IMPC Release Notes

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

Data release 6.0 includes: > 1k additional mouse lines with data. This represents a major release of new data from the IMPC consortium. There are 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

Data Type QC passed QC failed issues
categorical 11,129,732 3,389 * 14,775 *
unidimensional 8,151,407 24,321 * 188,283 *
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

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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

Status

Overall

By Center

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More charts and status information are available from iMits.

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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
ICSBrowseICS_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

Trends




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