The ENCODE Imputation Challenge: a critical assessment of methods for cross-cell type imputation of epigenomic profiles.
Journal
Genome biology
ISSN: 1474-760X
Titre abrégé: Genome Biol
Pays: England
ID NLM: 100960660
Informations de publication
Date de publication:
18 04 2023
18 04 2023
Historique:
received:
30
07
2022
accepted:
24
03
2023
medline:
20
4
2023
pubmed:
19
4
2023
entrez:
19
04
2023
Statut:
epublish
Résumé
A promising alternative to comprehensively performing genomics experiments is to, instead, perform a subset of experiments and use computational methods to impute the remainder. However, identifying the best imputation methods and what measures meaningfully evaluate performance are open questions. We address these questions by comprehensively analyzing 23 methods from the ENCODE Imputation Challenge. We find that imputation evaluations are challenging and confounded by distributional shifts from differences in data collection and processing over time, the amount of available data, and redundancy among performance measures. Our analyses suggest simple steps for overcoming these issues and promising directions for more robust research.
Identifiants
pubmed: 37072822
doi: 10.1186/s13059-023-02915-y
pii: 10.1186/s13059-023-02915-y
pmc: PMC10111747
doi:
Types de publication
Journal Article
Research Support, U.S. Gov't, Non-P.H.S.
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
79Subventions
Organisme : NHGRI NIH HHS
ID : U24 HG009446
Pays : United States
Organisme : NHGRI NIH HHS
ID : R01 HG008155
Pays : United States
Organisme : NHGRI NIH HHS
ID : UM1 HG009444
Pays : United States
Organisme : NIGMS NIH HHS
ID : R35 GM124952
Pays : United States
Organisme : NHGRI NIH HHS
ID : U01 HG012069
Pays : United States
Organisme : NIGMS NIH HHS
ID : R35 GM133346
Pays : United States
Organisme : NHGRI NIH HHS
ID : T32 HG000044
Pays : United States
Organisme : NHGRI NIH HHS
ID : UM1 HG009442
Pays : United States
Organisme : NIGMS NIH HHS
ID : R35 GM134922
Pays : United States
Organisme : NHGRI NIH HHS
ID : R01 HG011466
Pays : United States
Organisme : NHGRI NIH HHS
ID : U24 HG009397
Pays : United States
Organisme : NHGRI NIH HHS
ID : UM1 HG009390
Pays : United States
Informations de copyright
© 2023. The Author(s).
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