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IMPC
- Release: 5.0
- Published: 2 August 2016
Statistical Package
- PhenStat
- Version: 2.3.3
Genome Assembly
- Mus musculus
- Version: GRCm38
Summary
- Number of phenotyped genes: 3,328
- Number of phenotyped mutant lines: 3,532
- Number of phenotype calls: 28,406
Data access
- Ftp site: ftp://ftp.ebi.ac.uk/pub/databases/impc/release-5.0
- RESTful interfaces: APIs
Highlights
Data release 5.0
Release notes:
Represents a major data release. Changes include:
- Data for an additional 1000 phenotyped lines
-
Additional control data for Grip strength procedures (protocol IMPC_GRS).
The following list of genes has had one or more phenotype associations removed:
- Abca13, Aif1l, Aldob, Alg10b, Anapc13, Arhgap23, Btbd16, Ccdc64, Ccdc94, Cdkl2, Cilp, Col14a1, Cox5b, Cyp2ab1, Cyp7b1, Dact2, Dst, Foxj3, Gstcd, Gstm4, Hip1r, Igfbp7, Il12rb1, Kcng2, Lss, Mmp15, Mogs, Nanos2, Nxn, Patl1, Podn, Psca, Rad9a, Rims3, Rps19bp1, Scarb1, Serpinf1, Skiv2l, Smo, Spata5, Spdye4b, Sptssa, Tas2r131, Wdr59
Data Reports
Lines and Specimens
| Phenotyping Center | Mutant Lines | Baseline Mice | Mutant Mice |
|---|---|---|---|
| JAX | 563 | 4,153 | 15,531 |
| NING | 157 | 1,321 | 2,337 |
| TCP | 291 | 4,692 | 12,426 |
| HMGU | 140 | 1,512 | 2,455 |
| MRC Harwell | 362 | 3,285 | 8,685 |
| RBRC | 42 | 1,217 | 972 |
| ICS | 129 | 1,306 | 1,990 |
| WTSI | 1,008 | 3,184 | 16,204 |
| BCM | 204 | 1,611 | 5,906 |
| UC Davis | 636 | 1,742 | 14,275 |
Experimental Data and Quality Checks
| Data Type | QC passed | QC failed | issues |
|---|---|---|---|
| categorical | 8,107,737 | 930 * | 10,766 * |
| unidimensional | 5,938,585 | 8,081 * | 154,942 * |
| time series | 8,772,128 | 190 * | 84,718 * |
| text | 111,319 | 14,784 * | 19,826 * |
| image record | 270,804 | 0 | 0 |
* Excluded from statistical analysis.
Procedures
Allele Types
| Mutation | Name | Mutant Lines |
|---|---|---|
| Targeted Mutation | a | 764 |
| Targeted Mutation | 1 | 921 |
| Targeted Mutation | b | 1670 |
| Targeted Mutation | 2 | 5 |
| Targeted Mutation | c | 2 |
| Targeted Mutation | d | 1 |
| Targeted Mutation | e | 52 |
Mouse knockout programs: KOMP,EUCOMM,NCOM,mirKO,IST12471H5
More charts and status information are available from iMits.
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 |