{"doi":"10.1111/jop.13329","title":"The regulatory role of\n                    <i>HOX</i>\n                    interacting lncRNA in oral cancer—An\n                    <i>in silico</i>\n                    analysis","abstract":"<jats:title>Abstract</jats:title>\n                  <jats:sec>\n                    <jats:title>Objectives</jats:title>\n                    <jats:p>\n                      We aim to elucidate the interaction of long noncoding RNAs with\n                      <jats:italic>HOX</jats:italic>\n                      genes and their regulatory role and potential drug candidates in oral cancer.\n                    </jats:p>\n                  </jats:sec>\n                  <jats:sec>\n                    <jats:title>Materials and Methods</jats:title>\n                    <jats:p>\n                      The interaction network was constructed using RNA Interactome and the RNA Interactome from the Sequencing Experiments database. The differential expression of\n                      <jats:italic>HOX</jats:italic>\n                      genes and\n                      <jats:italic>HOX</jats:italic>\n                      interacting lncRNAs was assessed using the TCGA‐Head and Neck Squamous Cell Carcinoma oral cancer dataset using DESeq2 R‐package. Further, the functional enrichment analysis was performed for the differentially expressed\n                      <jats:italic>HOX</jats:italic>\n                      genes and\n                      <jats:italic>HOX</jats:italic>\n                      ‐interacting lncRNAs using Gene Ontology, long noncoding RNA Set Enrichment Analysis, lncRNA ontology annotation extractor and repository (Lantern), and LncRNA Ontology tools. Drug‐lncRNA interaction and the effect of drugs on lncRNA expression were assessed from the D‐lnc tool.\n                    </jats:p>\n                  </jats:sec>\n                  <jats:sec>\n                    <jats:title>Results</jats:title>\n                    <jats:p>\n                      A total of 78 unique interactions were identified between\n                      <jats:italic>HOX</jats:italic>\n                      and lncRNAs. Differential expression analysis showed 27\n                      <jats:italic>HOX</jats:italic>\n                      genes and 10\n                      <jats:italic>HOX‐</jats:italic>\n                      interacting lncRNAs in oral cancer.\n                      <jats:italic>HOX</jats:italic>\n                      genes and\n                      <jats:italic>HOX‐</jats:italic>\n                      interacting lncRNAs were involved in crucial regulatory processes like cell cycle regulation, cell proliferation and migration, epithelial‐mesenchymal transition, angiogenesis, and cell signaling pathways. Cancer hallmark analysis from using long noncoding RNA Set Enrichment Analysis showed the involvement of HOTAIR, HOTTIP MIR503HG, and CDKN2B‐AS1 in proliferation, migration, and invasion. Panobinostat was the common drug that influenced the expression of HOTAIR, HOTAIRM1, HOTTIP and CDKN2B‐AS1.\n                    </jats:p>\n                  </jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions</jats:title>\n                    <jats:p>\n                      Differentially expressed\n                      <jats:italic>HOX‐</jats:italic>\n                      interacting lncRNAs are involved in various regulatory biological processes and cancer hallmark events in oral cancer.\n                    </jats:p>\n                  </jats:sec>\n                  <jats:sec>\n                    <jats:title>Clinical Relevance</jats:title>\n                    <jats:p>The creation of interaction networks may expand the existing knowledge of oral cancer signaling pathways and the discovery of novel targets.</jats:p>\n                  </jats:sec>","journal":"Journal of Oral Pathology &amp; Medicine","year":2022,"id":655378,"datarank":0.26876392038420827,"base_score":1.791759469228055,"endowment":1.791759469228055,"self_citation_contribution":0.26876392038420827,"citation_network_contribution":0.0,"self_endowment_contribution":0.26876392038420827,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":5,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":null,"is_data_producer":false,"deposit_databanks":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":null,"fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1710793,"name":"Kanaka Sai Ram Padam","orcid":"0000-0001-5983-0066","position":1,"is_corresponding":false},{"id":639077,"name":"Sanjiban Chakrabarty","orcid":"0000-0002-6018-8098","position":2,"is_corresponding":false},{"id":1710796,"name":"Naveena Kumar AN","orcid":"0000-0002-1759-1500","position":3,"is_corresponding":false},{"id":1710797,"name":"Raghu Radhakrishnan","orcid":"0000-0003-0088-4777","position":4,"is_corresponding":false},{"id":1710792,"name":"Dhanraj Salur Basavarajappa","orcid":"0000-0001-7731-0304","position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"title":"The regulatory role of\n                    <i>HOX</i>\n                    interacting lncRNA in oral cancer—An\n                    <i>in silico</i>\n                    analysis","abstract":"<jats:title>Abstract</jats:title>\n                  <jats:sec>\n                    <jats:title>Objectives</jats:title>\n                    <jats:p>\n                      We aim to elucidate the interaction of long noncoding RNAs with\n                      <jats:italic>HOX</jats:italic>\n                      genes and their regulatory role and potential drug candidates in oral cancer.\n                    </jats:p>\n                  </jats:sec>\n                  <jats:sec>\n                    <jats:title>Materials and Methods</jats:title>\n                    <jats:p>\n                      The interaction network was constructed using RNA Interactome and the RNA Interactome from the Sequencing Experiments database. The differential expression of\n                      <jats:italic>HOX</jats:italic>\n                      genes and\n                      <jats:italic>HOX</jats:italic>\n                      interacting lncRNAs was assessed using the TCGA‐Head and Neck Squamous Cell Carcinoma oral cancer dataset using DESeq2 R‐package. Further, the functional enrichment analysis was performed for the differentially expressed\n                      <jats:italic>HOX</jats:italic>\n                      genes and\n                      <jats:italic>HOX</jats:italic>\n                      ‐interacting lncRNAs using Gene Ontology, long noncoding RNA Set Enrichment Analysis, lncRNA ontology annotation extractor and repository (Lantern), and LncRNA Ontology tools. Drug‐lncRNA interaction and the effect of drugs on lncRNA expression were assessed from the D‐lnc tool.\n                    </jats:p>\n                  </jats:sec>\n                  <jats:sec>\n                    <jats:title>Results</jats:title>\n                    <jats:p>\n                      A total of 78 unique interactions were identified between\n                      <jats:italic>HOX</jats:italic>\n                      and lncRNAs. Differential expression analysis showed 27\n                      <jats:italic>HOX</jats:italic>\n                      genes and 10\n                      <jats:italic>HOX‐</jats:italic>\n                      interacting lncRNAs in oral cancer.\n                      <jats:italic>HOX</jats:italic>\n                      genes and\n                      <jats:italic>HOX‐</jats:italic>\n                      interacting lncRNAs were involved in crucial regulatory processes like cell cycle regulation, cell proliferation and migration, epithelial‐mesenchymal transition, angiogenesis, and cell signaling pathways. Cancer hallmark analysis from using long noncoding RNA Set Enrichment Analysis showed the involvement of HOTAIR, HOTTIP MIR503HG, and CDKN2B‐AS1 in proliferation, migration, and invasion. Panobinostat was the common drug that influenced the expression of HOTAIR, HOTAIRM1, HOTTIP and CDKN2B‐AS1.\n                    </jats:p>\n                  </jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions</jats:title>\n                    <jats:p>\n                      Differentially expressed\n                      <jats:italic>HOX‐</jats:italic>\n                      interacting lncRNAs are involved in various regulatory biological processes and cancer hallmark events in oral cancer.\n                    </jats:p>\n                  </jats:sec>\n                  <jats:sec>\n                    <jats:title>Clinical Relevance</jats:title>\n                    <jats:p>The creation of interaction networks may expand the existing knowledge of oral cancer signaling pathways and the discovery of novel targets.</jats:p>\n                  </jats:sec>","is_dataset_classified":null,"base_score":1.791759469228055,"endowment":1.791759469228055,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"35766359","pmcid":null,"openalex_id":"https://openalex.org/W4283721540","authors":[],"funders":[{"funder_name":"The Wellcome Trust DBT India Alliance","grant_id":"IA/CPHI/18/1/503927","title":null}],"total_grants":1,"fwci":0.4204,"citation_percentile":0.51802706,"influential_citations":0,"citation_trend":[{"year":2023,"count":2},{"year":2025,"count":3}],"oa_status":"closed","license":"http://onlinelibrary.wiley.com/termsAndConditions#vor","oa_locations":[{"url":"https://onlinelibrary.wiley.com/doi/pdf/10.1111/jop.13329","host_type":"publisher"},{"url":"https://onlinelibrary.wiley.com/doi/full-xml/10.1111/jop.13329","host_type":"publisher"},{"url":"https://doi.org/10.1111/jop.13329","host_type":"journal"},{"url":"https://pubmed.ncbi.nlm.nih.gov/35766359","host_type":"repository"}],"fields_of_study":["Cancer-related molecular mechanisms research","Head and Neck Cancer Studies","Oral Health Pathology and Treatment","Gene Expression Profiling","Gene Expression Regulation, Neoplastic","Head and Neck Neoplasms","Humans","Mouth Neoplasms","RNA, Long Noncoding"],"mesh_terms":["Head and Neck Neoplasms","Humans","Mouth Neoplasms","Gene Expression Regulation, Neoplastic","Gene Expression Profiling","RNA, Long Noncoding"],"keywords":["Hox gene","HOTAIR","Biology","Interactome","Computational biology","PRC2","Genetics","Long non-coding RNA","Gene","Epigenetics","Transcription factor","RNA","EZH2","Oral Cancer","Hox","Long Noncoding Rna","Hox-interacting Long Noncoding Rnas"],"sdg_mappings":[{"sdg_number":0,"sdg_label":"Good health and well-being"}],"linked_datasets":[],"clinical_trials":[],"software_tools":[],"database_accessions":[],"source":"live","citation_network_status":"fetched"},"created_at":"2026-08-11T10:39:46.882235Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}