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Previous IMPC Data Release 6.0 Notes

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IMPC

  • Release: 6.0
  • Published: 10 November 2017

Statistical Package

  • PhenStat
  • Version: 2.14.0

Genome Assembly

  • Mus musculus
  • Version: GRCm38

Summary

  • Number of phenotyped genes: 4,364
  • Number of phenotyped mutant lines: 4,745
  • Number of phenotype calls: 52,461

Data access

Highlights

Data release 6.0

Release notes: Represents a major data release. Changes include:
  • > 1k additional mouse lines with new data from the IMPC consortium
  • Several changes to the statistical analysis, including:
    • Analysis includes body weight as an effect in the statistical model with the result that several hundred genotype-phenotype associations became non-significant, while the increased sensitivity added several hundred phenotypes that were not previously detected due to weight confounding the analysis
    • Several count parameters (Number of digits, Number of ribs left, Number of ribs right, Number of caudal vertebrae, Number of cervical vertebrae, Number of lumbar vertebrae, Number of pelvic vertebrae, Number of thoracic vertebrae) are now analyzed using the more appropriate Reference Range+ framework resulting in more accurate detection of phenotype
    • All Auditory Brain Stem Response parameters are analyzed using Reference Range+ framework when enough data is available, falling back to a linear mixed model (including jitter when there is no variation) when there is not enough data to establish a reference range

Data Reports

Lines and Specimens

Phenotyping Center Mutant Lines Baseline Mice Mutant Mice
JAX 920 5,742 24,912
TCP 443 5,891 19,740
HMGU 227 2,264 4,156
KMPC 24 408 510
MARC 235 1,880 3,776
MRC Harwell 449 4,341 11,359
RBRC 71 1,674 1,509
ICS 170 1,861 2,682
WTSI 1,024 3,386 16,829
BCM 403 1,207 12,839
UC Davis 779 2,651 18,163

Experimental Data and Quality Checks

188,283 *
Data Type QC passed QC failed issues
categorical 11,129,732 3,389 * 14,775 *
unidimensional 8,151,407 24,321 *
time series 12,001,974 2,393 * 0
text 143,003 11,431 * 34,141 *
image record 327,658 0 0

* Excluded from statistical analysis.

Procedures

Created with Highcharts 6.0.2Number of linesLines per procedureCenter by centerJAXTCPHMGUMRC HarwellMARCKMPCRBRCICSWTSIBCMUC DavisAcoustic Startle and Pre-pulse Inhibition (PPI)Combined SHIRPA and DysmorphologyOpen FieldRotarodFACSOrgan WeightChallenge Whole Body PlethysmographyFear ConditioningHot PlateShock ThresholdAuditory Brain Stem ResponseAdult LacZTissue Embedding and Block BankingBody WeightIndirect CalorimetryClinical ChemistryBody Composition (DEXA lean/fat)Electrocardiogram (ECG)EchoEmbryo LacZEye MorphologyGross Morphology Embryo E9.5Gross Morphology Embryo E12.5Gross Morphology Embryo E14.5-E15.5Gross Morphology Embryo E18.5Gross Morphology Placenta E9.5Gross Morphology Placenta E12.5Gross Morphology Placenta E14.5-E15.5Grip StrengthHematologyHistopathologyHeart WeightImmunophenotypingInsulin Blood LevelIntraperitoneal glucose tolerance test (IPGTT)Gross Pathology and Tissue CollectionX-rayElectroconvulsive Threshold TestingElectroretinographyElectroretinography 2Hole-board ExplorationLight-Dark TestPlasma ChemistrySleep WakeTail SuspensionUrinalysisTail Flick050010001500200025003000350040004500
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Allele Types

Mutation Name Mutant Lines
Targeted Mutation a 1134
Targeted Mutation 1 1113
Targeted Mutation b 2213
Targeted Mutation 2 5
Targeted Mutation c 2
Targeted Mutation d 2
Targeted Mutation e 74
Mouse knockout programs:

RRG305,W062C05,FLP1,mirKO,EUCJ0019c12,IST12471H5,EUCJ0004f10,W096D02,EUCJ0079d10,YHD437, RRR454,Thy1-MAPT*P301S,pT1Betageo,RRH308,KOMP,CB0226,M076C04,EUC0047a08,EUC0027g03, EUC0050e03,XG716,EUCE0233a03,IMPC,RRJ142,EUCOMM,NCOM,YTC001,XG510,EUC0054a05

Distribution of Phenotype Annotations

Created with Highcharts 6.0.2Number of genotype-phenotype associationsDistribution of Phenotype Associations in IMPChemizygoteheterozygotehomozygoteadipose tissue phenotypebehavior/neurological phenotypecardiovascular system phenotypecraniofacial phenotypedigestive/alimentary phenotypeendocrine/exocrine gland phenotypegrowth/size/body region phenotypehearing/vestibular/ear phenotypehematopoietic system phenotypehomeostasis/metabolism phenotypeimmune system phenotypeintegument phenotypelimbs/digits/tail phenotypemortality/agingmuscle phenotypereproductive system phenotyperespiratory system phenotypeskeleton phenotypevision/eye phenotypeembryo phenotypeliver/biliary system phenotypemammalian phenotypenervous system phenotypepigmentation phenotyperenal/urinary system phenotype01k2k3k4k5k6k7k8k

Status

Overall

Created with Highcharts 6.0.2Number of genesGenotyping Status696931316 5826 5823 3513 351Micro-injection in progressChimeras obtainedGenotype confirmedCre Excision StartedCre Excision Complete02.5k5k7.5k
Created with Highcharts 6.0.2Number of genesPhenotyping Status1 0421 0421901904 3344 334Phenotype Attempt RegisteredPhenotyping StartedPhenotyping Complete02k4k6k

By Center

Created with Highcharts 6.0.2Genotyping Status by Center
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Created with Highcharts 6.0.2Phenotyping Status by Center
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More charts and status information are available from iMits.

Phenotype Associations

Created with Highcharts 6.0.2Number of phenotype callsPhenotype calls per procedureCenter by centerJAXTCPHMGUMARCMRC HarwellRBRCICSWTSIBCMUC DavisCombined SHIRPA and DysmorphologyOpen FieldAcoustic Startle and Pre-pulse Inhibition (PPI)Indirect CalorimetryClinical ChemistryBody Composition (DEXA lean/fat)Electrocardiogram (ECG)EchoEye MorphologyFertility of Homozygous Knock-out MiceGrip StrengthHematologyHeart WeightIntraperitoneal glucose tolerance test (IPGTT)Viability Primary ScreenX-rayAuditory Brain Stem ResponseInsulin Blood LevelRotarodElectroconvulsive Threshold TestingHole-board ExplorationLight-Dark TestPlasma ChemistrySleep WakeTail SuspensionUrinalysisOrgan WeightChallenge Whole Body Plethysmography05001000150020002500300035004000
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Phenotype Associations Overview

We provide a 'phenome' overview of statistically significant calls. By following the links below, you'll access the details of the phenotype calls for each center.

Phenotyping Center Significant MP Calls Pipeline
JAXBrowseIMPC_001
JAXBrowseJAX_001
TCPBrowseTCP_001
HMGUBrowseIMPC_001
HMGUBrowseHMGU_001
KMPCBrowseIMPC_001
MARCBrowseIMPC_001
MRC HarwellBrowseHRWL_001
RBRCBrowseIMPC_001
WTSIBrowseMGP_001
BCMBrowseIMPC_001
BCMBrowseBCM_001
UC DavisBrowseUCD_001

Statistical Analysis

Statistical Methods

Data Statistical Method
categorical Fisher's exact test
unidimensional Wilcoxon rank sum test with continuity correction
unidimensional Mixed Model framework, generalized least squares, equation withoutWeight
unidimensional Mixed Model framework, linear mixed-effects model, equation withoutWeight

P-value distributions

Created with Highcharts 6.0.2FrequencyP-value distributionFisher's exact testFisher's exact test0.020.040.060.080.10.120.140.160.180.20.220.240.260.280.30.320.340.360.380.40.420.440.460.480.50.520.540.560.580.60.620.640.660.680.70.720.740.760.780.80.820.840.860.880.90.920.940.960.9810
Created with Highcharts 6.0.2FrequencyP-value distributionWilcoxon rank sum test with continuity correctionWilcoxon rank sum test with continuity correction0.020.040.060.080.10.120.140.160.180.20.220.240.260.280.30.320.340.360.380.40.420.440.460.480.50.520.540.560.580.60.620.640.660.680.70.720.740.760.780.80.820.840.860.880.90.920.940.960.9810
Created with Highcharts 6.0.2FrequencyP-value distributionMixed Model framework, generalized least squares, equation withoutWeightMixed Model framework, generalized least squares, equation withoutWeight0.020.040.060.080.10.120.140.160.180.20.220.240.260.280.30.320.340.360.380.40.420.440.460.480.50.520.540.560.580.60.620.640.660.680.70.720.740.760.780.80.820.840.860.880.90.920.940.960.98102505007501000125015001750200022502500275030003250
Created with Highcharts 6.0.2FrequencyP-value distributionMixed Model framework, linear mixed-effects model, equation withoutWeightMixed Model framework, linear mixed-effects model, equation withoutWeight0.020.040.060.080.10.120.140.160.180.20.220.240.260.280.30.320.340.360.380.40.420.440.460.480.50.520.540.560.580.60.620.640.660.680.70.720.740.760.780.80.820.840.860.880.90.920.940.960.98102.5k5k7.5k10k12.5k15k17.5k20k22.5k25k27.5k30k

Trends

Created with Highcharts 6.0.2Genes/Mutant LinesPhenotype CallsGenes/Mutant Lines/MP CallsRelease by ReleasePhenotyped genesPhenotyped linesMP calls1.01.12.03.03.13.23.33.44.04.24.35.06.001500300045006000015000300004500060000
Created with Highcharts 6.0.2Data pointsData pointsCategorical (QC failed)Categorical (QC passed)Categorical (issues)Image record (QC failed)Image record (QC passed)Image record (issues)Text (QC failed)Text (QC passed)Text (issues)Time series (QC failed)Time series (QC passed)Time series (issues)Unidimensional (QC failed)Unidimensional (QC passed)Unidimensional (issues)1.01.12.03.03.13.23.33.44.04.24.35.06.00250000050000007500000100000001250000015000000

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