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, CXB
Database 3:		UCLA CXB Aorta 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: All Cases CXB Only Non-CXB Only    

Basic Table Probability Plot Bar Graph (by name) Bar Graph (by rank) Box Plot Statistic Value N of Samples 9 Mean 7.139 Median 7.076 Standard Error (SE) 0.086 Standard Deviation (SD) 0.258 Minimum 6.947 Maximum 7.776 Range (log2) 0.829 Range (fold) 1.776 Interquartile Range 1.149 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 8 Mean 7.130 Median 7.036 Standard Error (SE) 0.097 Standard Deviation (SD) 0.274 Minimum 6.947 Maximum 7.776 Range (log2) 0.829 Range (fold) 1.776 Interquartile Range 1.132 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-CXB case data were entered. No statistical analysis has been attempted.

  Calculate Correlations

Sample r Literature r Tissue r Database: CXB Published Phenotypes CXB Genotypes UCLA CXB Aorta Affy M430 2.0 (Jan16) RMA Hippocampus Consortium M430v2 CXB (Dec05) PDNN Hippocampus Consortium M430v2 CXB (Dec05) RMA UCLA CXB Liver Affy M430 2.0 (Jan16) RMA Stuart Spleen M430v2 (Nov07) RMA Return: top 25 top 50 top 100 top 200 top 500 top 1000 top 2000 top 5000 top 10000 top 15000 top 20000 top 30000 top 40000 top 60000 Samples: CXB Only Non-CXB Only All Cases 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: CXB Published Phenotypes CXB Genotypes UCLA CXB Aorta Affy M430 2.0 (Jan16) RMA Hippocampus Consortium M430v2 CXB (Dec05) PDNN Hippocampus Consortium M430v2 CXB (Dec05) RMA UCLA CXB Liver Affy M430 2.0 (Jan16) RMA Stuart Spleen M430v2 (Nov07) RMA Return: top 25 top 50 top 100 top 200 top 500 top 1000 top 2000 top 5000 top 10000 top 15000 top 20000 top 30000 top 40000 top 60000 Samples: CXB Only Non-CXB Only All Cases 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: CXB Published Phenotypes CXB Genotypes UCLA CXB Aorta Affy M430 2.0 (Jan16) RMA Hippocampus Consortium M430v2 CXB (Dec05) PDNN Hippocampus Consortium M430v2 CXB (Dec05) RMA UCLA CXB Liver Affy M430 2.0 (Jan16) RMA Stuart Spleen M430v2 (Nov07) RMA Return: top 25 top 50 top 100 top 200 top 500 top 1000 top 2000 top 5000 top 10000 top 15000 top 20000 top 30000 top 40000 top 60000 Samples: CXB Only Non-CXB Only All Cases 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: All 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 X Mapping Scale: Megabase Centimorgan 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: All 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 X Mapping Scale: Megabase Centimorgan 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: LRS Full LRS Interact Return: top 50 top 100 top 200 top 500 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:         CXB Only Non-CXB Only       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 CBF1 ± 2 BCF1 ± 3 C57BL/6ByJ ± 4 BALB/cByJ ± 5 CXB1 ± 6 CXB2 ± 7 CXB3 ± 8 CXB4 ± 9 CXB5 ± 10 CXB6 ± 11 CXB7 ± 12 CXB8 ± 13 CXB9 ± 14 CXB10 ± 15 CXB11 ± 16 CXB12 ± 17 CXB13 ±   Index Sample Value   SE N 1 CBF1 ± 2 BCF1 ± 3 C57BL/6ByJ ± 4 BALB/cByJ ± 5 CXB13 ±