117
4 SHR/OlaIpcv (SHR) ± RGD_631848
5 HXB31 ± RGD_2307081