Identification of the differential expression of genes and upstream microRNAs in small cell lung cancer compared with normal lung based on bioinformatics analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32176034", "kind": "science-record", "revision": 8, "content_hash": "sha256:1b27326e9b01754b0b5bb93f2534fded26e864300bb37402745184dab5734618", "created_at": "2026-11-01T15:40:57Z", "updated_at": "2026-11-01T22:44:39Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of the differential expression of genes and upstream microRNAs in small cell lung cancer compared with normal lung based on bioinformatics analysis.", "doi": "10.1097/MD.0000000000019086", "pmid": "32176034", "authors": ["Xiuwei Li", "Chao Ma", "Huan Luo", "Jian Zhang", "Jinan Wang", "Hongtao Guo"], "journal": "Medicine", "year": 2020, "abstract": "Small cell lung cancer (SCLC) is one of the most lethal cancer, mainly attributing to its high tendency to metastasis. Mounting evidence has demonstrated that genes and microRNAs (miRNAs) are related to human cancer onset and progression including invasion and metastasis.An eligible gene dataset and an eligible miRNA dataset were downloaded from the Gene Expression Omnibus (GEO) database based our screening criteria. Differentially expressed genes (DE-genes) or DE-miRNAs for each dataset obtained by the R software package. The potential target genes of the top 10 DE-miRNAs were predicted by multiple databases. For annotation, visualization and integrated discovery, Metascape 3.0 was introduced to perform enrichment analysis for the DE-genes and the predicted target genes of the selected top 10 DE-miRNAs, including Pathway and Process Enrichment Analysis or protein-protein interaction enrichment analysis. The intersection of predicted target genes and DE-genes was taken as the final DE-genes. Then apply the predicted miRNAs-targets relationship of top 10 DE-miRNAs to the final DE-genes to gain more convinced DE-miRNAs, DE-genes and their one to one relationship.GSE19945 (miRNA microarray) and GSE40275 (gene microarray) datasets were selected and downloaded. 56 DE-miRNAs and 861 DE-genes were discovered. 297 miRNAs-targets relationships (284 unique genes) were predicted as the target of top 10 upregulating DE-miRNAs. 245 miRNAs-targets relationships (238 unique genes) were identified as the target of top 10 downregulating DE-miRNAs. The key results of enrichment analysis include protein kinase B signaling, transmembrane receptor protein tyrosine kinase signaling pathway, negative regulation of cell differentiation, response to growth factor, cellular response to lipid, muscle structure development, response to growth factor, signaling by Receptor Tyrosine Kinases, epithelial cell migration, cellular response to organic cyclic compound, Cell Cycle (Mitotic), DNA conformation change, cell division, DNA replication, cell cycle phase transition, blood vessel development, inflammatory response, Staphylococcus aureus infection, leukocyte migration, and myeloid leukocyte activation. Differential expression of genes-upstream miRNAs (RBMS3-hsa-miR-7-5p, NEDD9-hsa-miR-18a-5p, CRIM1-hsa-miR-18a-5p, TGFBR2-hsa-miR-9-5p, MYO1C-hsa-miR-9-5p, KLF4-hsa-miR-7-5p, EMP2-hsa-miR-1290, TMEM2-hsa-miR-18a-5p, CTGF-hsa-miR-18a-5p, TNFAIP3-hsa-miR-18a-5p, THBS1-hsa-miR-182-5p, KPNA2-hsa-miR-144-3p, GPR137C-hsa-miR-1-3p, GRIK3-hsa-miR-144-3p, and MTHFD2-hsa-miR-30a-3p) were identified in SCLC.RBMS3, NEDD9, CRIM1, KPNA2, GPR137C, GRIK3, hsa-miR-7-5p, hsa-miR-18a-5p, hsa-miR-144-3p, hsa-miR-1-3p along with the pathways included protein kinase B signaling, muscle structure development, Cell Cycle (Mitotic) and blood vessel development may gain a high chance to play a key role in the prognosis of SCLC, but more studies should be conducted to reveal it more clearly.", "claims": [{"id": "claim-method", "statement": "The miRNA and gene differential expression analysis were conducted using the limma software package in the Bioconductor package (http://www.bioconductor.org/).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32176034", "locator": "sections[4] \"Screening for DE-miRNAs and DE-genes\" paragraph 2", "quote": "The miRNA and gene differential expression analysis were conducted using the limma software package in the Bioconductor package (http://www.bioconductor.org/)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data availability: All data reported have been obtained from GEO database.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32176034", "locator": "sections[21] \"Footnotes\" paragraph 2", "quote": "Data availability: All data reported have been obtained from GEO 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:32176034"], "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:GSE19945"], "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:GSE19945"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:32176034", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1097/MD.0000000000019086", "sha256": "sha256:aeae71cb2068b0815212c19b6557cf8f190d5f251abb663bdc31c0c0a7f2b9ea", "bytes": 44236, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1097/MD.0000000000019086", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7440067", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE19945", "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=GSE19945", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE19945", "version": null, "note": "Data availability: All data reported have been obtained from GEO database.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data availability: All data reported have been obtained from GEO database.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM498363", "GSM498364", "GSM498365", "GSM498366", "GSM498367", "GSM498368", "GSM498369", "GSM498370", "GSM498371", "GSM498372", "GSM498373", "GSM498374", "GSM498375", "GSM498376", "GSM498377", "GSM498378", "GSM498379", "GSM498380", "GSM498381", "GSM498382", "GSM498383", "GSM498384", "GSM498385", "GSM498386", "GSM498387", "GSM498388", "GSM498389", "GSM498390", "GSM498391", "GSM498392", "GSM498393", "GSM498394", "GSM498395", "GSM498396", "GSM498397", "GSM498398", "GSM498399", "GSM498400", "GSM498401", "GSM498402", "GSM498403", "GSM498404", "GSM498405", "GSM498406", "GSM498407", "GSM498408", "GSM498409", "GSM498410", "GSM498411", "GSM498412", "GSM498413", "GSM498414", "GSM498415", "GSM498416", "GSM498417", "GSM498418", "GSM498419", "GSM498420", "GSM498421", "GSM498422", "GSM498423", "GSM498424", "GSM498425"], "sample_count": 63, "group_sizes": null, "group_sizes_basis": null, "platform": "9948", "taxon": "Homo sapiens", "title": "A small-cell lung cancer subtype with good prognosis found by a three miRNA signature", "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:GSE40275", "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=GSE40275", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE40275", "version": null, "note": "Data availability: All data reported have been obtained from GEO database.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data availability: All data reported have been obtained from GEO database.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM990169", "GSM990170", "GSM990171", "GSM990172", "GSM990173", "GSM990174", "GSM990175", "GSM990176", "GSM990177", "GSM990178", "GSM990179", "GSM990180", "GSM990181", "GSM990182", "GSM990183", "GSM990184", "GSM990185", "GSM990186", "GSM990187", "GSM990188", "GSM990189", "GSM990190", "GSM990191", "GSM990192", "GSM990193", "GSM990194", "GSM990195", "GSM990196", "GSM990197", "GSM990198", "GSM990199", "GSM990200", "GSM990201", "GSM990202", "GSM990203", "GSM990204", "GSM990205", "GSM990206", "GSM990207", "GSM990208", "GSM990209", "GSM990210", "GSM990211", "GSM990212", "GSM990213", "GSM990214", "GSM990215", "GSM990216", "GSM990217", "GSM990218", "GSM990219", "GSM990220", "GSM990221", "GSM990222", "GSM990223", "GSM990224", "GSM990225", "GSM990226", "GSM990227", "GSM990228", "GSM990229", "GSM990230", "GSM990231", "GSM990232", "GSM990233", "GSM990234", "GSM990235", "GSM990236", "GSM990237", "GSM990238", "GSM990239", "GSM990240", "GSM990241", "GSM990242", "GSM990243", "GSM990244", "GSM990245", "GSM990246", "GSM990247", "GSM990248", "GSM990249", "GSM990250", "GSM990251", "GSM990252"], "sample_count": 84, "group_sizes": null, "group_sizes_basis": null, "platform": "15974", "taxon": "Homo sapiens", "title": "Gene expression of samples derived from normal lung and patients with small cell lung cancer (SCLC) or non-small cell lung cancer (NSCLC)", "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:32176034:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:c2a3778699d5a0b03c84dab6f8ef79ee4e44672417a6d49e01ff96a839e80d60", "bytes": 215, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[16]/table-wrap[1]#T12", "version": null, "note": "More convinced downregulated DE- genes and their upstream miRNAs.", "structure": {"pmcid": "PMC7440067", "section_index": 7, "section_title": "Conjoint analysis of DE-miRNAs and DE-genes", "row_count": 0, "column_count": 0}, "table": {"label": "Table 12", "caption": "More convinced downregulated DE- genes and their upstream miRNAs.", "rows": [], "row_count": 0, "column_count": 0, "numeric_cells": 0, "header_rows": 0, "locator": "section[16]/table-wrap[1]#T12"}}, {"id": "asset:table:pmid:32176034:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:102a5ef66b3612fdb64b6feee00245c0fc90df45fd37b4b5dca1f1e90e5fdf62", "bytes": 213, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[16]/table-wrap[2]#T13", "version": null, "note": "More convinced upregulated DE- genes and their upstream miRNAs.", "structure": {"pmcid": "PMC7440067", "section_index": 7, "section_title": "Conjoint analysis of DE-miRNAs and DE-genes", "row_count": 0, "column_count": 0}, "table": {"label": "Table 13", "caption": "More convinced upregulated DE- genes and their upstream miRNAs.", "rows": [], "row_count": 0, "column_count": 0, "numeric_cells": 0, "header_rows": 0, "locator": "section[16]/table-wrap[2]#T13"}}, {"id": "asset:table:pmid:32176034:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:77752343971704fc31f84167b945a456de73db89a780910b8dbcb53639fbf352", "bytes": 191, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[10]/table-wrap[1]#T1", "version": null, "note": "Basic information of the selected datasets.", "structure": {"pmcid": "PMC7440067", "section_index": 10, "section_title": "Microarrays", "row_count": 0, "column_count": 0}, "table": {"label": "Table 1", "caption": "Basic information of the selected datasets.", "rows": [], "row_count": 0, "column_count": 0, "numeric_cells": 0, "header_rows": 0, "locator": "section[10]/table-wrap[1]#T1"}}, {"id": "asset:table:pmid:32176034:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:e5de46d7d14ce344ae6df5b0ca7c9710e8b470638825bf18014fc86a93dbe8a6", "bytes": 212, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[11]/table-wrap[1]#T2", "version": null, "note": "The top 20 upregulated DE-miRNAs (ranked by |fold change [FC]|).", "structure": {"pmcid": "PMC7440067", "section_index": 11, "section_title": "Identification of DE-miRNAs and DE-genes", "row_count": 0, "column_count": 0}, "table": {"label": "Table 2", "caption": "The top 20 upregulated DE-miRNAs (ranked by |fold change [FC]|).", "rows": [], "row_count": 0, "column_count": 0, "numeric_cells": 0, "header_rows": 0, "locator": "section[11]/table-wrap[1]#T2"}}, {"id": "asset:table:pmid:32176034:5", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:48b7c31d32686692c6908c5962d681b44c236bfcf7c2fd8813c9d9ea11d8b409", "bytes": 213, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[11]/table-wrap[2]#T5", "version": null, "note": "The top 20 downregulated DE-genes (ranked by |fold change [FC]|).", "structure": {"pmcid": "PMC7440067", "section_index": 11, "section_title": "Identification of DE-miRNAs and DE-genes", "row_count": 0, "column_count": 0}, "table": {"label": "Table 5", "caption": "The top 20 downregulated DE-genes (ranked by |fold change [FC]|).", "rows": [], "row_count": 0, "column_count": 0, "numeric_cells": 0, "header_rows": 0, "locator": "section[11]/table-wrap[2]#T5"}}, {"id": "asset:table:pmid:32176034:6", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:6841bcf06a855d30f5092ea6d5b51a234c6863dbc3af99513b7f534e9357fc77", "bytes": 214, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[11]/table-wrap[3]#T3", "version": null, "note": "The top 20 downregulated DE-miRNAs (ranked by |fold change [FC]|).", "structure": {"pmcid": "PMC7440067", "section_index": 11, "section_title": "Identification of DE-miRNAs and DE-genes", "row_count": 0, "column_count": 0}, "table": {"label": "Table 3", "caption": "The top 20 downregulated DE-miRNAs (ranked by |fold change [FC]|).", "rows": [], "row_count": 0, "column_count": 0, "numeric_cells": 0, "header_rows": 0, "locator": "section[11]/table-wrap[3]#T3"}}, {"id": "asset:table:pmid:32176034:7", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:158f4dc4494ce8bfe5cf6542f30fbde1418a6a670ddb8cca1a5076a03ef1d6de", "bytes": 211, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[11]/table-wrap[4]#T4", "version": null, "note": "The top 20 upregulated DE-genes (ranked by |fold change [FC]|).", "structure": {"pmcid": "PMC7440067", "section_index": 11, "section_title": "Identification of DE-miRNAs and DE-genes", "row_count": 0, "column_count": 0}, "table": {"label": "Table 4", "caption": "The top 20 upregulated DE-genes (ranked by |fold change [FC]|).", "rows": [], "row_count": 0, "column_count": 0, "numeric_cells": 0, "header_rows": 0, "locator": "section[11]/table-wrap[4]#T4"}}, {"id": "asset:table:pmid:32176034:8", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:c5b530f8a9f4f069024c68b95b6c9b61359b05ffd4b80881746b9077e96fffac", "bytes": 269, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[14]/table-wrap[1]#T6", "version": null, "note": "Top 20 clusters with their representative enriched terms of the targets genes of upregulated DE-miRNAs (one per cluster).", "structure": {"pmcid": "PMC7440067", "section_index": 14, "section_title": "Pathway and process enrichment analysis", "row_count": 0, "column_count": 0}, "table": {"label": "Table 6", "caption": "Top 20 clusters with their representative enriched terms of the targets genes of upregulated DE-miRNAs (one per cluster).", "rows": [], "row_count": 0, "column_count": 0, "numeric_cells": 0, "header_rows": 0, "locator": "section[14]/table-wrap[1]#T6"}}, {"id": "asset:table:pmid:32176034:9", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:93398b6f0da1a73c55c5a510cdb5168951ad3c5abd092b61ca0aa3b1c0d49e0e", "bytes": 253, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[14]/table-wrap[2]#T9", "version": null, "note": "Top 20 clusters with their representative enriched terms of the downregulated DE-genes (one per cluster).", "structure": {"pmcid": "PMC7440067", "section_index": 14, "section_title": "Pathway and process enrichment analysis", "row_count": 0, "column_count": 0}, "table": {"label": "Table 9", "caption": "Top 20 clusters with their representative enriched terms of the downregulated DE-genes (one per cluster).", "rows": [], "row_count": 0, "column_count": 0, "numeric_cells": 0, "header_rows": 0, "locator": "section[14]/table-wrap[2]#T9"}}, {"id": "asset:table:pmid:32176034:10", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:3345c5e615c6879c7ff0c6049441f5433929b5aeb9fb79fc3d029b730a402ea7", "bytes": 271, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[14]/table-wrap[3]#T7", "version": null, "note": "Top 20 clusters with their representative enriched terms of the targets genes of downregulated DE-miRNAs (one per cluster).", "structure": {"pmcid": "PMC7440067", "section_index": 14, "section_title": "Pathway and process enrichment analysis", "row_count": 0, "column_count": 0}, "table": {"label": "Table 7", "caption": "Top 20 clusters with their representative enriched terms of the targets genes of downregulated DE-miRNAs (one per cluster).", "rows": [], "row_count": 0, "column_count": 0, "numeric_cells": 0, "header_rows": 0, "locator": "section[14]/table-wrap[3]#T7"}}, {"id": "asset:table:pmid:32176034:11", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:049295fa5f1dee7cb96c69fe6e6cf1e24910ba143f78d782f8f8944dc51f56eb", "bytes": 251, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[14]/table-wrap[4]#T8", "version": null, "note": "Top 20 clusters with their representative enriched terms of the upregulated DE-genes (one per cluster).", "structure": {"pmcid": "PMC7440067", "section_index": 14, "section_title": "Pathway and process enrichment analysis", "row_count": 0, "column_count": 0}, "table": {"label": "Table 8", "caption": "Top 20 clusters with their representative enriched terms of the upregulated DE-genes (one per cluster).", "rows": [], "row_count": 0, "column_count": 0, "numeric_cells": 0, "header_rows": 0, "locator": "section[14]/table-wrap[4]#T8"}}, {"id": "asset:table:pmid:32176034:12", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:af85be7856c794f5dc9887c63c841b44c6138b98b3360ec5ecd20bc130f1b045", "bytes": 200, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[15]/table-wrap[1]#T10", "version": null, "note": "Protein–protein interaction enrichment analysis.", "structure": {"pmcid": "PMC7440067", "section_index": 15, "section_title": "Protein–protein interaction enrichment analysis", "row_count": 0, "column_count": 0}, "table": {"label": "Table 10", "caption": "Protein–protein interaction enrichment analysis.", "rows": [], "row_count": 0, "column_count": 0, "numeric_cells": 0, "header_rows": 0, "locator": "section[15]/table-wrap[1]#T10"}}, {"id": "asset:table:pmid:32176034:13", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:51fc0d62eadd7dcb54aa6c497626108fcbd51ac9678da9d0f5cab1515b6eaf48", "bytes": 198, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[15]/table-wrap[2]#T11", "version": null, "note": "Protein-protein interaction enrichment analysis.", "structure": {"pmcid": "PMC7440067", "section_index": 15, "section_title": "Protein–protein interaction enrichment analysis", "row_count": 0, "column_count": 0}, "table": {"label": "Table 11", "caption": "Protein-protein interaction enrichment analysis.", "rows": [], "row_count": 0, "column_count": 0, "numeric_cells": 0, "header_rows": 0, "locator": "section[15]/table-wrap[2]#T11"}}, {"id": "asset:table:pmid:32176034:14", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:c2a3778699d5a0b03c84dab6f8ef79ee4e44672417a6d49e01ff96a839e80d60", "bytes": 215, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[16]/table-wrap[1]#T12", "version": null, "note": "More convinced downregulated DE- genes and their upstream miRNAs.", "structure": {"pmcid": "PMC7440067", "section_index": 16, "section_title": "Conjoint analysis of DE-miRNAs and DE-genes", "row_count": 0, "column_count": 0}, "table": {"label": "Table 12", "caption": "More convinced downregulated DE- genes and their upstream miRNAs.", "rows": [], "row_count": 0, "column_count": 0, "numeric_cells": 0, "header_rows": 0, "locator": "section[16]/table-wrap[1]#T12"}}, {"id": "asset:table:pmid:32176034:15", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:102a5ef66b3612fdb64b6feee00245c0fc90df45fd37b4b5dca1f1e90e5fdf62", "bytes": 213, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[16]/table-wrap[2]#T13", "version": null, "note": "More convinced upregulated DE- genes and their upstream miRNAs.", "structure": {"pmcid": "PMC7440067", "section_index": 16, "section_title": "Conjoint analysis of DE-miRNAs and DE-genes", "row_count": 0, "column_count": 0}, "table": {"label": "Table 13", "caption": "More convinced upregulated DE- genes and their upstream miRNAs.", "rows": [], "row_count": 0, "column_count": 0, "numeric_cells": 0, "header_rows": 0, "locator": "section[16]/table-wrap[2]#T13"}}], "gaps": ["asset:data:geo:GSE19945 not downloaded", "asset:data:geo:GSE19945 licence not read", "asset:data:geo:GSE40275 not downloaded", "asset:data:geo:GSE40275 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 miRNA and gene differential expression analysis were conducted using the limma software package in the Bioconductor package (http://www.bioconductor.org/)."}}, {"id": "method-2", "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": 0.8, "band": "high", "quote": "Student's t test"}}, {"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": ["GSE19945", "GSE40275"], "resolved_accessions": ["GSE19945", "GSE40275"], "statements": ["Data availability: All data reported have been obtained from GEO database."], "basis": "The paper names GSE19945, GSE40275 in NCBI Gene Expression Omnibus (GEO) 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:32176034", "data:geo:GSE19945", "asset:table:pmid:32176034:1", "asset:table:pmid:32176034:2", "asset:table:pmid:32176034:3", "asset:table:pmid:32176034:4", "asset:table:pmid:32176034:5", "asset:table:pmid:32176034:6", "asset:table:pmid:32176034:7", "asset:table:pmid:32176034:8", "asset:table:pmid:32176034:9", "asset:table:pmid:32176034:10", "asset:table:pmid:32176034:11", "asset:table:pmid:32176034:12", "asset:table:pmid:32176034:13", "asset:table:pmid:32176034:14", "asset:table:pmid:32176034:15"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE19945"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:18:45Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 34845, "completion_tokens": 1207, "cached_tokens": 792}}, "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:32176034", "type": "paper", "label": "pmid:32176034"}, {"id": "source:pmid:32176034", "type": "manuscript", "label": "PMID 32176034 full text"}, {"id": "data:geo:GSE19945", "type": "dataset", "label": "GEO GSE19945"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:32176034", "type": "paper", "label": "pmid:32176034"}, {"id": "source:pmid:32176034", "type": "manuscript", "label": "PMID 32176034 full text"}, {"id": "data:geo:GSE19945", "type": "dataset", "label": "GEO GSE19945"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-32176034", "type": "extraction", "used": ["source:pmid:32176034"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE19945", "type": "accession_resolution", "used": ["data:geo:GSE19945"], "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:32176034", "parent_hash": "sha256:4b9111305ef32fbb44299e1b8c4689d0d15a8ff112186edc9269b0ab687c0ba6", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:GSE19945 licence not read", "asset:data:geo:GSE19945 not downloaded", "asset:data:geo:GSE40275 licence not read", "asset:data:geo:GSE40275 not downloaded", "execution.not_run", "method.reader_differs_from_extractor", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"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 miRNA and gene differential expression analysis were conducted using the limma software package in the Bioconductor package (http://www.bioconductor.org/)."], "order_basis": "analysis_only", "id": "assay:1"}]}