{"doi":"10.1101/2022.03.09.483487","title":"Dynamic Network Curvature Analysis of RNA-Seq Data in Sarcoma","abstract":"Abstract In this work, we utilized network features of cancer gene interactomes to cluster pediatric sarcoma tumors and identify candidate therapeutic targets in an unsupervised manner. RNA-Seq data were mapped to protein-level interactomes to construct weighted networks for mathematical analysis. We employed a geometric approach centered on a discrete notion of curvature, which provides a measure of the functional association between genes in the context of their connectivity. Specifically, we adopted a recently proposed dynamic extension of graph curvature to extract features of the non-Euclidean, multiscale structure of genomic networks. We propose a hierarchical clustering approach to reveal preferential gene clustering according to their geometric cooperation which captured the characteristic EWSR1-FLI1 fusion in Ewing sarcoma. We also performed in silico edge perturbations to assess systemic response to simulated interventions quantified by changes in curvature. These results demonstrate that geometric network-based features can be useful for identifying non-trivial gene associations in an agnostic manner.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2022,"id":306696,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":0,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9304,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2022-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":307645,"name":"Jung Hun Oh","orcid":"0000-0001-8791-2755","position":1,"is_corresponding":false},{"id":574850,"name":"Filemon S. Dela Cruz","orcid":"0000-0002-8356-5191","position":2,"is_corresponding":false},{"id":87007,"name":"Joseph O. Deasy","orcid":"0000-0002-9437-266X","position":3,"is_corresponding":false},{"id":327025,"name":"Andrew L. Kung","orcid":"0000-0002-9091-488X","position":4,"is_corresponding":false},{"id":268388,"name":"Allen Tannenbaum","orcid":"0000-0002-0567-5256","position":5,"is_corresponding":false},{"id":268381,"name":"Rena Elkin","orcid":"0000-0003-2435-3399","position":0,"is_corresponding":true}],"reference_count":32,"raw_metadata":null,"created_at":"2026-07-19T00:32:52.703737Z","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":[]}