IMPC Release Notes

IMPC
  • Release: 1.1
  • Published: 26 June 2014
Statistical Package
  • PhenStat
  • Version: 1.2.0
Genome Assembly
  • Mus musculus
  • Version: GRCm38
Summary
  • Number of phenotyped genes: 470
  • Number of phenotyped mutant lines: 484
  • Number of phenotype calls: 2,732

Data access

Highlights

Phenotype Association Versioning

Many factors contribute to the identification of phenodeviants by statistical analysis. This includes the number of mutant and baseline mice, the statistical test used, the selected thresholds and changes to the underlying software that runs the analysis. For these reasons, we will be versioning genotype-to-phenotype associations from data release to data release. A given genotype-to-phenotype may change from release to release.

Statistical Tests

In general, we are applying a Fisher Exact Test for categorical data and linear regression for continuous data. In cases where there is no variability in values for a data parameter in a control or mutant mouse group, a rank sum test is applied instead of a linear regression. The statistical test used is always noted when displayed on the portal or when obtained by the API. Documentation on statistical analysis is available here: http://www.mousephenotype.org/data/documentation/statistics-help

P-value threshold

In this first release, we are using a p value threshold of ≤ 1 x10-4 for all statistical tests to make a phenotype call. This threshold may be adjusted for some parameters upon further review by statistical experts.

Clinical Blood Chemistry and Hematology

Review of PhenStat calls for clinical blood chemistry and hematology by phenotypers at WTSI suggest our current analysis maybe giving a high false positive rate. Alternative statistical approaches are being considered. We suggest looking at the underlying data that supports a phenotype association if it's critical to your research.

Data Reports

Lines and Specimens

Phenotyping Center Mutant Lines Baseline Mice Mutant Mice
MRC Harwell 47 1,945 1,122
HMGU 13 365 194
ICS 15 375 234
WTSI 301 1,469 4,463
JAX 18 1,004 514
UC Davis 37 1,018 807
TCP 49 288 987
BCM 5 224 121

Experimental Data and Quality Checks

Data Type QC passed QC failed issues
categorical 958,957 0 1,214 *
unidimensional 1,011,637 1,443 * 5,286 *
time series 1,451,844 13,176 * 83 *
text 12,803 0 0
image record 5,623 0 0

* Excluded from statistical analysis.

Procedures

Allele Types

Mutation Name Mutant Lines
Targeted Mutation 2 2
Targeted Mutation 1 63
Targeted Mutation e 17
Targeted Mutation b 139
Targeted Mutation a 263

Mouse knockout programs: EUCOMM,KOMP

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
MRC HarwellBrowseHRWL_001
HMGUBrowseIMPC_001
HMGUBrowseHMGU_001
ICSBrowseICS_001
ICSBrowseIMPC_001
WTSIBrowseMGP_001
JAXBrowseJAX_001
UC DavisBrowseUCD_001
TCPBrowseTCP_001
BCMBrowseIMPC_001

Statistical Analysis

Statistical Methods

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

P-value distributions

Trends

Previous Releases