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IMPC
- Release: 4.2
- Published: 08 December 2015
Statistical Package
- PhenStat
- Version: 2.2.0
Genome Assembly
- Mus musculus
- Version: GRCm38
Summary
- Number of phenotyped genes: 2,432
- Number of phenotyped mutant lines: 2,577
- Number of phenotype calls: 13,008
Data access
- Ftp site: ftp://ftp.ebi.ac.uk/pub/databases/impc/release-4.2
- RESTful interfaces: APIs
Highlights
Data release 4.2
Release notes: Represents a minor data release. Changes include:- More final QCed data
- Corrected genetic background strain for some legacy lines
Data Reports
Lines and Specimens
| Phenotyping Center | Mutant Lines | Baseline Mice | Mutant Mice |
|---|---|---|---|
| JAX | 429 | 2,649 | 10,249 |
| NING | 93 | 985 | 1,362 |
| TCP | 254 | 3,885 | 10,582 |
| HMGU | 126 | 1,277 | 2,189 |
| MRC Harwell | 309 | 2,982 | 7,212 |
| RBRC | 32 | 968 | 696 |
| ICS | 104 | 1,038 | 1,655 |
| WTSI | 611 | 2,664 | 13,944 |
| BCM | 144 | 919 | 3,719 |
| UC Davis | 475 | 1,319 | 10,362 |
Experimental Data and Quality Checks
| Data Type | QC passed | QC failed | issues |
|---|---|---|---|
| categorical | 6,431,595 | 756 * | 4,776 * |
| unidimensional | 4,797,248 | 7,553 * | 113,998 * |
| time series | 9,138,387 | 128 * | 413 * |
| text | 89,172 | 14,643 * | 17,178 * |
| image record | 208,924 | 0 | 0 |
* Excluded from statistical analysis.
Procedures
Allele Types
| Mutation | Name | Mutant Lines |
|---|---|---|
| Targeted Mutation | a | 433 |
| Targeted Mutation | 1 | 733 |
| Targeted Mutation | b | 1327 |
| Targeted Mutation | 2 | 5 |
| Targeted Mutation | c | 2 |
| Targeted Mutation | d | 1 |
| Targeted Mutation | e | 44 |
Mouse knockout programs: KOMP,EUCOMM,NCOM,mirKO,IST12471H5
Distribution of Phenotype Annotations
Status
Overall
Phenotype Associations
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 |
|---|---|---|
| JAX | Browse | IMPC_001 |
| JAX | Browse | JAX_001 |
| NING | Browse | IMPC_001 |
| TCP | Browse | TCP_001 |
| HMGU | Browse | IMPC_001 |
| HMGU | Browse | HMGU_001 |
| MRC Harwell | Browse | HRWL_001 |
| RBRC | Browse | IMPC_001 |
| ICS | Browse | IMPC_001 |
| ICS | Browse | ICS_001 |
| WTSI | Browse | MGP_001 |
| BCM | Browse | IMPC_001 |
| BCM | Browse | BCM_001 |
| UC Davis | Browse | UCD_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 |