In silico analysis of CSF2RB from cancer genomic databases reveals a heterogeneous role in different breast cancer subtypes.

{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:40837403", "kind": "science-record", "revision": 1, "content_hash": "sha256:8c7a41e89b03913c77bd82f819e83190bca2a27c34eef4504aad6d877bf9010f", "created_at": "2026-11-01T10:25:52Z", "updated_at": "2026-11-01T10:25:52Z", "generator": {"name": "corpus-assay-engine", "converter": "sep_to_sci_v1", "source_package_schema": "urn:bntrg:sep:1.0.0"}, "paper": {"state": "partial", "title": "In silico analysis of CSF2RB from cancer genomic databases reveals a heterogeneous role in different breast cancer subtypes.", "doi": "10.3389/fbinf.2025.1606828", "pmid": "40837403", "authors": null, "journal": "Frontiers in bioinformatics", "year": 2025, "abstract": null, "claims": [{"id": "claim-1", "statement": "the headline numerical result the paper states for its main finding", "kind": "qualitative", "state": "blocked", "target": {"value": null, "unit": null, "tolerance": null, "source": null}, "evidence": []}], "gaps": ["abstract", "authors"]}, "experiment": {"state": "partial", "objective": "the headline numerical result the paper states for its main finding", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate and its interval from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The number a replication must land on, and the sentence it came from.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:40837403"], "outputs": ["the published estimate, its unit and its interval"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data behind the published result", "kind": "data-preparation", "state": "blocked", "blocked_on": "data:not_downloaded", "description": "The published result cannot be recomputed without the data the paper analysed.", "duration_hours": null, "parameters": {}, "inputs": [], "outputs": ["the source data with its provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the analysis programme", "kind": "analysis", "state": "blocked", "blocked_on": "no owned computational capability is bound to this experiment", "description": "Re-run the paper's analysis on the source data and produce the registered result. | SEP input not carried into the asset list: materials:the source data behind the published result in pmid:40837403", "duration_hours": null, "parameters": {}, "inputs": [], "outputs": ["the registered result"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:obtain_source_data blocked on data:not_downloaded", "step:run_analysis blocked on no owned computational capability is bound to this experiment", "step:run_analysis input 'materials:the source data behind the published result in pmid:40837403' does not resolve to a declared asset"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:40837403", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fbinf.2025.1606828", "sha256": "sha256:c28108d5b65776d5baee4424e6cb1a3024fc38ae7bae2ec61f8a06a020053620", "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fbinf.2025.1606828", "version": null, "note": "Source read by the package builder: full_text.", "structure": {"access_state": "full_text"}}], "gaps": ["asset:source:pmid:40837403 not verified"]}, "analysis": {"state": "absent", "methods": [], "targets": [], "gaps": ["method", "targets"]}, "capability": {"state": "absent", "requirements": [], "gaps": ["capability"]}, "readiness": {"state": "partial", "tier": null, "blocking_axis": null, "blocked_on": null, "axes": {}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:40837403"], "steps": ["read_published_estimate"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": ["xml"], "capabilities": [], "data_gaps": ["source:pmid:40837403"]}, "gaps": ["corpus_record_absent"]}, "review": {"state": "partial", "machine_critique": {"status": "passed", "providers": [{"provider": "minimax", "model": "MiniMax-M3.1-Flash", "prompt_version": "full-text-reading-v1", "prompt_hash": "42c2769af291cd22fe84e30afd17a918f4152590b566a2ac662200db0ea835fa", "source_hash": "c28108d5b65776d5baee4424e6cb1a3024fc38ae7bae2ec61f8a06a020053620", "raw_response_sha256": "sha256:521545370441683fece223427bf9f12f035bc95192ea3f9d6713f02bf9370dbb", "raw_response_chars": 6540}, {"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "full-text-reading-v1", "prompt_hash": "c74160f63018c65620dc6210c29e793532f9cbaaf40cd27eb6a7b89f72a61942", "source_hash": "c28108d5b65776d5baee4424e6cb1a3024fc38ae7bae2ec61f8a06a020053620", "raw_response_sha256": "sha256:b6350b829ba4ebd9ada8bf2f642dbb3c3c6d574e210dfa295c2ee499966d3e82", "raw_response_chars": 56918}], "target_providers": [{"provider": "minimax", "model": "MiniMax-M3.1-Flash", "prompt_version": "replication-target-v2", "prompt_hash": "b1b2a76ff28f81c34e8190adb840e5b5f4f62a8034124217e65dbe55868421b1", "source_hash": "c28108d5b65776d5baee4424e6cb1a3024fc38ae7bae2ec61f8a06a020053620", "raw_response": "{\"parent_value\":0,\"unit\":\"\",\"evidence\":\"\",\"target_result\":\"The paper states qualitative findings but no numerical result for the registered target.\",\"number_stated\":false}", "reading": {"parent_value": 0, "unit": "", "evidence": "", "target_result": "The paper states qualitative findings but no numerical result for the registered target.", "number_stated": false, "source_locator": null}, "recorded_at": "2026-10-31T15:30:56.662190+00:00"}, {"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "replication-target-v2", "prompt_hash": "1fc72b1029bd3b300405564acd96679069990af5a332a007ff7d4bdb8bda60cc", "source_hash": "c28108d5b65776d5baee4424e6cb1a3024fc38ae7bae2ec61f8a06a020053620", "raw_response": "<think>We need answer JSON only. Need interpret task. Registered target headline numerical result paper states for main finding. Source text appears abstract/results prose, no numerical headline result. Numbers embedded? CSF2RB, CD8+, maybe database names versions, but no quantitative result with number. Thus number_stated false, parent 0, unit \"\", evidence \"\". target_result says text states overexpression AML, decreased BRCA, elevated methylation, favorable but nonsignificant prognosis, high CD8 infiltration correlation, WT > mutant, no significant OS effect, subtype expression differences; no headline numerical result. Need ensure JSON valid and only source claims. \"If no number ... say in target_result what text does state instead.\" Could quote exact perhaps. We should not claim no number? target_result maybe \"The text states qualitative findings...\" Since no numerical. Need perhaps exact contiguous quote? Evidence empty as instructed. JSON.\n\nCould there be \"single numerical result\" hidden e.g. CD8+ is number but not numerical result. Title no. The text perhaps source truncated excludes detailed result? No. So false.\n\nNeed target_result perhaps succinctly mention main finding: \"The text states that CSF2RB was overexpressed in AML and downregulated in BRCA versus matched normal samples, with elevated promoter methylation and subtype-dependent expression; it reports no headline numerical result.\" The instruction says say what text does state instead. We can use wording closely. Unit empty.\n\nLet's ensure no issue target_result itself perhaps must state no numerical result and findings. Evidence exact quote impossible. Use source wording maybe exact sentence(s): \"Our in silico analyses showed overexpression of CSF2RB in acute myeloid leukemia (AML) and decreased expression in breast invasive carcinoma (BRCA) compared to matched normal samples.\" Then additional. But target_result field can contain quotes? Fine.\n\nJSON number parent_value 0. number_stated false.</think>\n\n{\"parent_value\":0,\"unit\":\"\",\"evidence\":\"\",\"target_result\":\"The text states qualitative findings: “Our in silico analyses showed overexpression of CSF2RB in acute myeloid leukemia (AML) and decreased expression in breast invasive carcinoma (BRCA) compared to matched normal samples.” No headline numerical result is stated.\",\"number_stated\":false}", "reading": {"parent_value": 0, "unit": "", "evidence": "", "target_result": "The text states qualitative findings: “Our in silico analyses showed overexpression of CSF2RB in acute myeloid leukemia (AML) and decreased expression in breast invasive carcinoma (BRCA) compared to matched normal samples.” No headline numerical result is stated.", "number_stated": false, "source_locator": null}, "recorded_at": "2026-10-31T15:31:00.025747+00:00"}], "agreement": true, "disagreements": {"target_result": {"minimax": "No numerical value for the headline result is reported. The stated main finding is heterogeneous CSF2RB expression across breast cancer subtypes: expression is downregulated in luminal and HER2-positive breast cancer and upregulated in triple-negative breast cancer relative to normal samples.", "minimax_alt": "unclear", "decisive": false}, "analysis_methods": {"minimax": ["In silico analysis of CSF2RB genetic changes", "mRNA expression analysis", "DNA methylation analysis", "prognostic analysis", "immune infiltration analysis", "tumor-versus-matched-normal expression comparison", "comparison of wild-type and mutated CSF2RB expression"], "minimax_alt": ["in silico analysis", "analysis of CSF2RB genetic changes, mRNA expression, DNA methylation, prognosis, and immune infiltration levels across different tumor types", "analysis using publicly available cancer genomics databases and web-based interactive portals"], "decisive": false}}, "agreement_basis": {"policy": "decisive_fields", "decisive_fields": ["work_type", "number_stated", "parent_value", "unit"]}, "blinded": true}, "human_critique": {"status": "not_run", "reviewer": null, "signed_at": null, "conflict_checked": false, "commentary": null}, "stages": [{"key": "target_materials", "status": "pending", "reason": null, "evidence": null}, {"key": "independent_readings", "status": "passed", "reason": "The independent readings are incomplete or disagree; the source evidence must resolve the difference.", "evidence": {"provider_errors": []}}, {"key": "source_resolution", "status": "pending", "reason": null, "evidence": null}, {"key": "protocol_reconstruction", "status": "pending", "reason": null, "evidence": null}, {"key": "control_execution", "status": "pending", "reason": null, "evidence": null}, {"key": "control_comparison", "status": "pending", "reason": null, "evidence": null}, {"key": "publication", "status": "pending", "reason": null, "evidence": null}], "gaps": ["review.human_critique", "review.machine_critique.passed"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "package:483f1e29bd40c02073503b8d3e991141f94f671dedad07ab37c85b86f6b05a2d", "type": "sep_package", "label": "SEP v1 package for pmid:40837403"}], "activities": [{"id": "activity:conversion:pmid:40837403", "type": "conversion", "used": ["package:483f1e29bd40c02073503b8d3e991141f94f671dedad07ab37c85b86f6b05a2d"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:minimax", "type": "model", "label": "minimax"}, {"id": "agent:minimax_alt", "type": "model", "label": "minimax_alt"}, {"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}], "source_run_id": "run-20261023T122449232913", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "d47eba0d-f217-4469-91a8-0a3215d5b61c", "parent_hash": "483f1e29bd40c02073503b8d3e991141f94f671dedad07ab37c85b86f6b05a2d", "fork_of": null, "generation": 1}, "gaps": ["abstract", "asset:source:pmid:40837403 not verified", "authors", "capability", "corpus_record_absent", "execution.not_run", "method", "review.human_critique", "review.machine_critique.passed", "step:obtain_source_data blocked on data:not_downloaded", "step:run_analysis blocked on no owned computational capability is bound to this experiment", "step:run_analysis input 'materials:the source data behind the published result in pmid:40837403' does not resolve to a declared asset", "targets"]}