Genome-wide expression reveals potential biomarkers in breast cancer bone metastasis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35388653", "kind": "science-record", "revision": 4, "content_hash": "sha256:b1176f4ab6aff0c1f4aae4c1db55959c74e95a580e685745ca891084c0a0809a", "created_at": "2026-11-01T18:14:12Z", "updated_at": "2026-11-01T22:06:15Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Genome-wide expression reveals potential biomarkers in breast cancer bone metastasis.", "doi": "10.1515/jib-2021-0041", "pmid": "35388653", "authors": ["Yashbir Singh", "Naidu Subbarao", "Abhinav Jaimini", "Quincy A Hathaway", "Amina Kunovac", "Bradley Erickson", "Vishnu Swarup", "Himanshu Narayan Singh"], "journal": "Journal of integrative bioinformatics", "year": 2022, "abstract": "Breast cancer metastases are most commonly found in bone, an indication of poor prognosis. Pathway-based biomarkers identification may help elucidate the cellular signature of breast cancer metastasis in bone, further characterizing the etiology and promoting new therapeutic approaches. We extracted gene expression profiles from mouse macrophages from the GEO dataset, GSE152795 using the GEO2R webtool. The differentially expressed genes (DEGs) were filtered by log2 fold-change with threshold 1.5 (FDR < 0.05). STRING database and Enrichr were used for GO-term analysis, miRNA and TF analysis associated with DEGs. Autodock Vienna was exploited to investigate interaction of anti-cancer drugs, Actinomycin-D and Adriamycin. Sensitivity and specificity of DEGs was assessed using receiver operating characteristic (ROC) analyses. A total of 61 DEGs, included 27 down-regulated and 34 up-regulated, were found to be significant in breast cancer bone metastasis. Major DEGs were associated with lipid metabolism and immunological response of tumor tissue. Crucial DEGs, Bcl3, ADGRG7, FABP4, VCAN, and IRF4 were regulated by miRNAs, miR-497, miR-574, miR-138 and TFs, CCDN1, STAT6, IRF8. Docking analysis showed that these genes possessed strong binding with the drugs. ROC analysis demonstrated Bcl3 is specific to metastasis. DEGs Bcl3, ADGRG7, FABP4, IRF4, their regulating miRNAs and TFs have strong impact on proliferation and metastasis of breast cancer in bone tissues. In conclusion, present study revealed that DEGs are directly involved in of breast tumor metastasis in bone tissues. Identified genes, miRNAs, and TFs can be possible drug targets that may be used for the therapeutics. However, further experimental validation is necessary.", "claims": [{"id": "claim-method", "statement": "The Benjamini and Hochberg false discovery rate (FDR) method was used to filter out false-positive results, and the adjusted p values were calculated.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35388653", "locator": "sections[4] \"Identification of differential expressed genes (DEGs)\" paragraph 2", "quote": "The Benjamini and Hochberg false discovery rate (FDR) method was used to filter out false-positive results, and the adjusted p values were calculated."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The expression profile information of mouse macrophages was extracted from the GEO dataset, GSE152795 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE152795).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35388653", "locator": "sections[2] \"Materials\" paragraph 2", "quote": "The expression profile information of mouse macrophages was extracted from the GEO dataset, GSE152795 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE152795)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "A total of 61 DEGs, included 27 down-regulated and 34 up-regulated, were found to be significant in breast cancer bone metastasis.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35388653", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "A total of 61 DEGs, included 27 down-regulated and 34 up-regulated, were found to be significant in breast cancer bone metastasis."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "A total of 61 DEGs, included 27 down-regulated and 34 up-regulated, were found to be significant in breast cancer bone metastasis.", "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:35388653"], "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:GSE152795"], "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:GSE152795"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:35388653", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1515/jib-2021-0041", "sha256": "sha256:ff63d8d208727a49d27d67fa713585ef6d325865cd6adc2580a5415d4f573767", "bytes": 40736, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1515/jib-2021-0041", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9521824", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE152795", "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=GSE152795", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE152795", "version": null, "note": "The expression profile information of mouse macrophages was extracted from the GEO dataset, GSE152795 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE152795).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The expression profile information of mouse macrophages was extracted from the GEO dataset, GSE152795 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE152795).", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM4626676", "GSM4626677", "GSM4626678", "GSM4626679", "GSM4626680", "GSM4626681", "GSM4626682", "GSM4626683", "GSM4626684", "GSM4626685", "GSM4626686", "GSM4626687", "GSM4626688", "GSM4626689", "GSM4626690", "GSM4626691", "GSM4626692", "GSM4626693", "GSM4626694"], "sample_count": 19, "group_sizes": null, "group_sizes_basis": null, "platform": "28716", "taxon": "Mus musculus", "title": "Transcriptome profiling of inflammatory monocytes and macrophages in breast cancer bone metastasis", "resolution_checked_at": "2026-11-01T18:06:43Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE152795 not downloaded", "asset:data:geo:GSE152795 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "diagnostic_evaluation", "specific": "roc", "label": "Diagnostic test evaluation", "dsl_operations": ["confusion_counts", "roc_curve", "sensitivity_specificity", "solve_confusion_matrix", "classification_metrics", "published_precision_envelope"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["reference_standard_and_test"], "evidence": {"score": 0.7, "band": "medium", "quote": "ROC analysis"}}, {"id": "method-2", "family": null, "specific": null, "label": "Benjamini and Hochberg false discovery rate (FDR) method", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The Benjamini and Hochberg false discovery rate (FDR) method was used to filter out false-positive results, and the adjusted p values were calculated."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "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": ["confusion_counts", "roc_curve", "sensitivity_specificity", "solve_confusion_matrix", "classification_metrics", "published_precision_envelope"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: roc."}, "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": ["GSE152795"], "resolved_accessions": ["GSE152795"], "statements": ["The expression profile information of mouse macrophages was extracted from the GEO dataset, GSE152795 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE152795)."], "basis": "The paper names GSE152795 in GEO and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["confusion_counts", "roc_curve", "sensitivity_specificity", "solve_confusion_matrix", "classification_metrics", "published_precision_envelope"], "assets": ["source:pmid:35388653", "data:geo:GSE152795"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE152795"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T17:40:56Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 5, "usage": {"prompt_tokens": 12575, "completion_tokens": 1084, "cached_tokens": 128}}, "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:35388653", "type": "paper", "label": "pmid:35388653"}, {"id": "source:pmid:35388653", "type": "manuscript", "label": "PMID 35388653 full text"}, {"id": "data:geo:GSE152795", "type": "dataset", "label": "GEO GSE152795"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:35388653", "type": "paper", "label": "pmid:35388653"}, {"id": "source:pmid:35388653", "type": "manuscript", "label": "PMID 35388653 full text"}, {"id": "data:geo:GSE152795", "type": "dataset", "label": "GEO GSE152795"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-35388653", "type": "extraction", "used": ["source:pmid:35388653"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE152795", "type": "accession_resolution", "used": ["data:geo:GSE152795"], "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:35388653", "parent_hash": "sha256:6471aa69f116ee63ff2c79a9ea02b7edefea4823f5e288256fe7ea6cb6b360b1", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE152795 licence not read", "asset:data:geo:GSE152795 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "animal_model", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": [". We extracted gene expression profiles from mouse macrophages from the GEO dataset, GSE152795", "s into 4-week-old female mice, while healthy mice were not subjected to intra-cardiac injection. Me", "erials The expression profile information of mouse macrophages was extracted from the GEO datas", "ion was performed using Affymetrix GeneChip® Mouse Gene 2.0ST Array. The dataset included breas"], "order_basis": "paper_text_order:372", "id": "assay:1"}, {"role": "data_generation", "definition_id": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.77, "evidence": ["E152795). The annotation was performed using Affymetrix GeneChip® Mouse Gene 2.0ST Array. The datase"], "order_basis": "paper_text_order:2003", "id": "assay:2"}, {"role": "analysis", "definition_id": "diagnostic_evaluation", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["confusion_counts", "roc_curve", "sensitivity_specificity", "solve_confusion_matrix", "classification_metrics", "published_precision_envelope"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.7, "evidence": ["ROC analysis"], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}