An Integrated Bioinformatics Approach to Identify Network-Derived Hub Genes in Starving Zebrafish.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36230465", "kind": "science-record", "revision": 4, "content_hash": "sha256:a7a35da6593609b9cc2e13bf9892a5d85f5ebc5a1fa16e19719375ca384b7155", "created_at": "2026-11-01T18:15:35Z", "updated_at": "2026-11-01T22:07:49Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "An Integrated Bioinformatics Approach to Identify Network-Derived Hub Genes in Starving Zebrafish.", "doi": "10.3390/ani12192724", "pmid": "36230465", "authors": ["Amin Mortazavi", "Mostafa Ghaderi-Zefrehei", "Mustafa Muhaghegh Dolatabady", "Mahdi Golshan", "Sajad Nazari", "Ayeh Sadat Sadr", "Saeid Kadkhodaei", "Ikhide G Imumorin", "Sunday O Peters", "Jacqueline Smith"], "journal": "Animals : an open access journal from MDPI", "year": 2022, "abstract": "The present study was aimed at identifying causative hub genes within modules formed by co-expression and protein-protein interaction (PPI) networks, followed by Bayesian network (BN) construction in the liver transcriptome of starved zebrafish. To this end, the GSE11107 and GSE112272 datasets from the GEO databases were downloaded and meta-analyzed using the MetaDE package, an add-on R package. Differentially expressed genes (DEGs) were identified based upon expression intensity N(µ = 0.2, σ2 = 0.4). Reconstruction of BNs was performed by the bnlearn R package on genes within modules using STRINGdb and CEMiTool. ndufs5 (shared among PPI, BN and COEX), rps26, rpl10, sdhc (shared between PPI and BN), ndufa6, ndufa10, ndufb8 (shared between PPI and COEX), skp1, atp5h, ndufb10, rpl5b, zgc:193613, zgc:123327, zgc:123178, wu:fc58f10, zgc:111986, wu:fc37b12, taldo1, wu:fb62f08, zgc:64133 and acp5a (shared between COEX and BN) were identified as causative hub genes affecting gene expression in the liver of starving zebrafish. Future work will shed light on using integrative analyses of miRNA and DNA microarrays simultaneously, and performing in silico and experimental validation of these hub-causative (CST) genes affecting starvation in zebrafish.", "claims": [{"id": "claim-method", "statement": "The Random Effect Model (REM) method of MetaDE with FDR < 0.01 was used to integrate related samples from GSE11107 and GSE112272 datasets [39].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36230465", "locator": "sections[3] \"2.1. Data and Methods\" paragraph 3", "quote": "The Random Effect Model (REM) method of MetaDE with FDR < 0.01 was used to integrate related samples from GSE11107 and GSE112272 datasets [39]."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data that support the findings of this article are available from GEO database of the NCBI with accession number GSE11107 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE11107 (accessed on 9 April 2018)) and GSE112272 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi (accessed on 23 March 2018)).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36230465", "locator": "sections[19] \"notes\" paragraph 1", "quote": "The data that support the findings of this article are available from GEO database of the NCBI with accession number GSE11107 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE11107 (accessed on 9 April 2018)) and GSE112272 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi (accessed on 23 March 2018))."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Meta-analysis of two GEO microarray datasets followed by co-expression, protein–protein interaction, and Bayesian network reconstruction identified causative hub genes associated with starvation in the zebrafish liver.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:36230465", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "Differentially expressed genes (DEGs) were identified based upon expression intensity N(µ = 0.2, σ2 = 0.4)."}, {"asset": "source:pmid:36230465", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "Reconstruction of BNs was performed by the bnlearn R package on genes within modules using STRINGdb and CEMiTool."}, {"asset": "source:pmid:36230465", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "ndufs5 (shared among PPI, BN and COEX), rps26, rpl10, sdhc (shared between PPI and BN), ndufa6, ndufa10, ndufb8 (shared between PPI and COEX), skp1, atp5h, ndufb10, rpl5b, zgc:193613, zgc:123327, zgc:123178, wu:fc58f10, zgc:111986, wu:fc37b12, taldo1, wu:fb62f08, zgc:64133 and acp5a (shared between COEX and BN) were identified as causative hub genes affecting gene expression in the liver of starving zebrafish."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Meta-analysis of two GEO microarray datasets followed by co-expression, protein–protein interaction, and Bayesian network reconstruction identified causative hub genes associated with starvation in the zebrafish liver.", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:36230465"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. 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