Details and Links

Gene Symbol:		Chrna3
Aliases:		(a)3; A730007P14Rik; Acra-3; Acra3
Description:		cholinergic receptor, nicotinic, alpha polypeptide 3
Location:		Chr 9 @ 55.011424 Mb
Target Score:		BLAT specificity: 3.0   Score: 60
Species and Group:		Mouse, MDP
Database 3:		Harrill-Rusyn MDP Liver Acetaminophen Tox Study (G4121A, 2009)
Resource Links:		Gene  OMIM  GenBank  HomoloGene
		UCSC  BioGPS  STRING  PANTHER  Gemma  ABA  EBI GWAS  Wiki-Pi

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  Basic Statistics

Include: All Cases MDP Only Non-MDP Only    

Basic Table Probability Plot Bar Graph (by name) Bar Graph (by rank) Box Plot Statistic Value N of Samples 36 Mean -0.139 Median -0.143 Standard Error (SE) 0.023 Standard Deviation (SD) 0.139 Minimum -0.568 Maximum 0.315 Range (log2) 0.883 Range (fold) 1.844 Interquartile Range 1.088 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 35 Mean -0.141 Median -0.147 Standard Error (SE) 0.024 Standard Deviation (SD) 0.141 Minimum -0.568 Maximum 0.315 Range (log2) 0.883 Range (fold) 1.844 Interquartile Range 1.087 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-MDP case data were entered. No statistical analysis has been attempted.

  Calculate Correlations

Sample r Literature r Tissue r Database: Mouse Phenome Mouse Diversity Panel Genotype UCLA GSE27483 MDP Bone Femur ILM Mouse WG-6 v1, v1.1 (Jan13) RSN TSRI DRG Affy Mouse Genome 430 2.0 (Jan13) RMA MDP UMUTAffy Hippocampus Exon (Feb09) RMA MDP Hippocampus Consortium M430v2 (Jun06) RMA MDP UFL MDP Hippocampus Antidepressant Affy Mouse 430 2.0 (Aug14) RMA GSE16780 UCLA Mouse MDP Liver Affy HT M430A (Sep11) RMA JAX Liver Affy M430 2.0 (Jul11) MDP JAX Liver HF Affy M430 2.0 (Jul11) MDP JAX Liver 6C Affy M430 2.0 (Jul11) MDP Harrill-Rusyn MDP Liver Acetaminophen Tox Study (G4121A, 2009) HMS Spleen CD4+ T cells MDP Affy Mouse Gene 1.0 ST (Jul16) Gene Level 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: MDP Only Non-MDP 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: Mouse Phenome Mouse Diversity Panel Genotype UCLA GSE27483 MDP Bone Femur ILM Mouse WG-6 v1, v1.1 (Jan13) RSN TSRI DRG Affy Mouse Genome 430 2.0 (Jan13) RMA MDP UMUTAffy Hippocampus Exon (Feb09) RMA MDP Hippocampus Consortium M430v2 (Jun06) RMA MDP UFL MDP Hippocampus Antidepressant Affy Mouse 430 2.0 (Aug14) RMA GSE16780 UCLA Mouse MDP Liver Affy HT M430A (Sep11) RMA JAX Liver Affy M430 2.0 (Jul11) MDP JAX Liver HF Affy M430 2.0 (Jul11) MDP JAX Liver 6C Affy M430 2.0 (Jul11) MDP Harrill-Rusyn MDP Liver Acetaminophen Tox Study (G4121A, 2009) HMS Spleen CD4+ T cells MDP Affy Mouse Gene 1.0 ST (Jul16) Gene Level 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: MDP Only Non-MDP 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: Mouse Phenome Mouse Diversity Panel Genotype UCLA GSE27483 MDP Bone Femur ILM Mouse WG-6 v1, v1.1 (Jan13) RSN TSRI DRG Affy Mouse Genome 430 2.0 (Jan13) RMA MDP UMUTAffy Hippocampus Exon (Feb09) RMA MDP Hippocampus Consortium M430v2 (Jun06) RMA MDP UFL MDP Hippocampus Antidepressant Affy Mouse 430 2.0 (Aug14) RMA GSE16780 UCLA Mouse MDP Liver Affy HT M430A (Sep11) RMA JAX Liver Affy M430 2.0 (Jul11) MDP JAX Liver HF Affy M430 2.0 (Jul11) MDP JAX Liver 6C Affy M430 2.0 (Jul11) MDP Harrill-Rusyn MDP Liver Acetaminophen Tox Study (G4121A, 2009) HMS Spleen CD4+ T cells MDP Affy Mouse Gene 1.0 ST (Jul16) Gene Level 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: MDP Only Non-MDP 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:         MDP Only Non-MDP 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 129P1/ReJ ± 2 129P3/J ± 3 129PFVBF1-TgN(MMTV) ± 4 129S1/SvImJ ± 5 129S4/SvJae ± 6 129S6/SvEv ± 7 129S6/SvEvTac ± 8 129T2/SvEmsJ ± 9 129X1/SvJ ± 10 A/HeJ ± 11 A/J ± 12 A/WySnJ ± 13 AFVBF1-TgN(MMTV) ± 14 AKFVBF1-TgN(MMTV) ± 15 AKR/J ± 16 ALR/LtJ ± 17 ALS/LtJ ± 18 B6D2F1 ± 19 B6AF1/J ± 20 B6C3F1/J ± 21 B6SJLF1/J ± 22 B10FVBF1-TgN(MMTV) ± 23 B6.Cg-A<y>/J ± 24 B6.Cg-Tub<tub>/J ± 25 B6.Cg-m +/+ Lepr<db>/J ± 26 B6.V-Lep<ob>/J ± 27 B6129XF1 ± 28 B6CBAF1/J ± 29 B6IcrFVBF1-TgN(MMTV) ± 30 BALB/cByJ ± 31 BALB/cJ ± 32 BDP/J ± 33 BFM/2Ms ± 34 BKS.Cg-m +/+ Lepr<db>/J ± 35 BKS.HRS-Cpe<fat>/J ± 36 BLG2/Ms ± 37 BPH/2J ± 38 BPL/1J ± 39 BPN/3J ± 40 BRFVBF1-TgN(MMTV) ± 41 BTBRT<+>tf/J ± 42 BUB/BnJ ± 43 BUFVBF1-TgN(MMTV) ± 44 BXSB/MpJ ± 45 C3H/HeJ ± 46 C3H/HeOuJ ± 47 C3H/HeSnJ ± 48 C3HeB/FeJ ± 49 C3IcrFVBF1-TgN(MMTV) ± 50 C57BL/10J ± 51 C57BL/10ScSn ± 52 C57BL/10SnJ ± 53 C57BL/6ByJ ± 54 C57BL/6J ± 55 C57BLKS/J ± 56 C57BR/cdJ ± 57 C57L/J ± 58 C58/J ± 59 C58FVBF1-TgN(MMTV) ± 60 CAF1/J ± 61 CAFVBF1-TgN(MMTV) ± 62 CaJFVBF1-TgN(MMTV) ± 63 CALB/RkJ ± 64 CASA/RkJ ± 65 CAST/EiJ ± 66 CB6F1/J ± 67 CBA/CaJ ± 68 CBA/J ± 69 CE/J ± 70 CEFVBF1-TgN(MMTV) ± 71 CIM ± 72 Clcn3<KO> ± 73 CIcrFVBF1-TgN(MMTV) ± 74 CTP ± 75 CZECHI/EiJ ± 76 CZECHII/EiJ ± 77 D1FVBF1-TgN(MMTV) ± 78 D2B6F1 ± 79 D2FVBF1-TgN(MMTV) ± 80 DBA/1J ± 81 DBA/1LacJ ± 82 DBA/2HaSmnJ ± 83 DBA/2J ± 84 DDK/Pas ± 85 FVB-Tg(MMTV) ± 86 FVB/NJ ± 87 Gabbr1<KO> ± 88 Garba1<KO> ± 89 Gnb5<KO> ± 90 Gpr19<KO> ± 91 HMI/Ms ± 92 I/LnJ ± 93 IDH2/Ei ± 94 IFVBF1-TgN(MMTV) ± 95 ILS ± 96 ILS/Bg ± 97 IS/CamRkJ ± 98 ISS ± 99 ISS/Bg ± 100 JF1/Ms ± 101 KJR/Ms ± 102 KK/HlJ ± 103 KKFVBF1-TgN(MMTV) ± 104 LEWES/EiJ ± 105 LG/J ± 106 LP/J ± 107 LPFVBF1-TgN(MMTV) ± 108 MA/MyJ ± 109 MAI ± 110 MAI/Pas ± 111 MBT ± 112 MOFVBF1-TgN(MMTV) ± 113 MOLC/RkJ ± 114 MOLD/RkJ ± 115 MOLF/EiJ ± 116 MRL/MpJ ± 117 MRL/MpJ-Fas<lpr>/J ± 118 MSM/Ms ± 119 MusSpretusOutbred1 ± 120 MusSpretusOutbred2 ± 121 NJL/Ms ± 122 NOD.NON-H2<nb1>/LtJ ± 123 NOD/ShiLtJ ± 124 NOFVBF1-TgN(MMTV) ± 125 NON/LtJ ± 126 NOR/LtJ ± 127 NZB/BlNJ ± 128 NZBFVBF1-TgN(MMTV) ± 129 NZO/HlLtJ ± 130 NZW/LacJ ± 131 NZWFVBF1-TgN(MMTV) ± 132 Nyx<nob> ± 133 O20 ± 134 P/J ± 135 PANCEVO/EiJ ± 136 PERA/EiJ ± 137 PERC/EiJ ± 138 PFVBF1-TgN(MMTV) ± 139 PL/J ± 140 PWD/PhJ ± 141 PWK/Pas ± 142 PWK/PhJ ± 143 PWK/Rbrc ± 144 PWK/Ros ± 145 Qsi5 ± 146 RBA/DnJ ± 147 RBF/DnJ ± 148 RF/J ± 149 RFFVBF1-TgN(MMTV) ± 150 RIIIS/J ± 151 Rpe65<rd12> ± 152 SB/LeJ ± 153 SEA/GnJ ± 154 SEC/1ReJ ± 155 SEFVBF1-TgN(MMTV) ± 156 SEG/Pas ± 157 SENCARA/PtJ ± 158 SENCARB/PtJ ± 159 SENCARC/PtJ ± 160 SF/CamEiJ ± 161 SJL/Bm ± 162 SJL/J ± 163 SKH2/J ± 164 SKIVE/EiJ ± 165 SM/J (SM/J) ± 166 SPRET/EiJ ± 167 ST/bJ ± 168 STFVBF1-TgN(MMTV) ± 169 SWFVBF1-TgN(MMTV) ± 170 SWN/Ms ± 171 SWR/J ± 172 SWRB6F1 ± 173 SWRD2F1 ± 174 SWXL4/TyJ ± 175 TIRANO/EiJ ± 176 WMP/PasDnJ ± 177 WSB/EiJ ± 178 YBR/EiJ ± 179 ZALENDE/EiJ ±   Index Sample Value   SE N 1 SM/J ±