CellKb release notes

CellKb Version 2.7
Release Date: 28 Feb 2024
  • Contents: Version 2.7 of CellKb includes 80,142 marker gene sets representing 5,326 unique cell types from 12 species collected from 1298 publications.
CellKb Version 2.6
Release Date: 7 Oct 2023
  • Contents: Version 2.6 of CellKb includes 70,963 marker gene sets representing 4,968 unique cell types from 10 species collected from 1155 publications.
CellKb Version 2.5
Release Date: 29 June 2023
  • Contents: Version 2.5 of CellKb includes 66,205 marker gene sets representing 4,685 unique cell types from 10 species collected from 1052 publications.
  • Canonical markers of cell types: Canonical markers used by authors to annotate cell types in publications are now indicated in the Results heatmap. The matching cell types in Results heatmap can be sorted by the number of matching canonical markers present in the user query.
CellKb Version 2.4
Release Date: 13 February 2023
  • Contents: Version 2.4 of CellKb includes 60,715 marker gene sets representing 4,387 unique cell types from 10 species collected from 975 publications.
CellKb Version 2.3
Release Date: 20 October 2022
  • Contents: Version 2.3 of CellKb includes 49,445 marker gene sets representing 3,479 unique cell types from 10 species collected from 882 publications.
  • Comparing marker gene sets and consensus signatures: Comparison of marker gene sets between publications, comparison of marker gene sets between diseases and tissues is now possible. Advanced features allowing users to find common genes or unique genes between conditions have been included.
CellKb Version 2.2.3
Release Date: 11 August 2022
  • Updated the CellKb Pro license. See pricing page for the latest set of features in the CellKb Pro license.
CellKb Version 2.2.2
Release Date: 15 July 2022
  • Contents: Improved ontologies and consensus, CellKb now has 2,812 unique cell types.
CellKb Version 2.2.1
Release Date: 2 June 2022
  • Contents: Version 2.2.1 of CellKb includes 37,571 marker gene sets representing 2,742 unique cell types from 10 species collected from 774 publications.
  • Exploring marker gene sets and consensus signatures: Users can now explore cell types and anatomical structures along with their consensus signatures across diseases. Comparison of consensus signatures between species and disease conditions is also available.
CellKb Version 2.2.0
Release Date: 10 February 2022
  • Contents: Version 2.2 of CellKb includes 35,149 marker gene sets representing 2,481 unique cell types from 10 species collected from 714 publications.
  • Viewing and downloading search history: In this version, we introduce the History tab in CellKb where the user search history is recorded. Users can view, download, delete or edit their search history. Viewing previous search results and searching again with a previous query is also possible.
CellKb Version 2.1.3
Release Date: 21 October 2021
  • Contents: Version 2.1.3 of CellKb includes 33,064 marker gene sets representing 2,407 unique cell types from 10 species collected from 663 publications.
CellKb Version 2.1.2
Release Date: 5 June 2021
  • Contents: Version 2.1.2 of CellKb includes 28,897 marker gene sets representing 2,215 unique cell types from 9 species collected from 576 publications.
CellKb Version 2.1.1
Release Date: 3 April 2021
  • Search: We have enhanced the search options to allow filtering search results by celltypes/anatomical structures/publications/diseases/genes/other keywords.
CellKb Version 2.1
Release Date: 21 February 2021
  • Contents: Version 2.1 of CellKb contains 610,407 protein-protein interactions from the HitPredict database.
  • Viewing interaction network of query genes: We have integrated the contents of HitPredict, a protein-protein interactions database, into CellKb. When searching for matching cell types using a gene list, users can now see an interaction network of the query gene list with the marker genes of the matching cell type. Interactions are assigned a reliability score as calculated by HitPredict.
CellKb Version 2.0.3
Release Date: 10 January 2021
  • Contents: Version 2.0.3 of CellKb includes 24,818 marker gene sets representing 2,038 unique cell types from 9 species collected from 477 publications. Cell types from Macaca mulatta were added in this version, while those from Xenopus tropicalis, Nematostella vectensis and Schmidtea mediterranea were excluded due to insufficient cell type annotations.
  • Searching consensus signatures: Starting from this version, we aggregate the database signatures by calculating a unique consensus marker gene set for each annotated cell type. This consensus signature is calculated for each cell/uberon ontology using the ranks of marker genes of each cell type associated with the ontology. We chose a weighted rank-based approach over machine learning to account for cell types having incomplete marker gene sets. Users can select the "Consensus signatures" option on the Search interface and enter one or more gene lists as input to CellKb search to find matching consensus cell type signatures. This allows rapid cell type annotation for user gene lists.
CellKb Version 2.0.2
Release Date: 30 October 2020
  • Heatmap: We have added a heatmap on the search results page to summarize the matching cell types.
CellKb Version 2.0.1
Release Date: 12 October 2020
  • Update: The terms of service for the trial license has been updated on 25th Oct 2020.
  • Contents: Version 2.01 of CellKb includes 22,528 marker gene sets representing 1,802 unique cell types from 11 species collected from 403 publications. Cell types from Macaca fascicularis were added in this version.
  • Searching multiple gene clusters in a single query: Users can give multiple gene lists as input to CellKb search to find matching cell types in one query. Users need to specify a cluster or cell type identifier for each gene list that is ranked by significance of the genes.
  • Submitting genes in any column: Users can submit the input with the genes listed in any column. CellKb no longer requires users to submit genes in the first column. Instead, it prompts the user to select the column type before submitting a search query.
CellKb Version 2.0
Release Date: 26 August 2020
  • Contents: Version 2.0 of CellKb includes 22,528 marker gene sets representing 1,802 unique cell types from 11 species collected from 403 publications. Cell types from Macaca fascicularis were added in this version.
  • Free Trial license: A trial version has been introduced, that gives access to the explore and search functionality. Search results are limited to the top 20 matching cell types. The facility to download results is not available in this license.
  • Browsing cell types: All cell types and their marker gene sets can be viewed with the browsing facility in CellKb. Users can access cell types based on categories such a species, publications, disease, anatomical structure and cell type.
  • Viewing complete marker gene sets: Users can now navigate to a cell type and see its complete marker gene set along with associated values as in the original manuscript.
  • Searching matching cell types: Users can enter a gene list, with associated values such as log fold changes and p-values, to find matching cell type marker gene sets in CellKb. Match score is calculated using a variation of the Rank Bias Overlap method.
  • Searching cell types using a keyword: Cell types can be searched for a particular species using its name, anatomical structure, disease condition, publication details, a gene from its marker set and other experimental conditions. Keyword search suggests context-sensitive keywords to users.
  • Searching cell types across species: Users can give a gene list from one species and select another species to search cell types in. During search for matching cell type, genes from the query cell type are converted to orthologous genes from the target species.
  • Selection of experiment type: Cell type search using gene lists and keywords can be limited to cell types identified in single cell and/or bulk experiments.
  • Download search results: All search results can be downloaded in a tab-delimited format.
CellKb Version 1.0
Release Date: 26 April 2020
  • Contents: Version 1.0 of CellKb includes 18,985 marker gene sets representing 1,072 unique cell types from 10 species collected from 316 publications. Most of the data is collected from cell types identified in single-cell experiments. Signatures from some bulk experiments in public databases like MSigDB and Human Protein Atlas are included in the database.
  • Searching matching cell types: Users can enter a gene list, with associated values such as log fold changes and p-values, to find matching cell type marker gene sets in CellKb. Match score is calculated using a variation of the Rank Bias Overlap method. Users can search for matching cell types from single-cell experiments and bulk experiments through separate interfaces.
  • Searching cell types using a keyword: Cell types can be searched for a particular species using its name, anatomical structure, disease condition, publication details, a gene from its marker set and other experimental conditions. Keyword search suggests context-sensitive keywords to users.
  • Searching cell types across species: Users can give a gene list from one species and select another species to search cell types in. During search for matching cell type, genes from the query cell type are converted to orthologous genes from the target species.
  • Searching consensus signatures: Consensus signatures were calculated for all unique cell types by combining the marker gene sets from multiple experiments using logistic regression. Users can search the consensus signatures using gene lists or keywords.
  • Download search results: All search results can be downloaded in a tab-delimited format.