{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,9,14]],"date-time":"2024-09-14T11:12:57Z","timestamp":1726312377902},"reference-count":40,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2023,9,22]],"date-time":"2023-09-22T00:00:00Z","timestamp":1695340800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/pages\/standard-publication-reuse-rights"}],"funder":[{"name":"Natural Science Foundation of Guangdong Province of China","award":["2022A1515110759"]},{"name":"Guangdong Provincial Key Laboratory of Human Digital Twin","award":["2022B1212010004"]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["12271180","62172164","12322119"],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,9,22]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>The critical point or pivotal threshold of cell transition occurs in early embryonic development when cell differentiation culminates in its transition to specific cell fates, at which the cell population undergoes an abrupt and qualitative shift. Revealing such critical points of cell transitions can track cellular heterogeneity and shed light on the molecular mechanisms of cell differentiation. However, precise detection of critical state transitions proves challenging when relying on single-cell RNA sequencing data due to their inherent sparsity, noise, and heterogeneity. In this study, diverging from conventional methods like differential gene analysis or static techniques that emphasize classification of cell types, an innovative computational approach, single-cell gene association entropy (SGAE), is designed for the analysis of single-cell RNA-seq data and utilizes gene association information to reveal critical states of cell transitions. More specifically, through the translation of gene expression data into local SGAE scores, the proposed SGAE can serve as an index to quantitatively assess the resilience and critical properties of genetic regulatory networks, consequently detecting the signal of cell transitions. Analyses of five single-cell datasets for embryonic development demonstrate that the SGAE method achieves better performance in facilitating the characterization of a critical phase transition compared with other existing methods. Moreover, the SGAE value can effectively discriminate cellular heterogeneity over time and performs well in the temporal clustering of cells. Besides, biological functional analysis also indicates the effectiveness of the proposed approach.<\/jats:p>","DOI":"10.1093\/bib\/bbad366","type":"journal-article","created":{"date-parts":[[2023,10,14]],"date-time":"2023-10-14T03:19:29Z","timestamp":1697253569000},"source":"Crossref","is-referenced-by-count":3,"title":["SGAE: single-cell gene association entropy for revealing critical states of cell transitions during embryonic development"],"prefix":"10.1093","volume":"24","author":[{"given":"Jiayuan","family":"Zhong","sequence":"first","affiliation":[{"name":"Foshan University School of Mathematics and Big Data, , Foshan 528000 , China"}]},{"given":"Chongyin","family":"Han","sequence":"additional","affiliation":[{"name":"South China University of Technology School of Biology and Biological Engineering, , Guangzhou 510640 , China"}]},{"given":"Pei","family":"Chen","sequence":"additional","affiliation":[{"name":"South China University of Technology School of Mathematics, , Guangzhou 510640 , China"}]},{"given":"Rui","family":"Liu","sequence":"additional","affiliation":[{"name":"South China University of Technology School of Mathematics, , Guangzhou 510640 , China"}]}],"member":"286","published-online":{"date-parts":[[2023,10,13]]},"reference":[{"issue":"7260","key":"2023101403191472500_ref1","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1038\/nature08227","article-title":"Early-warning signals for critical transitions","volume":"461","author":"Scheffer","year":"2009","journal-title":"Nature"},{"issue":"9","key":"2023101403191472500_ref2","doi-asserted-by":"crossref","first-page":"2271","DOI":"10.1073\/pnas.1621412114","article-title":"Cell population structure prior to bifurcation predicts efficiency of directed differentiation in human induced pluripotent cells","volume":"114","author":"Bargaje","year":"2017","journal-title":"Proc Natl Acad Sci U S 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