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IMPC
- Release: 3.0
- Published: 06 February 2015
Statistical Package
- PhenStat
- Version: 2.0.1
Genome Assembly
- Mus musculus
- Version: GRCm38
Summary
- Number of phenotyped genes: 1,458
- Number of phenotyped mutant lines: 1,528
- Number of phenotype calls: 6,114
Data access
- Ftp site: ftp://ftp.ebi.ac.uk/pub/databases/impc/release-3.0
- RESTful interfaces: APIs
Highlights
Data release 3.0
Release notes:
Represents a major data release. Changes include:
- 1,456 mouse lines with phenotype data that has passed quality control. This is a marked increase since data release 2.0 and demonstrates the acceleration of data generation for the IMPC effort.
Statistical Analysis
The statistical analysis package used in data release 2.0 (PhenStat) has been updated to Version: 2.0.1.
Data Reports
Lines and Specimens
| Phenotyping Center | Mutant Lines | Baseline Mice | Mutant Mice |
|---|---|---|---|
| MRC Harwell | 186 | 2,520 | 4,191 |
| RBRC | 13 | 523 | 244 |
| NING | 6 | 142 | 98 |
| HMGU | 86 | 818 | 1,429 |
| ICS | 65 | 675 | 1,007 |
| WTSI | 434 | 1,751 | 6,380 |
| JAX | 232 | 1,322 | 4,678 |
| UC Davis | 273 | 883 | 6,320 |
| TCP | 161 | 571 | 2,824 |
| BCM | 72 | 464 | 1,487 |
Experimental Data and Quality Checks
| Data Type | QC passed | QC failed | issues |
|---|---|---|---|
| categorical | 3,935,293 | 0 | 3,426 * |
| unidimensional | 2,782,486 | 3,724 * | 38,737 * |
| time series | 7,237,320 | 9 * | 82 * |
| text | 51,283 | 18,591 * | 161 * |
| image record | 106,682 | 0 | 0 |
* Excluded from statistical analysis.
Procedures
Allele Types
| Mutation | Name | Mutant Lines |
|---|---|---|
| Targeted Mutation | 2 | 5 |
| Targeted Mutation | d | 1 |
| Targeted Mutation | 1 | 413 |
| Targeted Mutation | e | 24 |
| Targeted Mutation | b | 775 |
| Targeted Mutation | c | 2 |
| Targeted Mutation | a | 359 |
Mouse knockout programs: KOMP,EUCOMM,NCOM,IST12471H5
Distribution of Phenotype Annotations
Status
Overall
By Center
More charts and status information are available from iMits.
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 | IMPC_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 |
| 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 |