Identification and diagnostic potential of hsa_circ_101303 in colorectal cancer: unraveling a regulatory network.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38824581", "kind": "science-record", "revision": 5, "content_hash": "sha256:b2d2a6e8546caf90927335b835209d14737b69693f1eed81486578d36369e2c0", "created_at": "2026-11-01T19:20:47Z", "updated_at": "2026-11-01T22:54:26Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification and diagnostic potential of hsa_circ_101303 in colorectal cancer: unraveling a regulatory network.", "doi": "10.1186/s12885-024-12458-5", "pmid": "38824581", "authors": ["Ke-Zhi Li", "Xiao-Min Liao", "Si-Qi Li", "Hao-Tang Wei", "Zhi-Jian Liang", "Liu-Xin Ge", "Su-Fang Zhou", "Bang-Li Hu"], "journal": "BMC cancer", "year": 2024, "abstract": "BACKGROUND: The role of novel circular RNAs (circRNAs) in colorectal cancer (CRC) remains to be determined. This study aimed to identify a novel circRNA involved in CRC pathogenesis, assess its diagnostic value, and construct a regulatory network.\nMETHODS: Differential expression analysis was conducted using circRNA datasets to screen for differentially expressed circRNAs. The expression of selected circRNAs was validated in external datasets and clinical samples. Diagnostic value of plasma circRNA levels in CRC was assessed. A competing endogenous RNA (ceRNA) network was constructed for the circRNA using TCGA dataset.\nRESULTS: Analysis of datasets revealed that hsa_circ_101303 was significantly overexpressed in CRC tissues compared to normal tissues. The upregulation of hsa_circ_101303 in CRC tissues was further confirmed through the GSE138589 dataset and clinical samples. High expression of hsa_circ_101303 was associated with advanced N stage, M stage, and tumor stage in CRC. Plasma levels of hsa_circ_101303 were markedly elevated in CRC patients and exhibited moderate diagnostic ability for CRC (AUC = 0.738). The host gene of hsa_circ_101303 was also found to be related to the TNM stage of CRC. Nine miRNAs were identified as target miRNAs for hsa_circ_101303, and 27 genes were identified as targets of these miRNAs. Subsequently, a ceRNA network for hsa_circ_101303 was constructed to illustrate the interactions between the nine miRNAs and 27 genes.\nCONCLUSIONS: The study identifies hsa_circ_101303 as a highly expressed circRNA in CRC, which is associated with the progression of the disease. Plasma levels of hsa_circ_101303 show promising diagnostic potential for CRC. The ceRNA network for hsa_circ_101303 provides valuable insights into the regulatory mechanisms underlying CRC.", "claims": [{"id": "claim-method", "statement": "Differential expression analysis was then carried out on the GSE126094 dataset using the “limma” package to identify differentially expressed circRNAs (DEcircRNAs) between tumor and control tissues.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38824581", "locator": "sections[3] \"The acquisition of circRNA datasets in CRC\" paragraph 2", "quote": "Differential expression analysis was then carried out on the GSE126094 dataset using the “limma” package to identify differentially expressed circRNAs (DEcircRNAs) between tumor and control tissues."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data used to support the findings of this study are available from the corresponding author upon reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38824581", "locator": "sections[23] \"notes\" paragraph 1", "quote": "The data used to support the findings of this study are available from the corresponding author upon reasonable request."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Differential expression analysis identified hsa_circ_101303 as significantly overexpressed in CRC tissues compared with normal tissues.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38824581", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Analysis of datasets revealed that hsa_circ_101303 was significantly overexpressed in CRC tissues compared to normal tissues."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Differential expression analysis identified hsa_circ_101303 as significantly overexpressed in CRC tissues compared with normal tissues.", "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:38824581"], "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:GSE100186"], "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:GSE100186"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:38824581", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s12885-024-12458-5", "sha256": "sha256:0a87e17a4f9ea1796a7f0a5bab3962b8464c5cf9c80389cf074958ed1904cbca", "bytes": 31710, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s12885-024-12458-5", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC11144310", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE100186", "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=GSE100186", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE100186", "version": null, "note": "The data used to support the findings of this study are available from the corresponding author upon reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data used to support the findings of this study are available from the corresponding author upon reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2674259", "GSM2674260", "GSM2674261", "GSM2674262", "GSM2674263", "GSM2674264", "GSM2674265", "GSM2674266"], "sample_count": 8, "group_sizes": null, "group_sizes_basis": null, "platform": "21825", "taxon": "Homo sapiens", "title": "circRNA expression in renal cell carcinoma and mached non-tumor tissues", "resolution_checked_at": "2026-11-01T20:16:08Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE126094", "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=GSE126094", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE126094", "version": null, "note": "The data used to support the findings of this study are available from the corresponding author upon reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data used to support the findings of this study are available from the corresponding author upon reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM3591546", "GSM3591547", "GSM3591548", "GSM3591549", "GSM3591550", "GSM3591551", "GSM3591552", "GSM3591553", "GSM3591554", "GSM3591555", "GSM3591556", "GSM3591557", "GSM3591558", "GSM3591559", "GSM3591560", "GSM3591561", "GSM3591562", "GSM3591563", "GSM3591564", "GSM3591565"], "sample_count": 20, "group_sizes": null, "group_sizes_basis": null, "platform": "19978", "taxon": "Homo sapiens", "title": "Hsa_circ_101555 functions as a competing endogenous RNA of miR-597-5p to promote colorectal cancer progression [Circular RNAs]", "resolution_checked_at": "2026-11-01T18:06:43Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE138589", "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=GSE138589", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE138589", "version": null, "note": "The data used to support the findings of this study are available from the corresponding author upon reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data used to support the findings of this study are available from the corresponding author upon reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM4113975", "GSM4113976", "GSM4113977", "GSM4113978", "GSM4113979", "GSM4113980", "GSM4113981", "GSM4113982", "GSM4113983", "GSM4113984", "GSM4113985", "GSM4113986"], "sample_count": 12, "group_sizes": null, "group_sizes_basis": null, "platform": "19978", "taxon": "Homo sapiens", "title": "circRNA Microarray for human colorectal adenocarcinoma and normal mucosa", "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:GSE142837", "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=GSE142837", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE142837", "version": null, "note": "The data used to support the findings of this study are available from the corresponding author upon reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data used to support the findings of this study are available from the corresponding author upon reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM4240790", "GSM4240791", "GSM4240792", "GSM4240793", "GSM4240794", "GSM4240795", "GSM4240796", "GSM4240797", "GSM4240798", "GSM4240799"], "sample_count": 10, "group_sizes": null, "group_sizes_basis": null, "platform": "19978", "taxon": "Homo sapiens", "title": "circRNA expression data from human colorectal cancer tissues and the correponding non-cancerous tissues", "resolution_checked_at": "2026-11-01T19:09:46Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE97332", "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=GSE97332", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE97332", "version": null, "note": "The data used to support the findings of this study are available from the corresponding author upon reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data used to support the findings of this study are available from the corresponding author upon reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2561829", "GSM2561830", "GSM2561831", "GSM2561832", "GSM2561833", "GSM2561834", "GSM2561835", "GSM2561836", "GSM2561837", "GSM2561838", "GSM2561839", "GSM2561840", "GSM2561841", "GSM2561842"], "sample_count": 14, "group_sizes": null, "group_sizes_basis": null, "platform": "19978", "taxon": "Homo sapiens", "title": "circRNA expression in HCC and matched non-tumor tissues", "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:GSE100186 not downloaded", "asset:data:geo:GSE100186 licence not read", "asset:data:geo:GSE126094 not downloaded", "asset:data:geo:GSE126094 licence not read", "asset:data:geo:GSE138589 not downloaded", "asset:data:geo:GSE138589 licence not read", "asset:data:geo:GSE142837 not downloaded", "asset:data:geo:GSE142837 licence not read", "asset:data:geo:GSE97332 not downloaded", "asset:data:geo:GSE97332 licence not read"]}, "analysis": {"state": "partial", "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": "Differential expression analysis was then carried out on the GSE126094 dataset using the “limma” package to identify differentially expressed circRNAs (DEcircRNAs) between tumor and control tissues."}}, {"id": "method-2", "family": "group_comparison", "specific": "mann_whitney", "label": "Group comparison", "dsl_operations": [], "missing_operations": ["group_comparison_mann_whitney"], "expressible": false, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 0.8, "band": "high", "quote": "Mann-Whitney"}}, {"id": "method-3", "family": "group_comparison", "specific": "anova", "label": "Group comparison", "dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 0.8, "band": "high", "quote": "analysis of variance"}}], "targets": [], "gaps": ["method.reader_differs_from_extractor"]}, "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": ["GSE126094", "GSE138589", "GSE142837", "GSE97332", "GSE100186"], "resolved_accessions": ["GSE126094", "GSE138589", "GSE142837", "GSE97332", "GSE100186"], "statements": ["The data used to support the findings of this study are available from the corresponding author upon reasonable request."], "basis": "The paper names GSE126094, GSE138589, GSE142837, GSE97332, GSE100186 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:38824581", "data:geo:GSE100186"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE100186"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:20:16Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 10014, "completion_tokens": 1639, "cached_tokens": 264}}, "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:38824581", "type": "paper", "label": "pmid:38824581"}, {"id": "source:pmid:38824581", "type": "manuscript", "label": "PMID 38824581 full text"}, {"id": "data:geo:GSE100186", "type": "dataset", "label": "GEO GSE100186"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:38824581", "type": "paper", "label": "pmid:38824581"}, {"id": "source:pmid:38824581", "type": "manuscript", "label": "PMID 38824581 full text"}, {"id": "data:geo:GSE100186", "type": "dataset", "label": "GEO GSE100186"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-38824581", "type": "extraction", "used": ["source:pmid:38824581"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE100186", "type": "accession_resolution", "used": ["data:geo:GSE100186"], "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:38824581", "parent_hash": "sha256:114d616ce57dbd92cd02e0506c0b198b415d4aad85f7b4cb527739ea1f2cbecf", "fork_of": null, "generation": 4}, "gaps": ["asset:data:geo:GSE100186 licence not read", "asset:data:geo:GSE100186 not downloaded", "asset:data:geo:GSE126094 licence not read", "asset:data:geo:GSE126094 not downloaded", "asset:data:geo:GSE138589 licence not read", "asset:data:geo:GSE138589 not downloaded", "asset:data:geo:GSE142837 licence not read", "asset:data:geo:GSE142837 not downloaded", "asset:data:geo:GSE97332 licence not read", "asset:data:geo:GSE97332 not downloaded", "execution.not_run", "method.reader_differs_from_extractor", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "qpcr", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["cance (P > 0.05). Further validation through RT-qPCR assay on 60 CRC tumor tissues and correspond", "ce (P > 0.05). Further validation through RT-qPCR assay on 60 CRC tumor tissues and correspond"], "order_basis": "paper_text_order:5718", "id": "assay:1"}, {"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": ["Differential expression analysis was then carried out on the GSE126094 dataset using the “limma” package to identify differentially expressed circRNAs (DEcircRNAs) between tumor and control tissues."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}