About: Identifying key genes associated with Hirschsprung’s disease based on bioinformatics analysis of RNA-sequencing data

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About: Identifying key genes associated with Hirschsprung’s disease based on bioinformatics analysis of RNA-sequencing data Goto Sponge NotDistinct Permalink

An Entity of Type : schema:ScholarlyArticle, within Data Space : covidontheweb.inria.fr associated with source document(s)

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type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	Identifying key genes associated with Hirschsprung’s disease based on bioinformatics analysis of RNA-sequencing data
Creator	Li, Peng Yu, Hui Gao, Ya Ge, Xin Pan, Wei-Kang Xie, Chong Zhang, Ya-Fei Zheng, Bai-Jun
Source	PMC
abstract	BACKGROUND: Hirschsprung’s disease (HSCR) is a type of megacolon induced by deficiency or dysfunction of ganglion cells in the distal intestine and is associated with developmental disorders of the enteric nervous system. To explore the mechanisms of HSCR, we analyzed the RNA-sequencing data of the expansion and the narrow segments of colon tissues separated from children with HSCR. METHODS: RNA-sequencing of the expansion segments and the narrow segments of colon tissues isolated from children with HSCR was performed. After differentially expressed genes (DEGs) were identified using the edgeR package in R, functional and pathway enrichment analyses of DEGs were carried out using DAVID software. To further screen the key genes, protein-protein interaction (PPI) network and module analyses were conducted separately using Cytoscape software. RESULTS: A total of 117 DEGs were identified in the expansion segment samples, including 47 up-regulated and 70 down-regulated genes. Functional enrichment analysis suggested that FOS and DUSP1 were implicated in response to endogenous stimulus. In the PPI network analysis, FOS (degree=20), EGR1 (degree=16), ATF3 (degree=9), NOS1 (degree=8), CCL5 (degree=8), DUSP1 (degree=7), CXCL3 (degree=6), VIP (degree=6), FOSB (degree=5), and NOS2 (degree=4) had higher degrees, which could interact with other genes. In addition, two significant modules (module 1 and module 2) were identified from the PPI network. CONCLUSIONS: Several genes (including FOS, EGR1, ATF3, NOS1, CCL5, DUSP1, CXCL3, VIP, FOSB, and NOS2) might be involved in the development of HSCR through their effect on the nervous system.
has issue date	2017-01-25(xsd:dateTime)
bibo:doi	10.1007/s12519-017-0002-0
bibo:pmid	28120235
has license	no-cc
sha1sum (hex)	364cead576f72be17ef8bf8da931dfdca2aed5c6
schema:url	https://doi.org/10.1007/s12519-017-0002-0
resource representing a document's title	Identifying key genes associated with Hirschsprung’s disease based on bioinformatics analysis of RNA-sequencing data
has PubMed Central identifier	PMC7091079
has PubMed identifier	28120235
schema:publication	World J Pediatr
resource representing a document's body	covid:364cead576f72be17ef8bf8da931dfdca2aed5c6#body_text
is schema:about of	named entity 'HSCR' named entity 'mechanisms' named entity 'segments' named entity 'DYSFUNCTION' named entity 'NARROW' named entity 'HSCR' named entity 'MEGACOLON' named entity 'DATA' named entity 'ENTERIC NERVOUS SYSTEM' named entity 'DISEASE' named entity 'DEVELOPMENTAL DISORDERS' named entity 'ANALYZED' named entity 'ASSOCIATED WITH' named entity 'INDUCED' named entity 'IS A' named entity 'GANGLION CELLS' named entity 'EXPANSION' named entity 'SEQUENCING DATA' named entity '27S' named entity 'IDENTIFYING' named entity 'BACKGROUND' named entity 'CHILDREN' named entity 'COLON' covid:arg/364cead576f72be17ef8bf8da931dfdca2aed5c6 named entity 'RNA-SEQUENCING' named entity 'BIOINFORMATICS ANALYSIS' named entity 'KEY' named entity 'DISEASE' named entity 'BASED' named entity 'GENES' named entity 'ASSOCIATED WITH' named entity 'MECHANISMS' named entity 'SEGMENTS' named entity '27S' named entity 'TYPE' named entity 'TISSUES' named entity 'DISTAL INTESTINE' named entity 'INVOLVED' named entity 'SEPARATED FROM' named entity 'developmental disorders' named entity 'genes' named entity 'distal intestine' named entity 'ENS' named entity 'signal transduction' named entity 'CCL5' named entity 'EDNRB' named entity 'CCL5' named entity 'CCL5' named entity 'transcription factors' named entity 'ligand' named entity 'Nitric oxide' named entity 'CXC chemokine' named entity 'large intestine' named entity 'SRY' named entity 'mucosal' named entity 'somatic mutation' named entity 'San Diego' named entity 'endothelin 3' named entity 'nitric oxide' named entity 'up-regulated' named entity 'enrichment analyses' named entity 'NOS1' named entity 'abdominal distention' named entity 'RNA' named entity 'locus' named entity 'PPI' named entity 'enteric ganglia' named entity 'endothelin receptor type B' named entity 'NOS2' named entity 'Invitrogen' named entity 'CCL5' named entity 'CNS' named entity 'neurite' named entity 'endogenous'

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