Bioinformatics analysis of LINC01554 and its co‑expressed genes in hepatocellular carcinoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33000250", "kind": "science-record", "revision": 8, "content_hash": "sha256:c5bf087ff52213d3899f77081d2281a24cc4a1053d7c03065afa4274be42afcb", "created_at": "2026-11-01T15:41:12Z", "updated_at": "2026-11-01T22:45:24Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Bioinformatics analysis of LINC01554 and its co‑expressed genes in hepatocellular carcinoma.", "doi": "10.3892/or.2020.7779", "pmid": "33000250", "authors": ["Ling Li", "Kang Huang", "Zhongshan Lu", "Huijia Zhao", "Hao Li", "Qifa Ye", "Guizhu Peng"], "journal": "Oncology reports", "year": 2020, "abstract": "Hepatocellular carcinoma (HCC) is a leading cause of cancer‑related morbidity and mortality globally. Despite the remarkable improvements in comprehensive HCC treatment, the underlying mechanistic details of HCC remain elusive. We screened HCC patients for differentially expressed genes (DEGs) using the Gene Expression Omnibus (GSE113850) and The Cancer Genome Atlas (TCGA) datasets. LINC01554 expression in 40 paired samples was determined by quantitative reverse transcription polymerase chain reaction (RT‑qPCR), and its clinical significance was assessed. LINC01554 was found to have a gain‑of‑function role in HCC in vitro. Additionally, the bioinformatics analysis of the genes co‑expressed with LINC01554 was performed using the Co‑LncRNA website, and potential molecular mechanisms were investigated using the Gene Ontology and Kyoto Encyclopaedia of Genes and Genomes resources and validated by in vitro experiments. A total of 229 DEGs were identified from the GSE113850 dataset. Among the identified DEGs, three long non‑coding RNAs (lncRNAs) (DIO3OS, LINC01554, and LINC01093) with |logFC| ≥2 and P<0.05 were screened. A total of 148 lncRNAs with |logFC| ≥1 and P<0.05 were identified from TCGA dataset. Low LINC01554 expression levels were significantly correlated with overall survival, pathological stage, hepatitis B infection, tumour size, portal vein tumour thrombus, and TNM stage. Using gain‑of‑function assays, we further showed that LINC01554 inhibited the proliferation, migration, and invasion of the HCCLM9 and SK‑Hep1 cells and promoted G0/G1 arrest, but it did not significantly affect apoptosis. Western blotting revealed that LINC01554 overexpression resulted in increased ZO‑1 and E‑cadherin expression levels, but decreased N‑cadherin and vimentin expression levels. Moreover, LINC01554 overexpression inhibited Akt, p‑Akt, β‑catenin, and p‑Gsk3β expression. Our results showed that LINC01554 repressed HCC cell invasiveness and epithelial‑to‑mesenchymal transition partly by inhibiting Wnt and PI3K‑Akt signalling in vitro. Taken together, our findings provide new insights into the molecular mechanisms underlying HCC tumourigenesis and implicate LINC01554 as a potential target for HCC therapy.", "claims": [{"id": "claim-method", "statement": "We used the GEO2R statistical analysis tool (https://www.ncbi.nlm.nih.gov/geo/geo2r/) and Student's t-test to identify DEGs in the GSE113850 dataset. Data from the TCGA database were analysed using the R packages, DESeq and edgeR (https://www.bioconductor.org/), and Student's t-test to identify DEGs.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33000250", "locator": "sections[5] \"Screening of HCC patients for differentially expressed genes (DEGs)\" paragraph 2", "quote": "We used the GEO2R statistical analysis tool (https://www.ncbi.nlm.nih.gov/geo/geo2r/) and Student's t-test to identify DEGs in the GSE113850 dataset."}, {"asset": "source:pmid:33000250", "locator": "sections[5] \"Screening of HCC patients for differentially expressed genes (DEGs)\" paragraph 2", "quote": "Data from the TCGA database were analysed using the R packages, DESeq and edgeR (https://www.bioconductor.org/), and Student's t-test to identify DEGs."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets used during the present study are available from the corresponding author upon reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33000250", "locator": "sections[33] \"Availability of data and materials\" paragraph 2", "quote": "The datasets used during the present study are available from the corresponding author upon reasonable request."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "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:33000250"], "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:GSE113850"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "blocked", "blocked_on": "method:student_t", "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:GSE113850"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:run_analysis blocked on method:student_t"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:33000250", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3892/or.2020.7779", "sha256": "sha256:eb9d43861f8107299a0ad0e38894c14a377f2e429e7623d2df13d0f5970787ec", "bytes": 32793, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3892/or.2020.7779", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7551476", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE113850", "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=GSE113850", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE113850", "version": null, "note": "The datasets used during the present study are available from the corresponding author upon reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets used during the present study are available from the corresponding author upon reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM3121189", "GSM3121190", "GSM3121191", "GSM3121192", "GSM3121193", "GSM3121194", "GSM3121195", "GSM3121196", "GSM3121197", "GSM3121198", "GSM3121199", "GSM3121200", "GSM3121201", "GSM3121202", "GSM3121203", "GSM3121204", "GSM3121205", "GSM3121206", "GSM3121207", "GSM3121208", "GSM3121209", "GSM3121210", "GSM3121211", "GSM3121212", "GSM3121213", "GSM3121214", "GSM3121215", "GSM3121216", "GSM3121217", "GSM3121218", "GSM3121219", "GSM3121220", "GSM3121221", "GSM3121222", "GSM3121223", "GSM3121224", "GSM3121225", "GSM3121226", "GSM3121227"], "sample_count": 39, "group_sizes": null, "group_sizes_basis": null, "platform": "16847", "taxon": "Homo sapiens", "title": "Long non-coding RNA Expression Profiling in Hepatocellular Carcinoma (HCC) and in normal liver", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE113850 not downloaded", "asset:data:geo:GSE113850 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "student_t_test", "label": "Group comparison", "dsl_operations": [], "missing_operations": ["student_t"], "expressible": false, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 1.0, "band": "reordered", "quote": "We used the GEO2R statistical analysis tool (https://www.ncbi.nlm.nih.gov/geo/geo2r/) and Student's t-test to identify DEGs in the GSE113850 dataset. Data from the TCGA database were analysed using the R packages, DESeq and edgeR (https://www.bioconductor.org/), and Student's t-test to identify DEGs."}}, {"id": "method-2", "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"}}, {"id": "method-3", "family": "survival_analysis", "specific": "log_rank_test", "label": "Survival analysis", "dsl_operations": ["logrank_test"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.8, "band": "high", "quote": "log-rank"}}, {"id": "method-4", "family": "differential_expression", "specific": "deseq2", "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": 0.8, "band": "high", "quote": "DESeq"}}, {"id": "method-5", "family": "differential_expression", "specific": "edger", "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": 0.8, "band": "high", "quote": "edgeR"}}, {"id": "method-6", "family": "regression_modelling", "specific": "ols", "label": "Regression modelling", "dsl_operations": ["ols_fit"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["predictors_and_outcome"], "evidence": {"score": 0.8, "band": "high", "quote": "Linear Regression"}}, {"id": "method-7", "family": "clustering", "specific": "hierarchical", "label": "Clustering", "dsl_operations": ["hierarchical_cluster"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["feature_matrix"], "evidence": {"score": 0.8, "band": "high", "quote": "hierarchical clustering"}}], "targets": [], "gaps": ["method.student_t"]}, "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": false, "required_operations": [], "missing_operations": ["student_t"], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: student_t_test."}, "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": ["GSE113850"], "resolved_accessions": ["GSE113850"], "statements": ["The datasets used during the present study are available from the corresponding author upon reasonable request."], "basis": "The paper names GSE113850 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": [], "assets": ["source:pmid:33000250", "data:geo:GSE113850"], "steps": []}, "must_build": {"dsl_operations": [{"operation": "student_t", "unlocks_papers": null, "priority": null}], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE113850"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:22:57Z", "independence": "single_reader"}, "evidence_check": {"method": "reordered", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 26174, "completion_tokens": 2169, "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:33000250", "type": "paper", "label": "pmid:33000250"}, {"id": "source:pmid:33000250", "type": "manuscript", "label": "PMID 33000250 full text"}, {"id": "data:geo:GSE113850", "type": "dataset", "label": "GEO GSE113850"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:33000250", "type": "paper", "label": "pmid:33000250"}, {"id": "source:pmid:33000250", "type": "manuscript", "label": "PMID 33000250 full text"}, {"id": "data:geo:GSE113850", "type": "dataset", "label": "GEO GSE113850"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-33000250", "type": "extraction", "used": ["source:pmid:33000250"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE113850", "type": "accession_resolution", "used": ["data:geo:GSE113850"], "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:33000250", "parent_hash": "sha256:db1a42411ec01e33ae1998307db8d9564f7c9487b254e76907121718c7d9fca3", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:GSE113850 licence not read", "asset:data:geo:GSE113850 not downloaded", "execution.not_run", "method.student_t", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:run_analysis blocked on method:student_t"], "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": ["transcription polymerase chain reaction (RT‑qPCR), and its clinical significance was assessed", "and normal tumour-adjacent tissue samples by RT-qPCR. The results showed that LINC01554 expressio", "cer cell lines (SK-Hep1, HepG2, and HCCLM9). RT-qPCR results showed that LINC01554 expression was", "Transfection efficiencies were confirmed by RT-qPCR (P<0.01; Fig. 3D). Supplementary Material Su"], "order_basis": "paper_text_order:560", "id": "assay:1"}, {"role": "data_generation", "definition_id": "apoptosis_assay", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.69, "evidence": ["arrest, but it did not significantly affect apoptosis. Western blotting revealed that LINC01554 ov"], "order_basis": "paper_text_order:1664", "id": "assay:2"}, {"role": "data_generation", "definition_id": "western_blot", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["t it did not significantly affect apoptosis. Western blotting revealed that LINC01554 overexpression resul"], "order_basis": "paper_text_order:1674", "id": "assay:3"}, {"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": ["line tool used for analysing RNA sequencing (RNA-Seq) data from TCGA and GTEx databases. It inclu", "le or multiple lncRNAs. We analysed the same RNA-Seq datasets to identify the CEGs. The regressio", "x.html) is an online tool used for analysing RNA sequencing (RNA-Seq) data from TCGA and GTEx databases.", "ta from TCGA and GTEx databases. It includes RNA sequencing expression data of 9,736 tumors and 8,587 no"], "order_basis": "paper_text_order:3131", "id": "assay:4"}, {"role": "data_generation", "definition_id": "cell_culture", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["my of Sciences, Shanghai, China). Cells were cultured in Dulbecco's modified Eagles medium (DMEM; Inv", "Liver cancer cell lines (SK-Hep1, HCCLM9 and HepG2) were obtained from the Cell Bank of the Typ", "ion in the liver cancer cell lines (SK-Hep1, HepG2, and HCCLM9). RT-qPCR results showed that LI", "in the SK-Hep1 and HCCLM9 cells than in the HepG2 cells (Fig. 3C). Therefore, SK-Hep1 and HCCL"], "order_basis": "paper_text_order:4530", "id": "assay:5"}, {"role": "data_generation", "definition_id": "transfection", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["554 DNA sequence (Lv-NC), as a control, were transfected into HCC cells. Transfection efficiencies we", "a control, were transfected into HCC cells. Transfection efficiencies were confirmed by RT-qPCR (P<0."], "order_basis": "paper_text_order:8475", "id": "assay:6"}, {"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["We used the GEO2R statistical analysis tool (https://www.ncbi.nlm.nih.gov/geo/geo2r/) and Student's t-test to identify DEGs in the GSE113850 dataset. Data from the TCGA database were analysed using the R packages, DESeq and edgeR (https://www.bioconductor.org/), and Student's t-test to identify DEGs."], "order_basis": "consumes_earlier_output", "id": "assay:7"}]}