Identification of differentially expressed genes and signaling pathways in human conjunctiva and reproductive tract infected with Chlamydia trachomatis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33875006", "kind": "science-record", "revision": 8, "content_hash": "sha256:6e29e94958b4ba1f567909b6230a299887f50b3eea5760318d8d0165d0c27d4f", "created_at": "2026-11-01T15:41:33Z", "updated_at": "2026-11-01T22:46:33Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of differentially expressed genes and signaling pathways in human conjunctiva and reproductive tract infected with Chlamydia trachomatis.", "doi": "10.1186/s40246-021-00313-8", "pmid": "33875006", "authors": ["Guo-Dong Zhu", "Xun-Jie Cao", "Ya-Ping Li", "Jia-Xin Li", "Zi-Jian Leng", "Li-Min Xie", "Xu-Guang Guo"], "journal": "Human genomics", "year": 2021, "abstract": "BACKGROUND: Currently, Chlamydia trachomatis-specific host defense mechanisms in humans remain poorly defined. To study the characteristics of host cells infected early with Chlamydia trachomatis, we used bioinformatics methods to analyze the RNA transcription profiles of the conjunctiva, fallopian tubes, and endometrium in humans infected with Chlamydia trachomatis.\nMETHOD: The gene expression profiles of GSE20430, GSE20436, GSE26692, and GSE41075 were downloaded from the Gene Expression Synthesis (GEO) database. Then, we obtained the differentially expressed genes (DEGs) through the R 4.0.1 software. STRING was used to construct protein-protein interaction (PPI) networks; then, the Cytoscape 3.7.2 software was used to visualize the PPI and screen hub genes. GraphPad Prism 8.0 software was used to verify the expression of the hub gene. In addition, the gene-miRNA interaction was constructed on the NetworkAnalyst 3.0 platform using the miRTarBase v8.0 database.\nRESULTS: A total of 600 and 135 DEGs were screened out in the conjunctival infection group and the reproductive tract infection group, respectively. After constructing a PPI network and verifying the hub genes, CSF2, CD40, and CSF3 in the reproductive tract infection group proved to have considerable statistical significance.\nCONCLUSION: In our research, the key genes in the biological process of reproductive tract infection with Chlamydia trachomatis were clarified through bioinformatics analysis. These hub genes may be further used in clinical treatment and clinical diagnosis.", "claims": [{"id": "claim-method", "statement": "Then, the limma package was applied to identify the differentially expressed genes (DEGs).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33875006", "locator": "sections[4] \"Data processing and identification of DEGs\" paragraph 2", "quote": "Then, the limma package was applied to identify the differentially expressed genes (DEGs)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33875006", "locator": "sections[23] \"notes\" paragraph 1", "quote": "The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request."}], "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:33875006"], "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. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE20430"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE20430"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:33875006", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s40246-021-00313-8", "sha256": "sha256:f02938ff4a8043f461676dc7da8077eed4c95affac9032ac6a8ea490a1e7801b", "bytes": 23390, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s40246-021-00313-8", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8056519", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE20430", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE20430", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE20430", "version": null, "note": "The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM512409", "GSM512410", "GSM512411", "GSM512412", "GSM512413", "GSM512414", "GSM512415", "GSM512416", "GSM512417", "GSM512418", "GSM512419", "GSM512420", "GSM512421", "GSM512422", "GSM512423", "GSM512424", "GSM512425", "GSM512426", "GSM512427", "GSM512428", "GSM512429", "GSM512430", "GSM512431", "GSM512432", "GSM512433", "GSM512434", "GSM512435", "GSM512436", "GSM512437"], "sample_count": 29, "group_sizes": null, "group_sizes_basis": null, "platform": "201", "taxon": "Homo sapiens", "title": "Expression data from Gambian children with and without the clinical signs of active trachoma: HG-focus array", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE20436", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE20436", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE20436", "version": null, "note": "The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM512479", "GSM512480", "GSM512481", "GSM512482", "GSM512483", "GSM512484", "GSM512485", "GSM512486", "GSM512487", "GSM512488", "GSM512489", "GSM512490", "GSM512491", "GSM512492", "GSM512493", "GSM512494", "GSM512495", "GSM512496", "GSM512497", "GSM512498", "GSM512499", "GSM512500", "GSM512501", "GSM512502", "GSM512503", "GSM512504", "GSM512505", "GSM512506", "GSM512507", "GSM512508", "GSM512509", "GSM512510", "GSM512511", "GSM512512", "GSM512513", "GSM512514", "GSM512515", "GSM512516", "GSM512517", "GSM512518", "GSM512519", "GSM512520", "GSM512521", "GSM512522", "GSM512523", "GSM512524", "GSM512525", "GSM512526", "GSM512527", "GSM512528", "GSM512529", "GSM512530", "GSM512531", "GSM512532", "GSM512533", "GSM512534", "GSM512535", "GSM512536", "GSM512537", "GSM512538"], "sample_count": 60, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Expression data from Gambian children with and without the clinical signs of active trachoma: U133 Plus2.0 array", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE26692", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE26692", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE26692", "version": null, "note": "The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM657128", "GSM657129", "GSM657130", "GSM657131", "GSM657132", "GSM657133", "GSM657134", "GSM657135"], "sample_count": 8, "group_sizes": null, "group_sizes_basis": null, "platform": "4133", "taxon": "Homo sapiens", "title": "Chlamydia trachomatis serogroup D disturbs epithelial tissue homeostasis in Fallopian tubes via paracrine Wnt signalling", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE41075", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE41075", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE41075", "version": null, "note": "The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1008247", "GSM1008248", "GSM1008249", "GSM1008250", "GSM1008251", "GSM1008252", "GSM1008253", "GSM1008254", "GSM1008255", "GSM1008256", "GSM1008257", "GSM1008258", "GSM1008259", "GSM1008260", "GSM1008261", "GSM1008262", "GSM1008263", "GSM1008264", "GSM1008265", "GSM1008266", "GSM1008267", "GSM1008268"], "sample_count": 22, "group_sizes": null, "group_sizes_basis": null, "platform": "571", "taxon": "Homo sapiens", "title": "Transcriptome profiling of endometrial biopsies  inflammatory response to Chlamydia trachomatis genital tract infection", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE87110", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE87110", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE87110", "version": null, "note": "The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2322515", "GSM2322516", "GSM2322517", "GSM2322518", "GSM2322519", "GSM2322520", "GSM2322521", "GSM2322522", "GSM2322523", "GSM2322524", "GSM2322525", "GSM2322526", "GSM2322527", "GSM2322528", "GSM2322529", "GSM2322530", "GSM2322531", "GSM2322532"], "sample_count": 18, "group_sizes": null, "group_sizes_basis": null, "platform": "11154", "taxon": "Homo sapiens", "title": "Transcriptional response of human endocervical epithelial A2EN cells to infection with wild-type or CpoS-deficient Chlamydia trachomatis L2/434/Bu", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:33875006:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:1dce74c1c1b111a4fa4f5cf71961b5845a85d38aad0eb3898d197fb21c1b348c", "bytes": 214, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[13]/table-wrap[1]#Tab1", "version": null, "note": "The top 5 miRNA ranked by degree in reproductive tract infection", "structure": {"pmcid": "PMC8056519", "section_index": 7, "section_title": "Verification of intersection hub genes and construction of intersection gene–miRNA interaction", "row_count": 0, "column_count": 0}, "table": {"label": "Table 1", "caption": "The top 5 miRNA ranked by degree in reproductive tract infection", "rows": [], "row_count": 0, "column_count": 0, "numeric_cells": 0, "header_rows": 0, "locator": "section[13]/table-wrap[1]#Tab1"}}, {"id": "asset:table:pmid:33875006:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:eb5495e6d8af085dcfd52ed826c0570820476d2a1e94b820eb2509729e03f584", "bytes": 208, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[13]/table-wrap[2]#Tab2", "version": null, "note": "The top 5 miRNA ranked by degree in conjunctival infection", "structure": {"pmcid": "PMC8056519", "section_index": 7, "section_title": "Verification of intersection hub genes and construction of intersection gene–miRNA interaction", "row_count": 0, "column_count": 0}, "table": {"label": "Table 2", "caption": "The top 5 miRNA ranked by degree in conjunctival infection", "rows": [], "row_count": 0, "column_count": 0, "numeric_cells": 0, "header_rows": 0, "locator": "section[13]/table-wrap[2]#Tab2"}}, {"id": "asset:table:pmid:33875006:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:1dce74c1c1b111a4fa4f5cf71961b5845a85d38aad0eb3898d197fb21c1b348c", "bytes": 214, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[13]/table-wrap[1]#Tab1", "version": null, "note": "The top 5 miRNA ranked by degree in reproductive tract infection", "structure": {"pmcid": "PMC8056519", "section_index": 13, "section_title": "Verification of intersection hub genes and construction of intersection gene–miRNA interaction", "row_count": 0, "column_count": 0}, "table": {"label": "Table 1", "caption": "The top 5 miRNA ranked by degree in reproductive tract infection", "rows": [], "row_count": 0, "column_count": 0, "numeric_cells": 0, "header_rows": 0, "locator": "section[13]/table-wrap[1]#Tab1"}}, {"id": "asset:table:pmid:33875006:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:eb5495e6d8af085dcfd52ed826c0570820476d2a1e94b820eb2509729e03f584", "bytes": 208, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[13]/table-wrap[2]#Tab2", "version": null, "note": "The top 5 miRNA ranked by degree in conjunctival infection", "structure": {"pmcid": "PMC8056519", "section_index": 13, "section_title": "Verification of intersection hub genes and construction of intersection gene–miRNA interaction", "row_count": 0, "column_count": 0}, "table": {"label": "Table 2", "caption": "The top 5 miRNA ranked by degree in conjunctival infection", "rows": [], "row_count": 0, "column_count": 0, "numeric_cells": 0, "header_rows": 0, "locator": "section[13]/table-wrap[2]#Tab2"}}], "gaps": ["asset:data:geo:GSE20430 not downloaded", "asset:data:geo:GSE20430 licence not read", "asset:data:geo:GSE20436 not downloaded", "asset:data:geo:GSE20436 licence not read", "asset:data:geo:GSE26692 not downloaded", "asset:data:geo:GSE26692 licence not read", "asset:data:geo:GSE41075 not downloaded", "asset:data:geo:GSE41075 licence not read", "asset:data:geo:GSE87110 not downloaded", "asset:data:geo:GSE87110 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "differential_expression", "specific": "limma_voom", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Then, the limma package was applied to identify the differentially expressed genes (DEGs)."}}, {"id": "method-2", "family": "network_analysis", "specific": "ppi_network", "label": "Network / pathway analysis", "dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "protein-protein interaction"}}, {"id": "method-3", "family": "network_analysis", "specific": "pathway_enrichment", "label": "Network / pathway analysis", "dsl_operations": ["pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.8, "band": "high", "quote": "GO enrichment"}}], "targets": [], "gaps": []}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: limma_voom."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE20430", "GSE20436", "GSE26692", "GSE41075", "GSE87110"], "resolved_accessions": ["GSE20430", "GSE20436", "GSE26692", "GSE41075", "GSE87110"], "statements": ["The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request."], "basis": "The paper names GSE20430, GSE20436, GSE26692, GSE41075, GSE87110 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "assets": ["source:pmid:33875006", "data:geo:GSE20430", "asset:table:pmid:33875006:1", "asset:table:pmid:33875006:2", "asset:table:pmid:33875006:3", "asset:table:pmid:33875006:4"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE20430"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:29:15Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 17612, "completion_tokens": 1629, "cached_tokens": 784}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:33875006", "type": "paper", "label": "pmid:33875006"}, {"id": "source:pmid:33875006", "type": "manuscript", "label": "PMID 33875006 full text"}, {"id": "data:geo:GSE20430", "type": "dataset", "label": "GEO GSE20430"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:33875006", "type": "paper", "label": "pmid:33875006"}, {"id": "source:pmid:33875006", "type": "manuscript", "label": "PMID 33875006 full text"}, {"id": "data:geo:GSE20430", "type": "dataset", "label": "GEO GSE20430"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-33875006", "type": "extraction", "used": ["source:pmid:33875006"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE20430", "type": "accession_resolution", "used": ["data:geo:GSE20430"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:33875006", "parent_hash": "sha256:5caa4a900cf578c0c6c3bcf00dcce0a20b0d9b2b10d6cba935ed39ac3ace3a2d", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:GSE20430 licence not read", "asset:data:geo:GSE20430 not downloaded", "asset:data:geo:GSE20436 licence not read", "asset:data:geo:GSE20436 not downloaded", "asset:data:geo:GSE26692 licence not read", "asset:data:geo:GSE26692 not downloaded", "asset:data:geo:GSE41075 licence not read", "asset:data:geo:GSE41075 not downloaded", "asset:data:geo:GSE87110 licence not read", "asset:data:geo:GSE87110 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "analysis", "definition_id": "differential_expression", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Then, the limma package was applied to identify the differentially expressed genes (DEGs)."], "order_basis": "analysis_only", "id": "assay:1"}]}