The expression of miR-513c and miR-3163 was downregulated in tumor tissues compared with normal adjacent tissue of patients with breast cancer.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34233668", "kind": "science-record", "revision": 5, "content_hash": "sha256:e2d7159cddc75c66fe374ff04f722b7a5758af82b8db12d954f667465b6203f8", "created_at": "2026-11-01T15:41:42Z", "updated_at": "2026-11-01T22:04:08Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "The expression of miR-513c and miR-3163 was downregulated in tumor tissues compared with normal adjacent tissue of patients with breast cancer.", "doi": "10.1186/s12920-021-01029-3", "pmid": "34233668", "authors": ["Soheila Delgir", "Khandan Ilkhani", "Asma Safi", "Yazdan Rahmati", "Vahid Montazari", "Zahra Zaynali-Khasraghi", "Farhad Seif", "Milad Bastami", "Mohammad Reza Alivand"], "journal": "BMC medical genomics", "year": 2021, "abstract": "BACKGROUND: Breast cancer (BC) is the most invasive cancer with different subtypes that its metabolism is unique compared with normal cells. Glutamine is considered critical nutrition that many cancer cells, particularly BC cells, are dependent on it for growth and proliferation. Therefore, targeting glutamine metabolism, especially enzymes that are related to this pathway, can be beneficial to design anti-cancer agents. Recent evidence has shown that microRNAs (miRNAs), with a short length and single-strand properties, play a prominent role in regulating the genes related to glutamine metabolism, which may control the development of cancer.\nMETHODS: In silico analysis confirmed that miR-513c and miR-3163 might be involved in glutamine metabolism. The expression level of these two miRNAs was evaluated in eighty BC tissues and normal adjacent tissues. Furthermore, GSE38167, GSE38867, GSE42128, GSE45666, and GSE53179 were employed from gene expression omnibus (GEO). The Limma package was utilized to identify differentially expressed miRNAs (DEMs) of mentioned datasets to evaluate miR-513c and miR-3163 expression. Further, in silico analysis was utilized to predict the potential biological processes and molecular pathways of miR-513c and miR-3163, based on their target genes.\nRESULTS: In silico studies revealed top categories of biological processes and cellular pathways that might play a critical role in metabolism reprogramming and cancer development and were target genes for miR-513c and miR-3163. The current study showed that miR-513c (p value = 0.02062 and FC = - 2.3801) and miR-3163 (p value = 0.02034 and FC = - 2.3792) were downregulated in tumor tissues compared to normal adjacent tissues. The analysis of GEO microarray datasets showed that miR-513c was downregulated in GSE38167, GSE38867, GSE42128, GSE45666 and GSE53179, whereas there was a significant downregulation of miR-3163 in only two studies, including GSE38867 and GSE42128 that they were in accordance with our experimental results. Furthermore, the subgroup analysis did not show any substantial relationship between expression levels of these two miRNAs and factors such as age, family history of cancer, and abortion history.\nCONCLUSION: MiR-513c and miR-3163 were downregulated in BC tissues, which might serve as tumor suppressors. They are suggested as potential therapeutic targets for patients with BC.", "claims": [{"id": "claim-method", "statement": "Paired T-test and delta-CTs were used for comparison of the gene expressions between tumor and normal adjacent tissues.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34233668", "locator": "sections[8] \"Statistical analysis\" paragraph 2", "quote": "Paired T-test and delta-CTs were used for comparison of the gene expressions between tumor and normal adjacent tissues."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data that support the findings of this study are available on request from the corresponding author. The data are not publicly available due to privacy or ethical restrictions e.g. containing information that could compromise the privacy of research participants.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34233668", "locator": "sections[25] \"notes\" paragraph 1", "quote": "The data that support the findings of this study are available on request from the corresponding author. The data are not publicly available due to privacy or ethical restrictions e.g. containing information that could compromise the privacy of research participants."}], "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:34233668"], "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": "blocked", "blocked_on": "data:accession_absent", "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": [], "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": [], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:obtain_source_data blocked on data:accession_absent"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:34233668", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s12920-021-01029-3", "sha256": "sha256:1aa4b3a3e0402f78bbe632db2161afc1be52e715b91ab65a1137cdf08b0aea3c", "bytes": 33554, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s12920-021-01029-3", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8265124", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "asset:table:pmid:34233668:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:5040c36ebc33e1c810f672deb6d39b3ab0e437c125000b817510148103d1ef2d", "bytes": 557, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[4]/table-wrap[1]#Tab1", "version": null, "note": "Basis characteristics of the patients with breast cancer", "structure": {"pmcid": "PMC8265124", "section_index": 4, "section_title": "Clinical specimens", "row_count": 15, "column_count": 2}, "table": {"label": "Table 1", "caption": "Basis characteristics of the patients with breast cancer", "rows": [["Parameter", "Number (percentage)"], ["Tumor grade", "Grade 3 = 5%"], ["Grade 2 = 87.5%"], ["Grade 1 = 7.5%"], ["Lymph node", "Yes = 87.5%"], ["No = 12.5%"], ["Family cancer history", "Yes = 47.5%"], ["No = 41.3%"], ["Unknown = 11.2%"], ["Abortion history", "Yes = 36.2%"], ["No = 51.3%"], ["Unknown = 12.5%"], ["Age", "≤ 50 38.8%"], ["> 50 40%"], ["Unknown = 21.2%"]], "row_count": 15, "column_count": 2, "numeric_cells": 14, "header_rows": 1, "locator": "section[4]/table-wrap[1]#Tab1"}}, {"id": "asset:table:pmid:34233668:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:4b37c61e09078ef487fe65f4f81a4a95df98dbcc1436607e257b63c2180ba240", "bytes": 995, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[6]/table-wrap[1]#Tab2", "version": null, "note": "cDNA synthesis specific stem-loop primers and real-time PCR primer sequences", "structure": {"pmcid": "PMC8265124", "section_index": 6, "section_title": "cDNA synthesis and real-time PCR", "row_count": 9, "column_count": 4}, "table": {"label": "Table 2", "caption": "cDNA synthesis specific stem-loop primers and real-time PCR primer sequences", "rows": [["", "Noncoding-RNAs and their accession numbers", "Sequences"], ["cDNA synthesis reaction", "MiR-3163-5pNIMAT 0015037", "MiR-3163 (STL)", "5′-GTCGTATCCAGTGCAGGGTCCGAGGTATTCGCACTGGATACGACGTCTTAC-3′"], ["Mir-513c-5pNIMAT 0022728", "Mir-513c (STL)", "5′-GTCGTATCCAGTGCAGGGTCCGAGGTATTCGCACTGGATACGACATAAAC-3′"], ["RNU6NR_003027.2", "U6 (STL)", "5′-GTCGTATCCAGTGCAGGGTCCGAGGTATTCGCACTGGATACGACAAAAATAT-3′"], ["Real time PCR reaction", "MiR-3163-5pNIMAT 0015037", "Mir-3163 (F)", "5′-AGGGTATAAAATGAGGGCAGTAAGAC-3′"], ["Mir-513c-5pNIMAT 0022728", "Mir-513c (F)", "5′-GGGTTCTCAAGGAGGTGTCG-3′"], ["MiR-3163 and Mir-513c", "Common (R)", "5′-GTGCAGGGTCCGAGGT-3′"], ["RNU6NR_003027.2", "U6 (F)", "5′-GCTTCGGCAGCACATATACTAAAAT-3′"], ["U6 (R)", "5′-CGCTTCACGAATTTGCGTGTCAT-3′"]], "row_count": 9, "column_count": 4, "numeric_cells": 19, "header_rows": 1, "locator": "section[6]/table-wrap[1]#Tab2"}}, {"id": "asset:table:pmid:34233668:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:7803da2816c7d4c06eb6f4be12a5681f89dcf1cb4aa8672b29ea9ebfe61f4e5d", "bytes": 570, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[17]/table-wrap[1]#Tab3", "version": null, "note": "Pathways that are enriched among target genes of mir-513c", "structure": {"pmcid": "PMC8265124", "section_index": 7, "section_title": "In silico analysis", "row_count": 5, "column_count": 7}, "table": {"label": "Table 3", "caption": "Pathways that are enriched among target genes of mir-513c", "rows": [["No", "ID", "Pathway name", "O", "FDR", "E", "p valuea"], ["1", "hsa05222", "Small cell lung cancer", "92", "1", "0.34163", "0.0046026"], ["2", "hsa00130", "Ubiquinone and other terpenoid-quinone biosynthesis", "11", "1", "0.040847", "0.040124"], ["3", "hsa05200", "Pathways in cancer", "524", "1", "1.9458", "0.041062"], ["4", "hsa05032", "Morphine addiction", "91", "1", "0.33792", "0.044411"]], "row_count": 5, "column_count": 7, "numeric_cells": 24, "header_rows": 1, "locator": "section[17]/table-wrap[1]#Tab3"}}, {"id": "asset:table:pmid:34233668:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:ea4fb9b34ef042294ae52e6b4f9af0370219a68ff3a5abe9346093caa343b845", "bytes": 1177, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[17]/table-wrap[2]#Tab4", "version": null, "note": "Pathways that are enriched among target genes of miRNA-3163", "structure": {"pmcid": "PMC8265124", "section_index": 7, "section_title": "In silico analysis", "row_count": 11, "column_count": 8}, "table": {"label": "Table 4", "caption": "Pathways that are enriched among target genes of miRNA-3163", "rows": [["Nos", "Gene set", "Pathway name", "C", "E", "R", "FDR", "p valuea"], ["1", "hsa05170", "Human immunodeficiency virus 1 infection", "212", "3.6155", "3.3191", "0.081094", "2.5E−04"], ["2", "hsa04110", "Cell cycle", "124", "2.1147", "3.783", "0.09676", "1E−03"], ["3", "hsa04114", "Oocyte meiosis", "124", "2.1147", "3.783", "0.09676", "1E−03"], ["4", "hsa05202", "Transcriptional misregulation in cancer", "186", "3.1721", "3.1525", "0.09676", "1E−03"], ["5", "hsa04010", "MAPK signaling pathway", "295", "5.0309", "2.584", "0.09676", "1.5E−03"], ["6", "hsa05167", "Kaposi sarcoma-associated herpesvirus infection", "186", "3.1721", "2.8373", "0.2378", "4.4E−03"], ["7", "hsa04340", "Hedgehog signaling pathway", "47", "0.80154", "4.9904", "0.3802", "8.2E−03"], ["8", "hsa04310", "Wnt signaling pathway", "146", "2.4899", "2.8114", "0.49589", "1E−02"], ["9", "hsa05206", "MicroRNAs in cancer", "150", "2.5581", "2.7364", "0.50585", "1.4E−02"], ["10", "hsa04218", "Cellular senescence", "160", "2.7286", "2.5654", "0.58131", "2E−02"]], "row_count": 11, "column_count": 8, "numeric_cells": 71, "header_rows": 1, "locator": "section[17]/table-wrap[2]#Tab4"}}, {"id": "asset:table:pmid:34233668:5", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:0c5034a5a6d0829118fb937f7fd18a23a0845eeb3ed94b0cefbec2c34205600f", "bytes": 1270, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[17]/table-wrap[3]#Tab5", "version": null, "note": "Top ten enriched biological processes among target genes of miR-513c", "structure": {"pmcid": "PMC8265124", "section_index": 7, "section_title": "In silico analysis", "row_count": 11, "column_count": 8}, "table": {"label": "Table 5", "caption": "Top ten enriched biological processes among target genes of miR-513c", "rows": [["No", "GO ID", "Biological process", "O", "FDR", "E", "R", "p valuea"], ["1", "GO: 0042148", "Strand invasion", "5", "1", "0.024004", "83.32", "2.2E−04"], ["2", "GO: 0006612", "Protein targeting to membrane", "187", "1", "0.89774", "6.6834", "2.7E−04"], ["3", "GO: 0045047", "Protein targeting to ER", "107", "1", "0.51368", "7.7869", "1.7E−03"], ["4", "GO: 0072599", "Establishment of protein localization to endoplasmic reticulum", "111", "1", "0.53289", "7.5063", "1.9E−03"], ["5", "GO: 0008340", "Determination of adult lifespan", "17", "1", "0.081613", "24.506", "2.9−E3"], ["6", "GO: 0006605", "Protein targeting", "412", "1", "1.9779", "3.5391", "3.6E−03"], ["7", "GO: 0090150", "Establishment of protein localization to membrane", "313", "1", "1.5026", "3.993", "3.9–03"], ["8", "GO: 0070972", "Protein localization to endoplasmic reticulum", "137", "1", "0.65771", "6.0818", "4.2E−03"], ["9", "GO: 0031297", "Replication fork processing", "95", "1", "0.15362", "13.019", "1E−02"], ["10", "GO: 0006614", "SRP-dependent co-translational protein targeting to membrane", "95", "1", "0.45607", "6.5779", "1E−02"]], "row_count": 11, "column_count": 8, "numeric_cells": 70, "header_rows": 1, "locator": "section[17]/table-wrap[3]#Tab5"}}, {"id": "asset:table:pmid:34233668:6", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:93da04f037c7bd1c8dea0314251456fbed3b5da00dcdbc4b1b1615613e258364", "bytes": 1385, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[17]/table-wrap[4]#Tab6", "version": null, "note": "Top ten enriched biological processes among target genes of miR-3163", "structure": {"pmcid": "PMC8265124", "section_index": 7, "section_title": "In silico analysis", "row_count": 11, "column_count": 8}, "table": {"label": "Table 6", "caption": "Top ten enriched biological processes among target genes of miR-3163", "rows": [["No", "Gene set", "Biological pathways", "C", "E", "R", "FDR", "p value"], ["1", "GO: 0045934", "Negative regulation of nucleobase-containing compound metabolic process", "1418", "22.805", "1.9732", "0.04352", "8E−06"], ["2", "GO: 0033554", "Cellular response to stress", "1867", "30.026", "1.7984", "0.04352", "1E−05"], ["3", "GO: 0010629", "Negative regulation of gene expression", "1733", "27.871", "1.8299", "0.04352", "1E−05"], ["4", "GO: 1903311", "Regulation of mRNA metabolic process", "266", "4.278", "3.5063", "0.06326", "3E−05"], ["5", "GO: 0045935", "Positive regulation of nucleobase-containing compound metabolic process", "1847", "29.705", "1.7169", "0.12664", "8E−05"], ["6", "GO: 0000278", "Mitotic cell cycle", "927", "14.909", "2.0793", "0.12664", "9E−05"], ["7", "GO: 0051253", "Negative regulation of RNA metabolic process", "1295", "20.827", "1.8726", "0.12664", "1E−04"], ["8", "GO: 0000902", "Cell morphogenesis", "982", "15.793", "2.0262", "0.12664", "1E−04"], ["9", "GO: 0032989", "Cellular component morphogenesis", "1082", "17.401", "1.9539", "0.12664", "1E−04"], ["10", "GO: 2000113", "Negative regulation of cellular macromolecule biosynthetic process", "1359", "21.856", "1.8301", "0.12664", "1E−04"]], "row_count": 11, "column_count": 8, "numeric_cells": 70, "header_rows": 1, "locator": "section[17]/table-wrap[4]#Tab6"}}, {"id": "asset:table:pmid:34233668:7", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:7803da2816c7d4c06eb6f4be12a5681f89dcf1cb4aa8672b29ea9ebfe61f4e5d", "bytes": 570, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[17]/table-wrap[1]#Tab3", "version": null, "note": "Pathways that are enriched among target genes of mir-513c", "structure": {"pmcid": "PMC8265124", "section_index": 17, "section_title": "In silico analysis", "row_count": 5, "column_count": 7}, "table": {"label": "Table 3", "caption": "Pathways that are enriched among target genes of mir-513c", "rows": [["No", "ID", "Pathway name", "O", "FDR", "E", "p valuea"], ["1", "hsa05222", "Small cell lung cancer", "92", "1", "0.34163", "0.0046026"], ["2", "hsa00130", "Ubiquinone and other terpenoid-quinone biosynthesis", "11", "1", "0.040847", "0.040124"], ["3", "hsa05200", "Pathways in cancer", "524", "1", "1.9458", "0.041062"], ["4", "hsa05032", "Morphine addiction", "91", "1", "0.33792", "0.044411"]], "row_count": 5, "column_count": 7, "numeric_cells": 24, "header_rows": 1, "locator": "section[17]/table-wrap[1]#Tab3"}}, {"id": "asset:table:pmid:34233668:8", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:ea4fb9b34ef042294ae52e6b4f9af0370219a68ff3a5abe9346093caa343b845", "bytes": 1177, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[17]/table-wrap[2]#Tab4", "version": null, "note": "Pathways that are enriched among target genes of miRNA-3163", "structure": {"pmcid": "PMC8265124", "section_index": 17, "section_title": "In silico analysis", "row_count": 11, "column_count": 8}, "table": {"label": "Table 4", "caption": "Pathways that are enriched among target genes of miRNA-3163", "rows": [["Nos", "Gene set", "Pathway name", "C", "E", "R", "FDR", "p valuea"], ["1", "hsa05170", "Human immunodeficiency virus 1 infection", "212", "3.6155", "3.3191", "0.081094", "2.5E−04"], ["2", "hsa04110", "Cell cycle", "124", "2.1147", "3.783", "0.09676", "1E−03"], ["3", "hsa04114", "Oocyte meiosis", "124", "2.1147", "3.783", "0.09676", "1E−03"], ["4", "hsa05202", "Transcriptional misregulation in cancer", "186", "3.1721", "3.1525", "0.09676", "1E−03"], ["5", "hsa04010", "MAPK signaling pathway", "295", "5.0309", "2.584", "0.09676", "1.5E−03"], ["6", "hsa05167", "Kaposi sarcoma-associated herpesvirus infection", "186", "3.1721", "2.8373", "0.2378", "4.4E−03"], ["7", "hsa04340", "Hedgehog signaling pathway", "47", "0.80154", "4.9904", "0.3802", "8.2E−03"], ["8", "hsa04310", "Wnt signaling pathway", "146", "2.4899", "2.8114", "0.49589", "1E−02"], ["9", "hsa05206", "MicroRNAs in cancer", "150", "2.5581", "2.7364", "0.50585", "1.4E−02"], ["10", "hsa04218", "Cellular senescence", "160", "2.7286", "2.5654", "0.58131", "2E−02"]], "row_count": 11, "column_count": 8, "numeric_cells": 71, "header_rows": 1, "locator": "section[17]/table-wrap[2]#Tab4"}}, {"id": "asset:table:pmid:34233668:9", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:0c5034a5a6d0829118fb937f7fd18a23a0845eeb3ed94b0cefbec2c34205600f", "bytes": 1270, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[17]/table-wrap[3]#Tab5", "version": null, "note": "Top ten enriched biological processes among target genes of miR-513c", "structure": {"pmcid": "PMC8265124", "section_index": 17, "section_title": "In silico analysis", "row_count": 11, "column_count": 8}, "table": {"label": "Table 5", "caption": "Top ten enriched biological processes among target genes of miR-513c", "rows": [["No", "GO ID", "Biological process", "O", "FDR", "E", "R", "p valuea"], ["1", "GO: 0042148", "Strand invasion", "5", "1", "0.024004", "83.32", "2.2E−04"], ["2", "GO: 0006612", "Protein targeting to membrane", "187", "1", "0.89774", "6.6834", "2.7E−04"], ["3", "GO: 0045047", "Protein targeting to ER", "107", "1", "0.51368", "7.7869", "1.7E−03"], ["4", "GO: 0072599", "Establishment of protein localization to endoplasmic reticulum", "111", "1", "0.53289", "7.5063", "1.9E−03"], ["5", "GO: 0008340", "Determination of adult lifespan", "17", "1", "0.081613", "24.506", "2.9−E3"], ["6", "GO: 0006605", "Protein targeting", "412", "1", "1.9779", "3.5391", "3.6E−03"], ["7", "GO: 0090150", "Establishment of protein localization to membrane", "313", "1", "1.5026", "3.993", "3.9–03"], ["8", "GO: 0070972", "Protein localization to endoplasmic reticulum", "137", "1", "0.65771", "6.0818", "4.2E−03"], ["9", "GO: 0031297", "Replication fork processing", "95", "1", "0.15362", "13.019", "1E−02"], ["10", "GO: 0006614", "SRP-dependent co-translational protein targeting to membrane", "95", "1", "0.45607", "6.5779", "1E−02"]], "row_count": 11, "column_count": 8, "numeric_cells": 70, "header_rows": 1, "locator": "section[17]/table-wrap[3]#Tab5"}}, {"id": "asset:table:pmid:34233668:10", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:93da04f037c7bd1c8dea0314251456fbed3b5da00dcdbc4b1b1615613e258364", "bytes": 1385, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[17]/table-wrap[4]#Tab6", "version": null, "note": "Top ten enriched biological processes among target genes of miR-3163", "structure": {"pmcid": "PMC8265124", "section_index": 17, "section_title": "In silico analysis", "row_count": 11, "column_count": 8}, "table": {"label": "Table 6", "caption": "Top ten enriched biological processes among target genes of miR-3163", "rows": [["No", "Gene set", "Biological pathways", "C", "E", "R", "FDR", "p value"], ["1", "GO: 0045934", "Negative regulation of nucleobase-containing compound metabolic process", "1418", "22.805", "1.9732", "0.04352", "8E−06"], ["2", "GO: 0033554", "Cellular response to stress", "1867", "30.026", "1.7984", "0.04352", "1E−05"], ["3", "GO: 0010629", "Negative regulation of gene expression", "1733", "27.871", "1.8299", "0.04352", "1E−05"], ["4", "GO: 1903311", "Regulation of mRNA metabolic process", "266", "4.278", "3.5063", "0.06326", "3E−05"], ["5", "GO: 0045935", "Positive regulation of nucleobase-containing compound metabolic process", "1847", "29.705", "1.7169", "0.12664", "8E−05"], ["6", "GO: 0000278", "Mitotic cell cycle", "927", "14.909", "2.0793", "0.12664", "9E−05"], ["7", "GO: 0051253", "Negative regulation of RNA metabolic process", "1295", "20.827", "1.8726", "0.12664", "1E−04"], ["8", "GO: 0000902", "Cell morphogenesis", "982", "15.793", "2.0262", "0.12664", "1E−04"], ["9", "GO: 0032989", "Cellular component morphogenesis", "1082", "17.401", "1.9539", "0.12664", "1E−04"], ["10", "GO: 2000113", "Negative regulation of cellular macromolecule biosynthetic process", "1359", "21.856", "1.8301", "0.12664", "1E−04"]], "row_count": 11, "column_count": 8, "numeric_cells": 70, "header_rows": 1, "locator": "section[17]/table-wrap[4]#Tab6"}}], "gaps": []}, "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": 0.7, "band": "medium", "quote": "Limma"}}, {"id": "method-2", "family": null, "specific": null, "label": "Paired T-test", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Paired T-test and delta-CTs were used for comparison of the gene expressions between tumor and normal adjacent tissues."}}], "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": "data", "blocked_on": "data:accession_absent", "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": "R4", "reachable": false, "accessions": [], "resolved_accessions": [], "statements": ["The data that support the findings of this study are available on request from the corresponding author. The data are not publicly available due to privacy or ethical restrictions e.g. containing information that could compromise the privacy of research participants."], "basis": "The paper names no accession to its source data, so the data has to come from the authors."}}, "can_run": {"dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "assets": ["source:pmid:34233668", "asset:table:pmid:34233668:1", "asset:table:pmid:34233668:2", "asset:table:pmid:34233668:3", "asset:table:pmid:34233668:4", "asset:table:pmid:34233668:5", "asset:table:pmid:34233668:6", "asset:table:pmid:34233668:7", "asset:table:pmid:34233668:8", "asset:table:pmid:34233668:9", "asset:table:pmid:34233668:10"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:None"]}, "gaps": ["data:accession_absent"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:31:58Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 28027, "completion_tokens": 898, "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:34233668", "type": "paper", "label": "pmid:34233668"}, {"id": "source:pmid:34233668", "type": "manuscript", "label": "PMID 34233668 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:34233668", "type": "paper", "label": "pmid:34233668"}, {"id": "source:pmid:34233668", "type": "manuscript", "label": "PMID 34233668 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-34233668", "type": "extraction", "used": ["source:pmid:34233668"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-None", "type": "accession_resolution", "used": ["data:geo:None"], "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:34233668", "parent_hash": "sha256:2790dcf09fd5213a8c2b14a2e6b6096702652107781478583d86b857919124b5", "fork_of": null, "generation": 4}, "gaps": ["execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:obtain_source_data blocked on data:accession_absent"], "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": ["normal adjacent tissues. The analysis of GEO microarray datasets showed that miR-513c was downregula"], "order_basis": "paper_text_order:1843", "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": 0.7, "evidence": ["Limma"], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}