Bioinformatics analysis to identify the critical genes, microRNAs and long noncoding RNAs in melanoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:28723760", "kind": "science-record", "revision": 9, "content_hash": "sha256:b340ea0bca826e6700079381609462990736eec5c8a92cf9f63782fc14cee502", "created_at": "2026-11-01T15:40:27Z", "updated_at": "2026-11-01T22:43:03Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Bioinformatics analysis to identify the critical genes, microRNAs and long noncoding RNAs in melanoma.", "doi": "10.1097/MD.0000000000007497", "pmid": "28723760", "authors": ["Qian Zhang", "Yang Wang", "Jiulong Liang", "Yaguang Tian", "Yu Zhang", "Kai Tao"], "journal": "Medicine", "year": 2017, "abstract": "Melanoma, which is usually induced by ultraviolet light exposure and the following DNA damage, is the most dangerous skin cancer. The purpose of the present study was to screen key molecules involved in melanoma.Microarray data of E-MTAB-1862 were downloaded from the ArrayExpress database, which included 21 primary melanoma samples and 11 benign nevus samples. In addition, the RNASeq version 2 and microRNA (miRNA) sequencing data of cutaneous melanoma were downloaded from The Cancer Genome Atlas database. After identifying the differentially expressed genes (DEGs) using Limma package, enrichment analysis and protein-protein interaction (PPI) network analysis were performed separately for them using DAVID software and Cytoscape software. In addition, survival analysis and regulatory network analysis were further performed by log-rank test and Cytoscape software, respectively. Moreover, real-time reverse transcription polymerase chain reaction (RT-PCR) was performed to further verify the expression patterns of several selected DEGs.A total of 382 DEGs were identified in primary melanoma samples, including 206 upregulated genes and 176 downregulated genes. Functional enrichment analysis showed that COL17A1 was enriched in epidermis development. In the PPI network, CXCL8 (degree = 29) and STAT1 (degree = 28) had higher degrees and could interact with each other. Survival analysis showed that 21 DEGs, 55 long noncoding RNAs (lncRNAs) and 32 miRNAs were found to be associated with prognosis. Furthermore, several regulatory relationships were found in the lncRNA-gene regulatory network (such as RP11-361L15.4 targeting COL17A1) and the miRNA-gene regulatory network (such as hsa-miR-375 targeting CCL27 and hsa-miR-375 targeting insulin-like growth factor 1 receptor [IGF1R]). Real-time RT-PCR results showed that the overall direction of differential expression was consistent except COL17A1.CXCL8 interacted with STAT1, CCL27, and IGF1R targeted by hsa-miR-375, and COL17A1 targeted by RP11-361L15.4 might function in the development and progression of melanoma, which should be verified by more detailed experiments.", "claims": [{"id": "claim-method", "statement": "The DEGs between primary melanoma samples and benign nevus samples were screened by the linear models for microarray data (Limma) package[18,19] in R.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:28723760", "locator": "sections[4] \"Data preprocessing and DEGs screening\" paragraph 3", "quote": "The DEGs between primary melanoma samples and benign nevus samples were screened by the linear models for microarray data (Limma) package[18,19] in R."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Microarray data under the accession number of E-MTAB-1862 were extracted from the European Bioinformatics Institute ArrayExpress database (http://www.ebi.ac.uk/arrayexpress), which were sequenced on the platform of A-AFFY-44—Affymetrix GeneChip Human Genome U133 Plus 2.0 (HG-U133_Plus_2). The E-MTAB-1862 dataset included 21 primary melanoma samples (8 females and 13 males, mean Breslow thickness = 6.8) and 11 benign nevus samples (6 females and 5 males) isolated from skin. In addition, the RNASeqV2 and miRNASeq data of cutaneous melanoma were downloaded from TCGA database.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:28723760", "locator": "sections[3] \"Data source\" paragraph 2", "quote": "Microarray data under the accession number of E-MTAB-1862 were extracted from the European Bioinformatics Institute ArrayExpress database (http://www.ebi.ac.uk/arrayexpress), which were sequenced on the platform of A-AFFY-44—Affymetrix GeneChip Human Genome U133 Plus 2.0 (HG-U133_Plus_2). The E-MTAB-1862 dataset included 21 primary melanoma samples (8 females and 13 males, mean Breslow thickness = 6.8) and 11 benign nevus samples (6 females and 5 males) isolated from skin. In addition, the RNASeqV2 and miRNASeq data of cutaneous melanoma were downloaded from TCGA database."}], "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:28723760"], "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:E-MTAB-1862"], "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:E-MTAB-1862"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:28723760", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1097/MD.0000000000007497", "sha256": "sha256:a89fefa6e0306cca4cf6c508a3a5bdb0acb2f1a22ebded315347fb879c22eeb2", "bytes": 35094, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1097/MD.0000000000007497", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC5521900", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:E-MTAB-1862", "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=E-MTAB-1862", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "E-MTAB-1862", "version": null, "note": "Microarray data under the accession number of E-MTAB-1862 were extracted from the European Bioinformatics Institute ArrayExpress database (http://www.ebi.ac.uk/arrayexpress), which were sequenced on the platform of A-AFFY-44—Affymetrix GeneChip Human Genome U133 Plus 2.0 (HG-U133_Plus_2). The E-MTAB-1862 dataset included 21 primary melanoma samples (8 females and 13 males, mean Breslow thickness = 6.8) and 11 benign nevus samples (6 females and 5 males) isolated from skin. In addition, the RNASeqV2 and miRNASeq data of cutaneous melanoma were downloaded from TCGA database.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Microarray data under the accession number of E-MTAB-1862 were extracted from the European Bioinformatics Institute ArrayExpress database (http://www.ebi.ac.uk/arrayexpress), which were sequenced on the platform of A-AFFY-44—Affymetrix GeneChip Human Genome U133 Plus 2.0 (HG-U133_Plus_2). The E-MTAB-1862 dataset included 21 primary melanoma samples (8 females and 13 males, mean Breslow thickness = 6.8) and 11 benign nevus samples (6 females and 5 males) isolated from skin. In addition, the RNASeqV2 and miRNASeq data of cutaneous melanoma were downloaded from TCGA database.", "access_statement_kind": "repository_route_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": null, "resolution_checked_at": "2026-10-31T18:28:57Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:28723760:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:7a477526b02a64773a19bf879cef44b79956fceb12240674db652f13b3a07bf2", "bytes": 222, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[1]#T1", "version": null, "note": "The top 5 functional and pathway terms enriched for the upregulated genes.", "structure": {"pmcid": "PMC5521900", "section_index": 5, "section_title": "Functional and pathway enrichment analysis", "row_count": 0, "column_count": 0}, "table": {"label": "Table 1", "caption": "The top 5 functional and pathway terms enriched for the upregulated genes.", "rows": [], "row_count": 0, "column_count": 0, "numeric_cells": 0, "header_rows": 0, "locator": "section[12]/table-wrap[1]#T1"}}, {"id": "asset:table:pmid:28723760:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:ce26c193798e6964e8ee35b3b762b604fad63bd71f24cdcde9f01d455ccc676d", "bytes": 204, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[2]#T2", "version": null, "note": "The top 5 GO terms enriched for the downregulated genes.", "structure": {"pmcid": "PMC5521900", "section_index": 5, "section_title": "Functional and pathway enrichment analysis", "row_count": 0, "column_count": 0}, "table": {"label": "Table 2", "caption": "The top 5 GO terms enriched for the downregulated genes.", "rows": [], "row_count": 0, "column_count": 0, "numeric_cells": 0, "header_rows": 0, "locator": "section[12]/table-wrap[2]#T2"}}, {"id": "asset:table:pmid:28723760:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:7a477526b02a64773a19bf879cef44b79956fceb12240674db652f13b3a07bf2", "bytes": 222, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[1]#T1", "version": null, "note": "The top 5 functional and pathway terms enriched for the upregulated genes.", "structure": {"pmcid": "PMC5521900", "section_index": 12, "section_title": "Functional and pathway enrichment analysis", "row_count": 0, "column_count": 0}, "table": {"label": "Table 1", "caption": "The top 5 functional and pathway terms enriched for the upregulated genes.", "rows": [], "row_count": 0, "column_count": 0, "numeric_cells": 0, "header_rows": 0, "locator": "section[12]/table-wrap[1]#T1"}}, {"id": "asset:table:pmid:28723760:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:ce26c193798e6964e8ee35b3b762b604fad63bd71f24cdcde9f01d455ccc676d", "bytes": 204, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[2]#T2", "version": null, "note": "The top 5 GO terms enriched for the downregulated genes.", "structure": {"pmcid": "PMC5521900", "section_index": 12, "section_title": "Functional and pathway enrichment analysis", "row_count": 0, "column_count": 0}, "table": {"label": "Table 2", "caption": "The top 5 GO terms enriched for the downregulated genes.", "rows": [], "row_count": 0, "column_count": 0, "numeric_cells": 0, "header_rows": 0, "locator": "section[12]/table-wrap[2]#T2"}}], "gaps": ["asset:data:geo:E-MTAB-1862 not downloaded", "asset:data:geo:E-MTAB-1862 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": "The DEGs between primary melanoma samples and benign nevus samples were screened by the linear models for microarray data (Limma) package[18,19] in R."}}, {"id": "method-2", "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": 0.7, "band": "medium", "quote": "log-rank"}}, {"id": "method-3", "family": "network_analysis", "specific": "ppi_network", "label": "Network / pathway analysis", "dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "protein-protein interaction"}}], "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": ["E-MTAB-1862"], "resolved_accessions": ["E-MTAB-1862"], "statements": ["Microarray data under the accession number of E-MTAB-1862 were extracted from the European Bioinformatics Institute ArrayExpress database (http://www.ebi.ac.uk/arrayexpress), which were sequenced on the platform of A-AFFY-44—Affymetrix GeneChip Human Genome U133 Plus 2.0 (HG-U133_Plus_2). The E-MTAB-1862 dataset included 21 primary melanoma samples (8 females and 13 males, mean Breslow thickness = 6.8) and 11 benign nevus samples (6 females and 5 males) isolated from skin. In addition, the RNASeqV2 and miRNASeq data of cutaneous melanoma were downloaded from TCGA database."], "basis": "The paper names E-MTAB-1862 in European Bioinformatics Institute ArrayExpress database and TCGA database 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:28723760", "data:geo:E-MTAB-1862", "asset:table:pmid:28723760:1", "asset:table:pmid:28723760:2", "asset:table:pmid:28723760:3", "asset:table:pmid:28723760:4"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:E-MTAB-1862"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": null, "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 0, "usage": {}}, "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:28723760", "type": "paper", "label": "pmid:28723760"}, {"id": "source:pmid:28723760", "type": "manuscript", "label": "PMID 28723760 full text"}, {"id": "data:geo:E-MTAB-1862", "type": "dataset", "label": "GEO E-MTAB-1862"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:28723760", "type": "paper", "label": "pmid:28723760"}, {"id": "source:pmid:28723760", "type": "manuscript", "label": "PMID 28723760 full text"}, {"id": "data:geo:E-MTAB-1862", "type": "dataset", "label": "GEO E-MTAB-1862"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-28723760", "type": "extraction", "used": ["source:pmid:28723760"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-E-MTAB-1862", "type": "accession_resolution", "used": ["data:geo:E-MTAB-1862"], "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:28723760", "parent_hash": "sha256:fe53b9da8d191086f3c2ec99d883f0b6bcf1c1d0e48ef1d4363458e5b4e9114c", "fork_of": null, "generation": 8}, "gaps": ["asset:data:geo:E-MTAB-1862 licence not read", "asset:data:geo:E-MTAB-1862 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": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["to screen key molecules involved in melanoma.Microarray data of E-MTAB-1862 were downloaded from the"], "order_basis": "paper_text_order:270", "id": "assay:1"}, {"role": "data_generation", "definition_id": "rna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["nd 11 benign nevus samples. In addition, the RNASeq version 2 and microRNA (miRNA) sequencing da"], "order_basis": "paper_text_order:438", "id": "assay:2"}, {"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": ["The DEGs between primary melanoma samples and benign nevus samples were screened by the linear models for microarray data (Limma) package[18,19] in R."], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}