{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,2]],"date-time":"2026-06-02T09:23:48Z","timestamp":1780392228155,"version":"3.54.1"},"reference-count":87,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2024,5,13]],"date-time":"2024-05-13T00:00:00Z","timestamp":1715558400000},"content-version":"vor","delay-in-days":47,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2021YFF1200900"],"award-info":[{"award-number":["2021YFF1200900"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Outbound Postdoctoral Research Grant"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,3,27]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>The complicated process of neuronal development is initiated early in life, with the genetic mechanisms governing this process yet to be fully elucidated. Single-cell RNA sequencing (scRNA-seq) is a potent instrument for pinpointing biomarkers that exhibit differential expression across various cell types and developmental stages. By employing scRNA-seq on human embryonic stem cells, we aim to identify differentially expressed genes (DEGs) crucial for early-stage neuronal development. Our focus extends beyond simply identifying DEGs. We strive to investigate the functional roles of these genes through enrichment analysis and construct gene regulatory networks to understand their interactions. Ultimately, this comprehensive approach aspires to illuminate the molecular mechanisms and transcriptional dynamics governing early human brain development. By uncovering potential links between these DEGs and intelligence, mental disorders, and neurodevelopmental disorders, we hope to shed light on human neurological health and disease. In this study, we have used scRNA-seq to identify DEGs involved in early-stage neuronal development in hESCs. The scRNA-seq data, collected on days 26 (D26) and 54 (D54), of the in vitro differentiation of hESCs to neurons were analyzed. Our analysis identified 539 DEGs between D26 and D54. Functional enrichment of those DEG biomarkers indicated that the up-regulated DEGs participated in neurogenesis, while the down-regulated DEGs were linked to synapse regulation. The Reactome pathway analysis revealed that down-regulated DEGs were involved in the interactions between proteins located in synapse pathways. We also discovered interactions between DEGs and miRNA, transcriptional factors (TFs) and DEGs, and between TF and miRNA. Our study identified 20 significant transcription factors, shedding light on early brain development genetics. The identified DEGs and gene regulatory networks are valuable resources for future research into human brain development and neurodevelopmental disorders.<\/jats:p>","DOI":"10.1093\/bib\/bbae230","type":"journal-article","created":{"date-parts":[[2024,5,13]],"date-time":"2024-05-13T09:23:35Z","timestamp":1715592215000},"source":"Crossref","is-referenced-by-count":10,"title":["Single-cell RNA-seq data analysis reveals functionally relevant biomarkers of early brain development and their regulatory footprints in human embryonic stem cells (hESCs)"],"prefix":"10.1093","volume":"25","author":[{"given":"Md","family":"Alamin","sequence":"first","affiliation":[{"name":"Shenzhen Key Laboratory of Gene Regulation and Systems Biology , Department of Biology, , Southern University of Science and Technology, Shenzhen 518055, Guangdong , China"},{"name":"School of Life Sciences , Department of Biology, , Southern University of Science and Technology, Shenzhen 518055, Guangdong , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Most","family":"Humaira Sultana","sequence":"additional","affiliation":[{"name":"Institute of Bioinformatics, Zhejiang University , Hangzhou 310058 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Isaac Adeyemi","family":"Babarinde","sequence":"additional","affiliation":[{"name":"Shenzhen Key Laboratory of Gene Regulation and Systems Biology , Department of Biology, , Southern University of Science and Technology, Shenzhen 518055, Guangdong , China"},{"name":"School of Life Sciences , Department of Biology, , Southern University of Science and Technology, Shenzhen 518055, Guangdong , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"A K M","family":"Azad","sequence":"additional","affiliation":[{"name":"Department of Mathematics and Statistics , College of Science, , Riyadh 11432 , Saudi Arabia"},{"name":"Imam Muhammad Ibn Saud Islamic University , College of Science, , Riyadh 11432 , Saudi Arabia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mohammad Ali","family":"Moni","sequence":"additional","affiliation":[{"name":"Artificial Intelligence and Cyber Futures Institute, Charles Sturt University , Bathurst, NSW 2795 , Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Haiming","family":"Xu","sequence":"additional","affiliation":[{"name":"Institute of Bioinformatics, Zhejiang University , Hangzhou 310058 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2024,5,12]]},"reference":[{"key":"2024051308511125500_ref1","doi-asserted-by":"crossref","first-page":"9362","DOI":"10.1073\/pnas.0903103106","article-title":"Potential etiologic and functional implications of genome-wide association loci for human diseases and traits","volume":"106","author":"Hindorff","year":"2009","journal-title":"Proc Natl Acad Sci U S 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