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Previous IMPC Data Release 10.1 Notes

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IMPC

  • Release: 10.1
  • Published: 26 June 2019

Statistical Package

  • PhenStat
  • Version: 2.20.0

Genome Assembly

  • Mus musculus
  • Version: GRCm38

Summary

  • Number of phenotyped genes: 5,861
  • Number of phenotyped mutant lines: 6,255
  • Number of phenotype calls: 70,692

Data access

Highlights

Data release 10.1

Release notes: Represents a minor data release. Changes include:
  • Includes additional Acoustic Startle and Pre-pulse Inhibition (PPI) derived parameters for % Pre-pulse inhibition - Global. The formula was updated to relax derivation requirements. Specifically the update allows derivations to be calculated using 3 % PPI parameters rather than requiring all 4.
  • Updates to automated methods of detecting anomolous or missing data resulted in some extraneous datapoints being removed.
  • The embryonic day associated to Viability E14.5-E15.5 Secondary Screen was updated from E14.5 to E15.5
  • The process for generating genotype to phenotype associations for categorical parameters has been changed. A phenotpye call is made in the case where the data analysis for each individual sex is not significant, but analysis using the combined data from both sexes is significant.
  • Fixed issue analyzing Combined retina parameter resulting in more phenotype calls.

Data Reports

Lines and Specimens

Phenotyping Center Mutant Lines Baseline Mice Mutant Mice
JAX 1,226 8,413 35,252
TCP 546 7,104 24,892
HMGU 311 3,173 5,770
KMPC 43 869 1,067
MARC 232 1,877 3,776
MRC Harwell 596 5,893 15,626
RBRC 96 2,023 1,859
ICS 223 2,325 3,554
WTSI 1,329 4,540 21,316
BCM 597 4,572 17,476
UC Davis 1,056 4,156 23,749

Experimental Data and Quality Checks

Data Type QC passed QC failed issues
categorical 14,917,864 3,835 * 16,974 *
unidimensional 11,116,529 43,508 * 293,835 *
time series 13,444,019 2,615 * 11 *
text 192,175 11,124 * 45,751 *
image record 469,960 0 0

* Excluded from statistical analysis.

Distribution of Phenotype Annotations

Created with Highcharts 6.0.3Number of genotype-phenotype associationsChart context menuDistribution of Phenotype Associations in IMPChemizygoteheterozygotehomozygoteadipose tissue phenotypebehavior/neurological phenotypecardiovascular system phenotypecraniofacial phenotypedigestive/alimentary phenotypeembryo phenotypeendocrine/exocrine gland phenotypegrowth/size/body region phenotypehearing/vestibular/ear phenotypehematopoietic system phenotypehomeostasis/metabolism phenotypeimmune system phenotypeintegument phenotypelimbs/digits/tail phenotypemortality/agingmuscle phenotypenervous system phenotyperenal/urinary system phenotypereproductive system phenotyperespiratory system phenotypeskeleton phenotypevision/eye phenotypeliver/biliary system phenotypemammalian phenotypepigmentation phenotype01k2k3k4k5k6k7k8k

Status

Overall

Created with Highcharts 6.0.3Number of genesChart context menuGenotyping Status313145455 0775 0773 5073 507Micro-injection in progressChimeras obtainedGenotype confirmedCre Excision Complete02k4k6k
Created with Highcharts 6.0.3Number of genesChart context menuPhenotyping Status8848846976976 1476 147Phenotype Attempt RegisteredPhenotyping StartedPhenotyping Complete02k4k6k8k

By Center

Created with Highcharts 6.0.3Number of GenesChart context menuGenotyping Status by CenterJAXTCPMonterotondoVETMEDUNIHarwellMonterotondo R&DSEATMARCOuluBCMCDTAHMGUCAM-SU GRCCCP-IMGCIPHECNBKMPCUCDICSWTSINARLabsRIKEN BRCMonashMicro-injection in progressChimeras obtainedGenotype confirmedCre Excision Complete01k2k3k4k5k6k
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Created with Highcharts 6.0.3Number of GenesChart context menuPhenotyping Status by CenterJAXTCPMonterotondoHarwellSEATMARCBCMCDTAHMGUCCP-IMGCIPHEKMPCUCDICSWTSIRIKEN BRCPhenotype Attempt RegisteredPhenotyping StartedPhenotyping Complete01k2k3k4k5k6k7k8k
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More charts and status information are available from iMits.

Phenotype Associations

Created with Highcharts 6.0.3Number of phenotype callsChart context menuPhenotype calls per procedureCenter by center88192193197111234115511359951091711121314151619360484112221233451266712881299202223242526282913037325213313437725613813993530313233343537383914326538614430126814878840444647151274276431552433159439714505152535657581651661672883264483286061636667453103997470717374757879189223103620105801098283845088687BCM_CSD_001BCM_OFD_001IMPC_ACS_003IMPC_CAL_003IMPC_CBC_003IMPC_CSD_003IMPC_DXA_001IMPC_ECG_002IMPC_ECH_001IMPC_EYE_001IMPC_FER_001IMPC_GRS_001IMPC_HEM_002IMPC_HWT_001IMPC_LDT_001IMPC_OFD_001IMPC_OWT_001IMPC_VIA_001IMPC_XRY_001IMPC_ABR_002IMPC_CBC_002IMPC_CSD_002IMPC_ECG_001IMPC_INS_002IMPC_IPG_001ICS_ROT_001IMPC_ACS_002IMPC_CSD_001IMPC_EYE_002IMPC_HEM_001IMPC_INS_003JAX_ECT_001JAX_HBD_001JAX_LDT_001JAX_PLC_001JAX_ROT_001JAX_SLW_001JAX_TLS_001JAX_URI_001HRWL_OWT_001IMPC_ABR_001IMPC_CAL_002IMPC_FEA_001TCP_CHL_003IMPC_CBC_001MGP_CSD_001MGP_IPG_001MGP_MTB_001MGP_XRY_0010200400600800100012001400
IMPC_CBC_002
88: 0 calls
192: 0 calls
193: 0 calls
197: 0 calls
111: 0 calls
234: 0 calls
115: 0 calls
511: 0 calls
359: 0 calls
95: 0 calls
10: 0 calls
917: 0 calls
11: 0 calls
12: 0 calls
13: 0 calls
14: 0 calls
15: 0 calls
16: 0 calls
19: 0 calls
360: 0 calls
484: 0 calls
1: 135 calls
122: 0 calls
2: 0 calls
123: 0 calls
3: 0 calls
4: 0 calls
5: 0 calls
126: 0 calls
6: 0 calls
7: 0 calls
128: 0 calls
8: 0 calls
129: 0 calls
9: 0 calls
20: 0 calls
22: 0 calls
23: 0 calls
24: 0 calls
25: 0 calls
26: 0 calls
28: 0 calls
29: 43 calls
130: 0 calls
373: 0 calls
252: 0 calls
133: 0 calls
134: 0 calls
377: 0 calls
256: 0 calls
138: 0 calls
139: 0 calls
935: 0 calls
30: 0 calls
31: 0 calls
32: 0 calls
33: 0 calls
34: 0 calls
35: 0 calls
37: 0 calls
38: 0 calls
39: 0 calls
143: 0 calls
265: 0 calls
386: 0 calls
144: 0 calls
301: 0 calls
268: 0 calls
148: 0 calls
788: 0 calls
40: 0 calls
44: 0 calls
46: 0 calls
47: 0 calls
151: 0 calls
274: 0 calls
276: 0 calls
431: 119 calls
552: 0 calls
433: 0 calls
159: 0 calls
439: 0 calls
714: 0 calls
50: 0 calls
51: 0 calls
52: 0 calls
53: 0 calls
56: 0 calls
57: 0 calls
58: 0 calls
165: 0 calls
166: 0 calls
167: 0 calls
288: 0 calls
326: 0 calls
448: 0 calls
328: 0 calls
60: 0 calls
61: 0 calls
63: 0 calls
66: 0 calls
67: 0 calls
453: 0 calls
1039: 0 calls
974: 0 calls
70: 0 calls
71: 0 calls
73: 0 calls
74: 0 calls
75: 0 calls
78: 0 calls
79: 0 calls
189: 0 calls
223: 23 calls
103: 0 calls
620: 0 calls
105: 0 calls
80: 0 calls
109: 0 calls
82: 0 calls
83: 0 calls
84: 0 calls
508: 0 calls
86: 0 calls
87: 0 calls
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Trends

Created with Highcharts 6.0.3Genes/Mutant LinesPhenotype CallsChart context menuGenes/Mutant Lines/MP CallsRelease by ReleasePhenotyped genesPhenotyped linesMP calls1.01.12.03.03.13.23.33.44.04.24.35.06.06.17.08.09.19.210.010.1020004000600080000200004000060000800004.2● Phenotyped genes: 2 432 genes● Phenotyped lines: 2 577 lines● MP calls: 13 008 calls
Created with Highcharts 6.0.3Data pointsChart context menuData pointsCategorical (QC failed)Categorical (QC passed)Categorical (issues)Image record (QC failed)Image record (QC passed)Image record (issues)Text (QC failed)Text (QC passed)Text (issues)Time series (QC failed)Time series (QC passed)Time series (issues)Unidimensional (QC failed)Unidimensional (QC passed)Unidimensional (issues)1.01.12.03.03.13.23.33.44.04.24.35.06.06.17.08.09.19.210.010.105000000100000001500000020000000
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