A Comprehensive Analysis of Argonaute-CLIP Data Identifies Novel, Conserved and Species-Specific Targets of miR-21 in Human Liver and Hepatocellular Carcinoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:29538313", "kind": "science-record", "revision": 7, "content_hash": "sha256:7e4aa9d82b10a969fce2c3c59d7f081f76dc58461b31e0c8d14aa2680b26ec6b", "created_at": "2026-11-01T15:40:32Z", "updated_at": "2026-11-01T21:21:19Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "A Comprehensive Analysis of Argonaute-CLIP Data Identifies Novel, Conserved and Species-Specific Targets of miR-21 in Human Liver and Hepatocellular Carcinoma.", "doi": "10.3390/ijms19030851", "pmid": "29538313", "authors": ["Aaron Balasingam Koenig", "Juan Martín Barajas", "María Jose Guerrero", "Kalpana Ghoshal"], "journal": "International journal of molecular sciences", "year": 2018, "abstract": "MicroRNAs are ~22 nucleotide RNAs that regulate gene expression at the post-transcriptional level by binding messenger RNA transcripts. miR-21 is described as an oncomiR whose steady-state levels are commonly increased in many malignancies, including hepatocellular carcinoma (HCC). Methods known as cross-linking and immunoprecipitation of RNA followed by sequencing (CLIP-seq) have enabled transcriptome-wide identification of miRNA interactomes. In our study, we use a publicly available Argonaute-CLIP dataset (GSE97061), which contains nine HCC cases with matched benign livers, to characterize the miR-21 interactome in HCC. Argonaute-CLIP identified 580 miR-21 bound target sites on coding transcripts, of which 332 were located in the coding sequences, 214 in the 3'-untranslated region, and 34 in the 5'-untranslated region, introns, or downstream sequences. We compared the expression of miR-21 targets in 377 patients with liver cancer from the data generated by The Cancer Genome Atlas (TCGA) and found that mRNA levels of 402 miR-21 targets are altered in HCC. Expression of three novel predicted miR-21 targets (CAMSAP1, DDX1 and MARCKSL1) correlated with HCC patient survival. Analysis of RNA-seq data from SK-Hep1 cells treated with a miR-21 antisense oligonucleotide (GSE65892) identified RMND5A, an E3 ubiquitin ligase, as a strong miR-21 candidate target. Collectively, our analysis identified novel miR-21 targets that are likely to play a causal role in hepatocarcinogenesis.", "claims": [{"id": "claim-method", "statement": "Cox proportional hazards models were adjusted for age, sex and tumor grade. The significance of the Cox coefficient was corrected for the false-discovery rate as described [59].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29538313", "locator": "sections[14] \"4.3. Statistical Analysis\" paragraph 4", "quote": "Cox proportional hazards models were adjusted for age, sex and tumor grade. The significance of the Cox coefficient was corrected for the false-discovery rate as described [59]."}], "state": "complete"}, {"id": "claim-data-access", "statement": "RNA-seq RPKM data from The Cancer Genome Atlas (cancergenome.nih.gov) were downloaded from firebrowse.org and log2 transformed.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29538313", "locator": "sections[13] \"4.2. Gene Set Enrichment and Pathway Analysis\" paragraph 2", "quote": "RNA-seq RPKM data from The Cancer Genome Atlas (cancergenome.nih.gov) were downloaded from firebrowse.org and log2 transformed."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Headline result: “Collectively, our analysis identified novel miR-21 targets that are likely to play a causal role in hepatocarcinogenesis.” The statistical method was survival analysis using Cox proportional hazards models adjusted for age, sex, and tumor grade, with false-discovery-rate correction. The source data were TCGA liver hepatocellular carcinoma RNA-seq RPKM data downloaded from firebrowse.org, and the OncoLnc package was used for survival analysis.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:29538313", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Collectively, our analysis identified novel miR-21 targets that are likely to play a causal role in hepatocarcinogenesis."}, {"asset": "source:pmid:29538313", "locator": "sections[9] \"2.7. Elements of the miR-21 Interactome Predict Survival in HCC\" paragraph 2", "quote": "Next, we conducted a survival analysis on potential targets of miR-21 in 369 patients with HCC."}, {"asset": "source:pmid:29538313", "locator": "sections[9] \"2.7. Elements of the miR-21 Interactome Predict Survival in HCC\" paragraph 2", "quote": "Among miR-21 candidate targets, higher expression of CAMSAP2, DDX1, and MARCKSL1 predicted shorter survival."}, {"asset": "source:pmid:29538313", "locator": "sections[14] \"4.3. Statistical Analysis\" paragraph 4", "quote": "The OncoLnc package was used for survival analysis (www.oncolnc.org). Cox proportional hazards models were adjusted for age, sex and tumor grade. The significance of the Cox coefficient was corrected for the false-discovery rate as described [59]."}, {"asset": "source:pmid:29538313", "locator": "sections[13] \"4.2. Gene Set Enrichment and Pathway Analysis\" paragraph 2", "quote": "RNA-seq RPKM data from The Cancer Genome Atlas (cancergenome.nih.gov) were downloaded from firebrowse.org and log2 transformed."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Headline result: “Collectively, our analysis identified novel miR-21 targets that are likely to play a causal role in hepatocarcinogenesis.” The statistical method was survival analysis using Cox proportional hazards models adjusted for age, sex, and tumor grade, with false-discovery-rate correction. The source data were TCGA liver hepatocellular carcinoma RNA-seq RPKM data downloaded from firebrowse.org, and the OncoLnc package was used for survival analysis.", "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:29538313"], "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:GSE65892"], "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:GSE65892"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:29538313", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3390/ijms19030851", "sha256": "sha256:6263c35023f90a838707abe82061c9bd3d374905607976e465b970b77677a8c9", "bytes": 22589, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3390/ijms19030851", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC5877712", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE65892", "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=GSE65892", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE65892", "version": null, "note": "RNA-seq RPKM data from The Cancer Genome Atlas (cancergenome.nih.gov) were downloaded from firebrowse.org and log2 transformed.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "RNA-seq RPKM data from The Cancer Genome Atlas (cancergenome.nih.gov) were downloaded from firebrowse.org and log2 transformed.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM1608422", "GSM1608423", "GSM1608424", "GSM1608425", "GSM1608426", "GSM1608427"], "sample_count": 6, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Anti-miR-21 Suppresses Hepatocellular Carcinoma Growth via Broad Transcriptional Network De-regulation", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE97058", "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=GSE97058", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE97058", "version": null, "note": "RNA-seq RPKM data from The Cancer Genome Atlas (cancergenome.nih.gov) were downloaded from firebrowse.org and log2 transformed.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "RNA-seq RPKM data from The Cancer Genome Atlas (cancergenome.nih.gov) were downloaded from firebrowse.org and log2 transformed.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM2550642", "GSM2550643", "GSM2550644", "GSM2550645", "GSM2550646", "GSM2550647", "GSM2550648", "GSM2550649", "GSM2550650"], "sample_count": 9, "group_sizes": null, "group_sizes_basis": null, "platform": "17021", "taxon": "Mus musculus", "title": "Argonaute CLIP defines a deregulated miR-122 bound transcriptome that correlates with patient survival in human liver cancer (Mouse CLIP-Seq)", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE97061", "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=GSE97061", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE97061", "version": null, "note": "RNA-seq RPKM data from The Cancer Genome Atlas (cancergenome.nih.gov) were downloaded from firebrowse.org and log2 transformed.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "RNA-seq RPKM data from The Cancer Genome Atlas (cancergenome.nih.gov) were downloaded from firebrowse.org and log2 transformed.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM2550604", "GSM2550605", "GSM2550606", "GSM2550607", "GSM2550608", "GSM2550609", "GSM2550610", "GSM2550611", "GSM2550612", "GSM2550613", "GSM2550614", "GSM2550615", "GSM2550616", "GSM2550617", "GSM2550618", "GSM2550619", "GSM2550620", "GSM2550621", "GSM2550622", "GSM2550623", "GSM2550624", "GSM2550625", "GSM2550626", "GSM2550627", "GSM2550628", "GSM2550629", "GSM2550630", "GSM2550631", "GSM2550642", "GSM2550643", "GSM2550644", "GSM2550645", "GSM2550646", "GSM2550647", "GSM2550648", "GSM2550649", "GSM2550650", "GSM2550655", "GSM2550656", "GSM2550657", "GSM2550658", "GSM2550659", "GSM2550660", "GSM2550661", "GSM2550662", "GSM2550663"], "sample_count": 46, "group_sizes": null, "group_sizes_basis": null, "platform": "16791;17021", "taxon": "Homo sapiens; Mus musculus", "title": "Argonaute CLIP defines a deregulated miR-122 bound transcriptome that correlates with patient survival in human liver cancer", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE65892 not downloaded", "asset:data:geo:GSE65892 licence not read", "asset:data:geo:GSE97058 not downloaded", "asset:data:geo:GSE97058 licence not read", "asset:data:geo:GSE97061 not downloaded", "asset:data:geo:GSE97061 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "survival_analysis", "specific": "cox_proportional_hazards", "label": "Survival analysis", "dsl_operations": ["cox_ph"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Cox proportional hazards models were adjusted for age, sex and tumor grade. The significance of the Cox coefficient was corrected for the false-discovery rate as described [59]."}}, {"id": "method-2", "family": "contingency_analysis", "specific": "chi_square", "label": "Categorical (contingency table) analysis", "dsl_operations": ["chi_square_test"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["categorical_cross_tabulation"], "evidence": {"score": 0.8, "band": "high", "quote": "Chi square"}}], "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": ["cox_ph"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: cox_proportional_hazards."}, "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": ["GSE97061", "GSE97058", "GSE65892"], "resolved_accessions": ["GSE97061", "GSE97058", "GSE65892"], "statements": ["RNA-seq RPKM data from The Cancer Genome Atlas (cancergenome.nih.gov) were downloaded from firebrowse.org and log2 transformed."], "basis": "The paper names GSE97061, GSE97058, GSE65892 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": ["cox_ph"], "assets": ["source:pmid:29538313", "data:geo:GSE65892"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE65892"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:33:54Z", "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 8, "usage": {"prompt_tokens": 50201, "completion_tokens": 4618, "cached_tokens": 1832}}, "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:29538313", "type": "paper", "label": "pmid:29538313"}, {"id": "source:pmid:29538313", "type": "manuscript", "label": "PMID 29538313 full text"}, {"id": "data:geo:GSE65892", "type": "dataset", "label": "GEO GSE65892"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:29538313", "type": "paper", "label": "pmid:29538313"}, {"id": "source:pmid:29538313", "type": "manuscript", "label": "PMID 29538313 full text"}, {"id": "data:geo:GSE65892", "type": "dataset", "label": "GEO GSE65892"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-29538313", "type": "extraction", "used": ["source:pmid:29538313"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE65892", "type": "accession_resolution", "used": ["data:geo:GSE65892"], "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:29538313", "parent_hash": "sha256:1c7cc4b9022583321d9017d838ec0498909e9aba31c730168c4f4be0efc58ddd", "fork_of": null, "generation": 6}, "gaps": ["asset:data:geo:GSE65892 licence not read", "asset:data:geo:GSE65892 not downloaded", "asset:data:geo:GSE97058 licence not read", "asset:data:geo:GSE97058 not downloaded", "asset:data:geo:GSE97061 licence not read", "asset:data:geo:GSE97061 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "rna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["lated with HCC patient survival. Analysis of RNA-seq data from SK-Hep1 cells treated with a miR-2", "llowed by sequencing (CLIP-seq) have enabled transcriptome-wide identification of miRNA interactomes. I"], "order_basis": "paper_text_order:507", "id": "assay:1"}, {"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["cox_ph"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Cox proportional hazards models were adjusted for age, sex and tumor grade. The significance of the Cox coefficient was corrected for the false-discovery rate as described [59]."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}