Exploration of the involvement of LncRNA in HIV-associated encephalitis using bioinformatics.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:30345171", "kind": "science-record", "revision": 4, "content_hash": "sha256:c382b3c96b94b0d7d385958dc80995a5c30c00ccf335c37592e437c5c7da7c50", "created_at": "2026-11-01T15:40:38Z", "updated_at": "2026-11-01T21:21:43Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Exploration of the involvement of LncRNA in HIV-associated encephalitis using bioinformatics.", "doi": "10.7717/peerj.5721", "pmid": "30345171", "authors": ["Diangeng Li", "Pengtao Bao", "Zhiwei Yin", "Lei Sun", "Jin Feng", "Zheng He", "Meiling Jin", "Changting Liu"], "journal": "PeerJ", "year": 2018, "abstract": "BACKGROUND: HIV-associated encephalitis (HIVE) is one of the common complications of HIV infection, and the pathogenesis of HIVE remains unclear, while lncRNA might be involved it. In this study, we made re-annotation on the expression profiling from the HIVE study in the public database, identified the lncRNA that might be involved in HIVE, and explored the possible mechanism.\nMETHODS: In the GEO public database, the microarray expression profile (GSE35864) of three regions of brain tissues (white matter, frontal cortex and basal ganglia brain tissues) was chosen, updated annotation was performed to construct the non-cording-RNA (ncRNA) microarray data. Morpheus was used to identify the differential expressed ncRNA, and Genbank of NCBI was used to identify lncRNAs. The StarBase, PITA and miRDB databases were used to predict the target miRNAs of lncRNA. The TargetScan, PicTar and MiRanda databases were used to predict the target genes of miRNAs. The GO and KEGG pathway analysis were used to make function analysis on the targets genes.\nRESULTS: Seventeen differentially expressed lncRNAs were observed in the white matter of brain tissues, for which 352 target miRNAs and 6,659 target genes were predicted. The GO function analysis indicated that the lncRNAs were mainly involved in the nuclear transcription and translation processes. The KEGG pathway analysis showed that the target genes were significantly enriched in 33 signal pathways, of which 11 were clearly related to the nervous system function.\nDISCUSSION: The brand-new and different microarray results can be obtained through the updated annotation of the chips, and it is feasible to identify lncRNAs from ordinary chips. The results suggest that lncRNA may be involved in the occurrence and development of HIVE, which provides a new direction for further research on the diagnosis and treatment of HIVE.", "claims": [{"id": "claim-method", "statement": "This analysis was based on the t-test and adjusted according to the characteristic that the noise of microarray data was correlated with the peak value of expression data.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30345171", "locator": "sections[4] \"Identifying differentially expressed lncRNAs\" paragraph 2", "quote": "This analysis was based on the t-test and adjusted according to the characteristic that the noise of microarray data was correlated with the peak value of expression data."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The following information was supplied regarding data availability:The raw measurements are provided in Data S1.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30345171", "locator": "sections[15] \"Additional Information and Declarations\" paragraph 4", "quote": "The following information was supplied regarding data availability:The raw measurements are provided in Data S1."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "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:30345171"], "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:GSE35864"], "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:GSE35864"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:30345171", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.7717/peerj.5721", "sha256": "sha256:56c90b419df00df12a67549fdea01c08f6b10be3168598905e20e1784b52f699", "bytes": 25244, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.7717/peerj.5721", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC6187992", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE35864", "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=GSE35864", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE35864", "version": null, "note": "The following information was supplied regarding data availability:The raw measurements are provided in Data S1.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The following information was supplied regarding data availability:The raw measurements are provided in Data S1.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM876838", "GSM876839", "GSM876840", "GSM876841", "GSM876842", "GSM876843", "GSM876844", "GSM876845", "GSM876846", "GSM876847", "GSM876848", "GSM876849", "GSM876850", "GSM876851", "GSM876852", "GSM876853", "GSM876854", "GSM876855", "GSM876856", "GSM876857", "GSM876858", "GSM876859", "GSM876860", "GSM876861", "GSM876862", "GSM876863", "GSM876864", "GSM876865", "GSM876866", "GSM876867", "GSM876868", "GSM876869", "GSM876870", "GSM876871", "GSM876872", "GSM876873", "GSM876874", "GSM876875", "GSM876876", "GSM876877", "GSM876878", "GSM876879", "GSM876880", "GSM876881", "GSM876882", "GSM876883", "GSM876884", "GSM876885", "GSM876886", "GSM876887", "GSM876888", "GSM876889", "GSM876890", "GSM876891", "GSM876892", "GSM876893", "GSM876894", "GSM876895", "GSM876896", "GSM876897", "GSM876898", "GSM876899", "GSM876900", "GSM876901", "GSM876902", "GSM876903", "GSM876904", "GSM876905", "GSM876906", "GSM876907", "GSM876908", "GSM876909"], "sample_count": 72, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "The National NeuroAIDS Tissue Consortium Brain Gene Array: Two types of HIV-associated neurocognitive impairment", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:30345171:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:b4c13cdcf402dd6007309c3e931ec6aa83348499451e61cab8baf8c3bd390ffa", "bytes": 225, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[9]/table-wrap[1]#table-1", "version": null, "note": "Differentially expressed lncRNAs in white matter and their target miRNAs.", "structure": {"pmcid": "PMC6187992", "section_index": 9, "section_title": "Prediction of target miRNAs of lncRNAs and target genes", "row_count": 0, "column_count": 0}, "table": {"label": "Table 1", "caption": "Differentially expressed lncRNAs in white matter and their target miRNAs.", "rows": [], "row_count": 0, "column_count": 0, "numeric_cells": 0, "header_rows": 0, "locator": "section[9]/table-wrap[1]#table-1"}}, {"id": "asset:table:pmid:30345171:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:fff0c0c8fbf46490eb0eadbe829c48f078def0d6a4ec1166c52d46d90f9c78d0", "bytes": 211, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[10]/table-wrap[1]#table-2", "version": null, "note": "GO analysis of targeted genes of target miRNAs of lncRNAs.", "structure": {"pmcid": "PMC6187992", "section_index": 10, "section_title": "GO cluster analysis of target genes", "row_count": 0, "column_count": 0}, "table": {"label": "Table 2", "caption": "GO analysis of targeted genes of target miRNAs of lncRNAs.", "rows": [], "row_count": 0, "column_count": 0, "numeric_cells": 0, "header_rows": 0, "locator": "section[10]/table-wrap[1]#table-2"}}, {"id": "asset:table:pmid:30345171:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:f422b6192f0ff6424154b4ba549cadb657ccedeb7e1ad65876dd58e64057689f", "bytes": 221, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[10]/table-wrap[2]#table-3", "version": null, "note": "KEGG pathway analysis of targeted genes of target miRNAs of lncRNAs.", "structure": {"pmcid": "PMC6187992", "section_index": 10, "section_title": "GO cluster analysis of target genes", "row_count": 0, "column_count": 0}, "table": {"label": "Table 3", "caption": "KEGG pathway analysis of targeted genes of target miRNAs of lncRNAs.", "rows": [], "row_count": 0, "column_count": 0, "numeric_cells": 0, "header_rows": 0, "locator": "section[10]/table-wrap[2]#table-3"}}], "gaps": ["asset:data:geo:GSE35864 not downloaded", "asset:data:geo:GSE35864 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": null, "specific": null, "label": "t-test", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "This analysis was based on the t-test and adjusted according to the characteristic that the noise of microarray data was correlated with the peak value of expression data."}}], "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": "blocked", "tier": "R4", "blocking_axis": "method", "blocked_on": "method:not_determinable", "axes": {"method": {"tier": "R4", "expressible": false, "required_operations": [], "missing_operations": [], "basis": "The reader quoted the method the paper names (t-test), but the corpus's method extractor could not map it onto a DSL operation, so the method is published but not expressible."}, "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": ["GSE35864"], "resolved_accessions": ["GSE35864"], "statements": ["The following information was supplied regarding data availability:The raw measurements are provided in Data S1."], "basis": "The paper names GSE35864 in Gene Expression Omnibus (GEO), curated by the National Center for Biotechnology Information (NCBI) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:30345171", "data:geo:GSE35864", "asset:table:pmid:30345171:1", "asset:table:pmid:30345171:2", "asset:table:pmid:30345171:3"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE35864"]}, "gaps": ["method:not_determinable"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:12:41Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 18572, "completion_tokens": 1711, "cached_tokens": 640}}, "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:30345171", "type": "paper", "label": "pmid:30345171"}, {"id": "source:pmid:30345171", "type": "manuscript", "label": "PMID 30345171 full text"}, {"id": "data:geo:GSE35864", "type": "dataset", "label": "GEO GSE35864"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:30345171", "type": "paper", "label": "pmid:30345171"}, {"id": "source:pmid:30345171", "type": "manuscript", "label": "PMID 30345171 full text"}, {"id": "data:geo:GSE35864", "type": "dataset", "label": "GEO GSE35864"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-30345171", "type": "extraction", "used": ["source:pmid:30345171"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE35864", "type": "accession_resolution", "used": ["data:geo:GSE35864"], "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:30345171", "parent_hash": "sha256:e84541b78ffeead3a4f6a84fa4990da6f9eeba18c0ed87a950727f81d5836955", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE35864 licence not read", "asset:data:geo:GSE35864 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["sm. METHODS: In the GEO public database, the microarray expression profile (GSE35864) of three regio", "med to construct the non-cording-RNA (ncRNA) microarray data. Morpheus was used to identify the diff", "ion. DISCUSSION: The brand-new and different microarray results can be obtained through the updated"], "order_basis": "paper_text_order:471", "id": "assay:1"}]}