{"doi":"10.1101/2024.07.05.602230","title":"GeneSurfer Enables Transcriptome-wide Exploration and Functional Annotation of Gene Co-expression Modules in 3D Spatial Transcriptomics Data","abstract":"Gene co-expression provides crucial insights into biological functions, however, there is a lack of exploratory analysis tools for localized gene co-expression in large-scale datasets. We present GeneSurfer, an interactive interface designed to explore localized transcriptome-wide gene co-expression patterns in the 3D spatial domain. Key features of GeneSurfer include transcriptome-wide gene filtering and gene clustering based on spatial local co-expression within transcriptomically similar cells, multi-slice 3D rendering of average expression of gene clusters, and on-the-fly Gene Ontology term annotation of co-expressed gene sets. Additionally, GeneSurfer offers multiple linked views for investigating individual genes or gene co-expression in the spatial domain at each exploration stage. Demonstrating its utility with both spatial transcriptomics and single-cell RNA sequencing data from the Allen Brain Cell Atlas, GeneSurfer effectively identifies and annotates localized transcriptome-wide co-expression, providing biological insights and facilitating hypothesis generation and validation.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2024,"id":500516,"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":0.931,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2024-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1110830,"name":"Julian Thijssen","orcid":"0009-0007-7585-6451","position":1,"is_corresponding":false},{"id":983502,"name":"Thomas Kroes","orcid":"0000-0002-0658-2203","position":2,"is_corresponding":false},{"id":1349813,"name":"Ximaine van der Burg","orcid":"0009-0002-2609-4597","position":3,"is_corresponding":false},{"id":282550,"name":"Louise van der Weerd","orcid":"0000-0002-5997-2125","position":4,"is_corresponding":false},{"id":38378,"name":"Thomas Höllt","orcid":"0000-0001-8125-1650","position":5,"is_corresponding":false},{"id":37203,"name":"Boudewijn P. F. Lelieveldt","orcid":"0000-0001-8269-7603","position":6,"is_corresponding":false},{"id":1146797,"name":"Chang Li","orcid":"0000-0003-4743-0553","position":0,"is_corresponding":true}],"reference_count":24,"raw_metadata":null,"created_at":"2026-07-19T02:10:08.435215Z","pmid":"39005368","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":[]}