News:Cellosaurus release 38 is available
0
0
Entering edit mode
5 months ago
Amos Bairoch ▴ 110

Cellosaurus release 38 is available on the ExPASy server:

https://web.expasy.org/cellosaurus/

1) Statistics

  • 128806 cell lines (96820 human, 21791 mouse, 2444 rat)
  • 712 species represented
  • 91983 synonyms
  • 385950 cross-references to 94 ontologies, databases, catalogs, etc.
  • 132166 references to 21875 distinct publications (papers, patents, theses, etc.)
  • 13447 web links
  • 7758 human, mouse and dog cell lines with STR profiles (from 613 distinct sources)

Since release 37 of January 2021: 2307 entries were created and 31156 entries were updated

2) Changes in the CC "Sequence variation" lines

These lines have been completely structured, contains cross-references to HGNC, MGI, RGD, UniProtKB and to VGNC to indicate the variation target gene and to ClinVar or dbSNP when the variation is described in one of these resources.

In addition the "Sequence variation" topic now has 4 subtopics:

  1. Gene amplification
  2. Gene deletion
  3. Gene fusion
  4. Mutation

Format:

Sequence variation: Gene amplification; Resource_abbrev; %s; Gene_name; Duplication|Triplication; Zygosity=Zyg_value [; Note=Free_text] (Sources).
Sequence variation: Gene deletion; Resource_abbrev; %s; Gene_name; Zygosity=Zyg_value [; Note=Free_text] (Sources). 
Sequence variation: Gene fusion; Resource_abbrev; %s; Gene_name + Resource_abbrev; %s; Gene_name; Names(s)=Name1[, Name2][, NameX] [; Note=Free_text] (Sources).
Sequence variation: Mutation; Resource_abbrev; %s; Gene_name; Mutation_type; Mutation_description [; ClinVar=%s|dbSNP=%s]; Zygosity=Zyg_value [; Note=Free_text] (Sources).

Where:

Resource_abbrev is one of: HGNC|MGI|RGD|UniProtKB|VGNC
Mutation_type is one of: Simple|Simple_corrected|Simple_edited|Repeat_expansion|Repeat_expansion_corrected|Unexplicit|Unexplicit_corrected|None_reported
Mutation_description is: the description of the mutation using, when possible the HGVS nomenclature.
Zyg_value is one of: Hemizygous|Heteroplasmic|Heterozygous|Homoplasmic|Homozygous|Mosaic|Unspecified|-

Examples:

Sequence variation: Gene amplification; HGNC; 11138; SNCA; Triplication; Zygosity=Heterozygous (Coriell).
Sequence variation: Gene amplification; HGNC; 1960; CHRNA7; Duplication; Zygosity=Unspecified; Note=15q13.3 interstitial duplication (PubMed=30218896).
Sequence variation: Gene deletion; HGNC; 7765; NF1; Zygosity=Heterozygous; Note=Somatic LOH (PubMed=27617404).
Sequence variation: Gene deletion; MGI; MGI:104738; Cdkn2a; Zygosity=Homozygous (PubMed=28577549).
Sequence variation: Gene fusion; HGNC; 76; ABL1 + HGNC; 1014; BCR; Name(s)=BCR-ABL1, BCR-ABL (PubMed=10071072).
Sequence variation: Gene fusion; HGNC; 3508; EWSR1 + HGNC; 3749; FLI1; Name(s)=EWSR1-FLI1, EWS-FLI1; Note=Type 4 fusion (Ex10/Ex5) (PubMed=9738976).
Sequence variation: Mutation; HGNC; 11998; TP53; Simple; p.Tyr220Cys (c.659A>G); ClinVar=VCV000127819; Zygosity=Homozygous (PubMed=17260012; PubMed=21156289; PubMed=23851445; CCLE; Cosmic-CLP).
Sequence variation: Mutation; MGI; MGI:1913975; Lrrk2; Simple_edited; p.Thr1348Asn (c.4043A>C); Zygosity=Homozygous; Note=By ZFN (ATCC).
Sequence variation: Mutation; HGNC; 28337; C9orf72; Repeat_expansion; c.-45+163GGGGCC[>24] (GGGGCC repeat expansion); ClinVar=VCV000031151; Zygosity=Unspecified (PubMed=24704492).

Note that in this release the XML format file has not yet been modified to accomodate these changes and the sequence variation information is in the structured string format described above. We will make the changes to the XML format for the next release.

3) Changes in the DR lines

Cross-references were added to the PerkinElmer cell line collection. Up to now we provided web links to the product description pages but having found a way to use the PerkinElmer catalog number we have converted these links to cross-references.

Example: DR PerkinElmer; BW119262

news cell_line knowledgebase database • 185 views
ADD COMMENT

Login before adding your answer.

Traffic: 2505 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6