Identification of key regulatory genes connected to NF-κB family of proteins in visceral adipose tissues using gene expression and weighted protein interaction network.

{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:31013288", "kind": "science-record", "revision": 5, "content_hash": "sha256:5117205bf1f5a3da06345818bda37cf8c8aed7e50ceafa46c50eb7ac16a275ec", "created_at": "2026-11-01T15:40:44Z", "updated_at": "2026-11-01T21:22:09Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of key regulatory genes connected to NF-κB family of proteins in visceral adipose tissues using gene expression and weighted protein interaction network.", "doi": "10.1371/journal.pone.0214337", "pmid": "31013288", "authors": ["Jamal S M Sabir", "Abdelfatteh El Omri", "Noor A Shaik", "Babajan Banaganapalli", "Majed A Al-Shaeri", "Naser A Alkenani", "Nahid H Hajrah", "Zuhier A Awan", "Houda Zrelli", "Ramu Elango", "Muhummadh Khan"], "journal": "PloS one", "year": 2019, "abstract": "Obesity is connected to the activation of chronic inflammatory pathways in both adipocytes and macrophages located in adipose tissues. The nuclear factor (NF)-κB is a central molecule involved in inflammatory pathways linked to the pathology of different complex metabolic disorders. Investigating the gene expression data in the adipose tissue would potentially unravel disease relevant gene interactions. The present study is aimed at creating a signature molecular network and at prioritizing the potential biomarkers interacting with NF-κB family of proteins in obesity using system biology approaches. The dataset GSE88837 associated with obesity was downloaded from Gene Expression Omnibus (GEO) database. Statistical analysis represented the differential expression of a total of 2650 genes in adipose tissues (p = <0.05). Using concepts like correlation, semantic similarity, and theoretical graph parameters we narrowed down genes to a network of 23 genes strongly connected with NF-κB family with higher significance. Functional enrichment analysis revealed 21 of 23 target genes of NF-κB were found to have a critical role in the pathophysiology of obesity. Interestingly, GEM and PPP1R13L were predicted as novel genes which may act as potential target or biomarkers of obesity as they occur with other 21 target genes with known obesity relationship. Our study concludes that NF-κB and prioritized target genes regulate the inflammation in adipose tissues through several molecular signaling pathways like NF-κB, PI3K-Akt, glucocorticoid receptor regulatory network, angiogenesis and cytokine pathways. This integrated system biology approaches can be applied for elucidating functional protein interaction networks of NF-κB protein family in different complex diseases. Our integrative and network-based approach for finding therapeutic targets in genomic data could accelerate the identification of novel drug targets for obesity.", "claims": [{"id": "claim-method", "statement": "Further, the identification of statistically significant differentially expressed genes (DEGs) between the normal and obese samples was performed using unpaired t-statistic.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31013288", "locator": "sections[4] \"Expression data pre-processing and normalization\" paragraph 2", "quote": "Further, the identification of statistically significant differentially expressed genes (DEGs) between the normal and obese samples was performed using unpaired t-statistic."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The gene expression dataset GSE88837 associated with obesity was downloaded from Gene Expression Omnibus (GEO) database (www.ncbi.nlm.nih.gov/geo) [26].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31013288", "locator": "sections[3] \"Collection of datasets\" paragraph 2", "quote": "The gene expression dataset GSE88837 associated with obesity was downloaded from Gene Expression Omnibus (GEO) database (www.ncbi.nlm.nih.gov/geo) [26]."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "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:31013288"], "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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