Trait Data and Analysis Form
Trait ID 1415670_at : 269753 from Hippocampus Consortium M430v2 Probe (Jun06)Gene Symbol: Copg Gene Alias: Copg1, D6Ertd71e, D6Wsu16e, MGC66965Description: coatomer protein complex, subunit gamma; two of the three last exons and proximal 3' UTRLocation: Chr 6 @ 87.859681 Mb on the plus strand BLAT Score: 211 BLAT Specificity: 10.6 IDs: Gene 54161 UniGene Mm.258785 GenBank BC024686 HomoloGene 56745 Resource Links: UCSC BioGPS STRING PANTHER SynDB ABA Analysis Tools:To analyze a trait, select appropriate options and one or more function buttons (Basic Statisics, Trait Correlations, Pair-Scan, etc.). New windows will open to display results and provide you access to a series of additional analysis tools. To review and edit data, scroll down to the Trait Data section. Trait Correlations compares the values listed below with those of all other records in the database that you select to the right. You can edit values before initiating the analysis. Choose Database: BXD Published Phenotypes BXD Genotypes UCHSC BXD Whole Brain M430 2.0 (Nov06) RMA INIA Brain mRNA M430 (Jun06) RMA INIA Brain mRNA M430 (Jan06) PDNN INIA Brain mRNA M430 (Jan06) RMA UTHSC Brain mRNA U74Av2 (Nov05) PDNN UTHSC Brain mRNA U74Av2 (Aug05) RMA UTHSC Brain mRNA U74Av2 (Aug05) PDNN UTHSC Brain mRNA U74Av2 (Aug05) MAS5 INIA Brain mRNA M430 (Feb04) PDNN UCLA BXD and BXH Cartilage v2 ** UCLA BXD and BXH Cartilage ** UCLA BXD Cartilage ** GE-NIAAA Cerebellum mRNA M430v2 (May05) MAS5 GE-NIAAA Cerebellum mRNA M430v2 (May05) PDNN GE-NIAAA Cerebellum mRNA M430v2 (May05) RMA SJUT Cerebellum mRNA M430 (Mar05) MAS5 SJUT Cerebellum mRNA M430 (Mar05) PDNN SJUT Cerebellum mRNA M430 (Mar05) RMA SJUT Cerebellum mRNA M430 (Oct04) MAS5 SJUT Cerebellum mRNA M430 (Oct04) PDNN SJUT Cerebellum mRNA M430 (Oct04) RMA SJUT Cerebellum mRNA M430 (Oct03) MAS5 Eye M430v2 (Sep08) RMA Eye M430v2 Mutant Gpnmb (Sep08) RMA ** Eye M430v2 WT Gpnmb (Sep08) RMA ** UMCG Stem Cells ILM6v1.1 (Apr09) original UMCG Stem Cells ILM6v1.1 (Apr09) transformed UMCG Progenitor Cells ILM6v1.1 (Apr09) original UMCG Progenitor Cells ILM6v1.1 (Apr09) transformed UMCG Erythroid Cells ILM6v1.1 (Apr09) original UMCG Erythroid Cells ILM6v1.1 (Apr09) transformed UMCG Myeloid Cells ILM6v1.1 (Apr09) original UMCG Myeloid Cells ILM6v1.1 (Apr09) transformed GNF Stem Cells U74Av2 (Mar04) RMA Hippocampus Consortium M430v2 (Jun06) PDNN Hippocampus Consortium M430v2 (Jun06) MAS5 Hippocampus Consortium M430v2 (Jun06) RMA UMUTAffy Hippocampus Exon (Feb09) RMA UTHSC Hippocampus Illumina v6.1 NOE (Sep09) RankInv ** UTHSC Hippocampus Illumina v6.1 NON (Sep09) RankInv ** UTHSC Hippocampus Illumina v6.1 NOS (Sep09) RankInv ** UTHSC Hippocampus Illumina v6.1 RSE (Sep09) RankInv ** UTHSC Hippocampus Illumina v6.1 RSS (Sep09) RankInv ** Mouse kidney M430v2 Female (Aug06) RMA Mouse kidney M430v2 Male (Aug06) RMA Mouse kidney M430v2 Sex Balanced (Aug06) RMA Mouse Kidney M430v2 Sex Balanced (Aug06) PDNN Mouse Kidney M430v2 (Jul06) PDNN Mouse Kidney M430v2 (Jul06) RMA UWA Illumina PBL (Nov08) RSN ** UNC Agilent G4121A Liver LOWESS Stanford (Jan06) BothSexes UNC Agilent G4121A Liver LOWESS Stanford (Jan06) Females UNC Agilent G4121A Liver LOWESS Stanford (Jan06) Males HZI Lung M430v2 (Apr08) RMA ** HZI Lung M430v2 (Apr08) MAS5 ** HQF BXD Neocortex ILM6v1.1 (Feb08) RankInv VCU BXD NA EtOH M430 2.0 (Oct07) RMA ** VCU BXD NA Sal M430 2.0 (Oct07) RMA VCU BXD NA Et vs Sal M430 2.0 (Oct07) Sscore ** VCU BXD PFC Sal M430 2.0 (Dec06) RMA VCU BXD PFC EtOH M430 2.0 (Dec06) RMA ** VCU BXD PFC Et vs Sal M430 2.0 (Dec06) Sscore ** HZI Treg M430v2 (Nov06) RMA ** HEI Retina Illumina V6.2 (April 2010) RankInv HEI Retina Illumina V6.2 (Mar09) RankInv IoP Affy MOE 430v2 Spleen (May09) RMA UWA Illumina Spleen (Nov08) RSN ** UTK Spleen ILM6.1 (Jan10) VST HQF BXD Striatum ILM6.1 (Nov07) RankInv HBP Rosen Striatum M430V2 (Apr05) MAS5 Clean HBP Rosen Striatum M430V2 (Apr05) RMA Clean HBP Rosen Striatum M430V2 (Apr05) PDNN Clean HBP Rosen Striatum M430V2 (Apr05) SScore HBP Rosen Striatum M430V2 (Apr05) RMA Orig HQF Striatum Exon (Feb09) RMA UWA Illumina Thymus (Nov08) RSN ** VCU BXD VTA Sal M430 2.0 (Jun09) RMA ** VCU BXD VTA EtOH M430 2.0 (Jun09) RMA ** VCU BXD VTA Et vs Sal M430 2.0 (Jun09) Sscore ** Calculate: Genetic Correlation, Pearson's r Genetic Correlation, Spearman's rho SGO Literature Correlation Tissue Correlation, Pearson's r Tissue Correlation, Spearman's rho Samples: BXD Only MDP Only All Cases Return: top 100 top 200 top 500 top 1000 top 2000 Interval Mapping computes linkage maps for the entire genome or single chromosomes. Use permutation and bootstrap tests to assess strength and consistency of linkage for single traits.Chromosome: All 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 X Mapping Scale: Physical Genetic Options: Permutation test Bootstrap test Marker Regression plots permutation results, lists those markers linked to trait variation, and provides access to composite mapping functions. Display LRS greater than OR display all LRS Sort by LRS Full LRS Interact Return top 50 top 100 top 200 top 500 Permutation test Pair-Scan searches for pairs of chromosomal regions that may be involved in two-locus epistatic interactions. Basic Statistics Trait Correlations Interval Mapping Marker Regression Pair-ScanTrait Data: Review the data in the edit boxes below. Scan for outliers with the help of the Basic Statistics analysis option above. Edit or delete values in the Trait Data boxes, and use the Reset option, as needed. Sample Value SE1B6D2F1 ± 2D2B6F1 ± 3BXD1 ± 4BXD2 ± 5BXD5 ± 6BXD6 ± 7BXD8 ± 8BXD9 ± 9BXD11 ± 10BXD12 ± 11BXD13 ± 12BXD14 ± 13BXD15 ± 14BXD16 ± 15BXD18 ± 16BXD19 ± 17BXD20 ± 18BXD21 ± 19BXD22 ± 20BXD23 ± 21BXD24a ± 22BXD24 ± 23BXD25 ± 24BXD27 ± 25BXD28 ± 26BXD29 ± 27BXD30 ± 28BXD31 ± 29BXD32 ± 30BXD33 ± 31BXD34 ± 32BXD35 ± 33BXD36 ± 34BXD37 ± 35BXD38 ± 36BXD39 ± 37BXD40 ± 38BXD41 ± 39BXD42 ± 40BXD43 ± 41BXD44 ± 42BXD45 ± 43BXD48 ± 44BXD49 ± 45BXD50 ± 46BXD51 ± 47BXD52 ± 48BXD53 ± 49BXD54 ± 50BXD55 ± 51BXD56 ± 52BXD59 ± 53BXD60 ± 54BXD61 ± 55BXD62 ± 56BXD63 ± 57BXD64 ± 58BXD65 ± 59BXD66 ± 60BXD67 ± 61BXD68 ± 62BXD69 ± 63BXD70 ± 64BXD71 ± 65BXD72 ± 66BXD73 ± 67BXD74 ± 68BXD75 ± 69BXD76 ± 70BXD77 ± 71BXD78 ± 72BXD79 ± 73BXD80 ± 74BXD81 ± 75BXD83 ± 76BXD84 ± 77BXD85 ± 78BXD86 ± 79BXD87 ± 80BXD88 ± 81BXD89 ± 82BXD90 ± 83BXD91 ± 84BXD92 ± 85BXD93 ± 86BXD94 ± 87BXD95 ± 88BXD96 ± 89BXD97 ± 90BXD98 ± 91BXD99 ± 92BXD100 ± 93BXD101 ± 94BXD102 ± 95BXD103 ± 1B6D2F1 ± 2D2B6F1 ± 3C57BL/6J ± 4DBA/2J ± 5129S1/SvImJ ± 6A/J ± 7AKR/J ± 8BALB/cByJ ± 9BALB/cJ ± 10C3H/HeJ ± 11C57BL/6ByJ ± 12C57BL/6J ± 13CAST/EiJ ± 14CXB1 ± 15CXB10 ± 16CXB11 ± 17CXB12 ± 18CXB13 ± 19CXB2 ± 20CXB3 ± 21CXB4 ± 22CXB5 ± 23CXB6 ± 24CXB7 ± 25CXB8 ± 26CXB9 ± 27DBA/2J ± 28KK/HIJ ± 29LG/J ± 30NOD/LtJ ± 31NZO/HlLtJ ± 32PWD/PhJ ± 33PWK/PhJ ± 34WSB/EiJ ± Use SE or Variance for Weighted RegressionOptions:By default parents and F1 data are not used in Marker Regression and Interval Mapping because their inclusion would bias permutation tests. If you want to use those data anyway, please check this box. Enable Use of Parents in the Panel:
Trait ID 1415670_at : 269753 from Hippocampus Consortium M430v2 Probe (Jun06)
Analysis Tools:
To analyze a trait, select appropriate options and one or more function buttons (Basic Statisics, Trait Correlations, Pair-Scan, etc.). New windows will open to display results and provide you access to a series of additional analysis tools. To review and edit data, scroll down to the Trait Data section.
Trait Correlations compares the values listed below with those of all other records in the database that you select to the right. You can edit values before initiating the analysis.
Interval Mapping computes linkage maps for the entire genome or single chromosomes. Use permutation and bootstrap tests to assess strength and consistency of linkage for single traits.
Marker Regression plots permutation results, lists those markers linked to trait variation, and provides access to composite mapping functions.
Pair-Scan searches for pairs of chromosomal regions that may be involved in two-locus epistatic interactions.
Trait Data:
Review the data in the edit boxes below. Scan for outliers with the help of the Basic Statistics analysis option above. Edit or delete values in the Trait Data boxes, and use the Reset option, as needed.
Options:
By default parents and F1 data are not used in Marker Regression and Interval Mapping because their inclusion would bias permutation tests. If you want to use those data anyway, please check this box.
Enable Use of Parents in the Panel: