IMPC
- Release: 3.1
- Published: 29 April 2015
Statistical Package
- PhenStat
- Version: 2.2.0
Genome Assembly
- Mus musculus
- Version: GRCm38
Summary
- Number of phenotyped genes: 1,468
- Number of phenotyped mutant lines: 1,540
- Number of phenotype calls: 5,974
Data access
- Ftp site: ftp://ftp.ebi.ac.uk/pub/databases/impc/release-3.1
- RESTful interfaces: APIs
Highlights
Data release 3.1
- Exclusion of "no data" categories when calculating significance of categorical results
- 147 more 3I lines with 257,008 more data points
- Removal of legacy data for colony HEPD0522_7_H06_10308 at the request of the production center
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 | 13 | 142 | 196 |
HMGU | 86 | 818 | 1,429 |
ICS | 65 | 675 | 1,007 |
WTSI | 434 | 1,751 | 6,380 |
JAX | 232 | 1,322 | 4,675 |
UC Davis | 273 | 883 | 6,138 |
TCP | 166 | 571 | 2,917 |
BCM | 72 | 435 | 1,487 |
Experimental Data and Quality Checks
Data Type | QC passed | QC failed | issues |
---|---|---|---|
categorical | 3,956,068 | 0 | 3,426 * |
unidimensional | 2,970,851 | 3,726 * | 39,065 * |
time series | 7,415,471 | 9 * | 77,684 * |
text | 51,611 | 18,591 * | 161 * |
image record | 107,059 | 0 | 0 |
* Excluded from statistical analysis.
Procedures
Allele Types
Mutation | Name | Mutant Lines |
---|---|---|
Targeted Mutation | 2 | 5 |
Targeted Mutation | d | 1 |
Targeted Mutation | 1 | 420 |
Targeted Mutation | e | 25 |
Targeted Mutation | b | 779 |
Targeted Mutation | c | 2 |
Targeted Mutation | a | 359 |
Mouse knockout programs: EUCOMM,KOMP,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 | 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 |