Investigation of the underlying genes and mechanism of familial hypercholesterolemia through bioinformatics analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32938406", "kind": "science-record", "revision": 8, "content_hash": "sha256:64334fb225f162bc28488324fc8160902da7382f9eb494e81efce324f523e19b", "created_at": "2026-11-01T15:41:10Z", "updated_at": "2026-11-01T22:45:20Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Investigation of the underlying genes and mechanism of familial hypercholesterolemia through bioinformatics analysis.", "doi": "10.1186/s12872-020-01701-z", "pmid": "32938406", "authors": ["Dinghui Wang", "Bin Liu", "Tianhua Xiong", "Wenlong Yu", "Qiang She"], "journal": "BMC cardiovascular disorders", "year": 2020, "abstract": "BACKGROUND: Familial hypercholesterolemia (FH) is one of the commonest inherited metabolic disorders. Abnormally high level of low-density lipoprotein cholesterol (LDL-C) in blood leads to premature atherosclerosis onset and a high risk of cardiovascular disease (CVD). However, the specific mechanisms of the progression process are still unclear. Our study aimed to investigate the potential differently expressed genes (DEGs) and mechanism of FH using various bioinformatic tools.\nMETHODS: GSE13985 and GSE6054 were downloaded from the Gene Expression Omnibus (GEO) database for bioinformatic analysis in this study. First, limma package of R was used to identify DEGs between blood samples of patients with FH and those from healthy individuals. Then, the functional annotation of DEGs was carried out by Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis and Gene Ontology (GO) analysis. Based on Search Tool for the Retrieval of Interacting Genes (STRING) tool, we constructed the Protein-Protein Interactions (PPIs) network among DEGs and mined the core genes as well.\nRESULTS: A total of 102 communal DEGs (49 up-regulated and 53 down-regulated) are identified in FH samples compared with control samples. The functional changes of DEGs are mainly associated with the focal adhere and glucagon signaling pathway. Ten genes (ITGAL, TLN1, POLR2A, CD69, GZMA, VASP, HNRNPUL1, SF1, SRRM2, ITGAV) were identified as core genes. Bioinformatic analysis showed that the core genes are mainly enriched in numerous processes related to cell adhesion, integrin-mediated signaling pathway and cell-matrix adhesion. In the transcription factor (TF) target regulating network, 219 nodes were detected, including 214 DEGs and 5 TFs (SP1, EGR3, CREB, SEF1, HOX13). In conclusion, the DEGs and hub genes identified in this study may help us understand the potential etiology of the occurrence and development of AS.\nCONCLUSION: Up-regulated ITGAL, TLN1, POLR2A, VASP, HNRNPUL1, SF1, SRRM2, and down-regulated CD69, GZMA and ITGAV performed important promotional effects for the formation of atherosclerotic plaques those suffering from FH. Moreover, SP1, EGR3, CREB, SEF1 and HOX13 were the potential transcription factors for DEGs and could serve as underlying targets for AS rupture prevention. These findings provide a theoretical basis for us to understand the potential etiology of the occurrence and development of AS in FH patients and we may be able to find potential diagnostic and therapeutic targets.", "claims": [{"id": "claim-method", "statement": "DEGs between FH patients and those of matched controls of the two expression profile data sets were screened out respectively using the Linear Models for Microarray (LIMMA; Version: 3.30.3) affy in R package12 [19].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32938406", "locator": "sections[5] \"Screening genes of differential expression\" paragraph 2", "quote": "DEGs between FH patients and those of matched controls of the two expression profile data sets were screened out respectively using the Linear Models for Microarray (LIMMA; Version: 3.30.3) affy in R package12 [19]."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Availability of data and materialsThe gene expression profiles of GSE13985 and GSE6054 were downloaded from Gene Expression Omnibus (GEO) (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE13985 and https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6054).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32938406", "locator": "sections[21] \"notes\" paragraph 1", "quote": "Availability of data and materialsThe gene expression profiles of GSE13985 and GSE6054 were downloaded from Gene Expression Omnibus (GEO) (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE13985 and https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6054)."}], "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:32938406"], "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:GSE13985"], "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:GSE13985"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:32938406", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s12872-020-01701-z", "sha256": "sha256:43aeaad6cd69668dc8cd22e00656ed6104d927589a96bf43dcd4a33e34ca0340", "bytes": 38252, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s12872-020-01701-z", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7493348", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE13985", "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=GSE13985", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE13985", "version": null, "note": "Availability of data and materialsThe gene expression profiles of GSE13985 and GSE6054 were downloaded from Gene Expression Omnibus (GEO) (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE13985 and https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6054).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Availability of data and materialsThe gene expression profiles of GSE13985 and GSE6054 were downloaded from Gene Expression Omnibus (GEO) (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE13985 and https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6054).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM351336", "GSM351337", "GSM351338", "GSM351339", "GSM351340", "GSM351341", "GSM351342", "GSM351343", "GSM351344", "GSM351345"], "sample_count": 10, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Atherosclerotic markers in human blood - a study in patients with familial hypercholesterolemia ", "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:GSE6054", "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=GSE6054", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE6054", "version": null, "note": "Availability of data and materialsThe gene expression profiles of GSE13985 and GSE6054 were downloaded from Gene Expression Omnibus (GEO) (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE13985 and https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6054).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Availability of data and materialsThe gene expression profiles of GSE13985 and GSE6054 were downloaded from Gene Expression Omnibus (GEO) (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE13985 and https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6054).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM140232", "GSM140233", "GSM140234", "GSM140235", "GSM140236", "GSM140237", "GSM140239", "GSM140240", "GSM140241", "GSM140244", "GSM140245", "GSM140246", "GSM140247", "GSM140248", "GSM140249", "GSM140250", "GSM140251", "GSM140252", "GSM140253", "GSM140254", "GSM140255", "GSM140256", "GSM140257"], "sample_count": 23, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Monocytes of patients with familial hypercholesterolemia show alterations in cholesterol metabolism", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:32938406:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:1a3b516f4325b3b1e7bda069b53b6546a7767c57042f72201e0962c810275302", "bytes": 3829, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[11]/table-wrap[1]#Tab1", "version": null, "note": "The functional enrichment analyses of DEGs ranked by P-value", "structure": {"pmcid": "PMC7493348", "section_index": 11, "section_title": "Functional annotation of DEGs through GO and KEGG analysis", "row_count": 31, "column_count": 4}, "table": {"label": "Table 1", "caption": "The functional enrichment analyses of DEGs ranked by P-value", "rows": [["Term", "Count", "Genes", "P-Value"], ["GO-BPs"], ["GO:0001843 ~ neural tube closure", "4", "TMED2, SKI, PRKACB, VASP", "0.006332314"], ["GO:0010942 ~ positive regulation of cell death", "3", "AKR1C3, UCP2, TRIM13", "0.008780361"], ["GO:0007596 ~ blood coagulation", "5", "P2RX5, F5, ENPP4, PRKACB, WAS", "0.012574205"], ["GO:0007229 ~ integrin-mediated signaling pathway", "4", "ITGAL, ITGAV, PRAM1, ZYX", "0.012578224"], ["GO:0038027 ~ apolipoprotein A-I-mediated signaling pathway", "2", "ABCA7, ITGAV", "0.024181939"], ["GO:0051289 ~ protein homotetramerization", "3", "CRTC2, VASP, GOLGA2", "0.034735707"], ["GO:0048208 ~ COPII vesicle coating", "3", "F5, TMED2, GOLGA2", "0.035801513"], ["GO:0035019 ~ somatic stem cell population maintenance", "3", "BCL9L, SKI, POLR2A", "0.040189117"], ["GO:0006888 ~ ER to Golgi vesicle-mediated transport", "4", "F5, TMED2, GOLGA2, SPTAN1", "0.043542377"], ["GO:0098609 ~ cell-cell adhesion", "5", "PKM, BAG3, VASP, GOLGA2, SPTAN1", "0.043641603"], ["GO-CCs"], ["GO:0005913 ~ cell-cell adherens junction", "7", "PKM, TLN1, BAG3, ZYX, VASP, GOLGA2, SPTAN1", "0.004005355"], ["GO:0032587 ~ ruffle membrane", "4", "ABCA7, TLN1, ITGAV, IFIT5", "0.00665283"], ["GO:0005886 ~ plasma membrane", "30", "ABCA7, ITGAL, TLN1, LRRC8B, ENPP4, MMP25, PKM, DYSF, ITGAV, BAG3, ANKRD11, CD4, PRKACB, KLRF1, ZYX, FLVCR1, FMNL1, KLRB1, RHBDF2, CD160, EDA2R, VASP, P2RX5, LSP1, PRKD2, NEDD1, F5, IFIT5, P2RY14, CYBRD1", "0.010121246"], ["GO:0016020 ~ membrane", "19", "FMNL1, ITGAL, MOB4, ENPP4, MAP 4 K1, RPS9, PRRC2A, CAD, MMP25, TAPBP, LSP1, PIGK, F5, PEX2, ITGAV, CD4, KLRF1, NCOR2, SPTAN1", "0.011799738"], ["GO:0070062 ~ extracellular exosome", "22", "FMNL1, ITGAL, CRTC2, TLN1, ENPP4, RPS9, MINK1, PRRC2A, CAD, WAS, VASP, AKR1C3, PKM, LSP1, DYSF, CLIC3, UBA1, ITGAV, BEX5, CYBRD1, PRKACB, SPTAN1", "0.017083511"], ["GO:1903561 ~ extracellular vesicle", "3", "PKM, F5, SPTAN1", "0.022786951"], ["GO:0017053 ~ transcriptional repressor complex", "3", "MIER1, SKI, NCOR2", "0.027213685"], ["GO:0005654 ~ nucleoplasm", "21", "CRTC2, SF1, RPS9, CAD, SKI, BOD1L1, POLR2A, FEM1C, PRKD2, NEDD1, HNRNPUL1, MIER1, SRRM2, FYTTD1, ANKRD11, SP4, BCL9L, KPNA5, PRKACB, NCOR2, CHD3", "0.02939589"], ["GO:0033116 ~ endoplasmic reticulum-Golgi intermediate compartment membrane", "3", "F5, TMED2, GOLGA2", "0.035966686"], ["GO:0005737 ~ cytoplasm", "33", "CRTC2, TLN1, MOB4, LRRC8B, MAP 4 K1, TRIM13, PRRC2A, AKR1C3, DNAJC17, PKM, MIER1, BAG3, ANKRD11, HECTD3, ZYX, MTMR6, CHD3, C15ORF39, RPS9, MINK1, SKI, VASP, P2RX5, FEM1C, PRKD2, CLIC3, UBA1, RFK, SP4, BEX5, CMIP, KPNA5, FPGT", "0.045491399"], ["GO:0032580 ~ Golgi cisterna membrane", "3", "MOB4, TMED2, GOLGA2", "0.049065899"], ["GO-MFs"], ["GO:0005515 ~ protein binding", "62", "RARRES3, TLN1, LRRC8B, HMGN4, TAPBP, PKM, PIGK, DYSF, PEX2, MIER1, BAG3, ZYX, PRKACB, MATK, FLVCR1, GOLGA2, FMNL1, GZMA, SF1, CD160, MINK1, LENG8, WAS, VASP, PRKD2, F5, CLIC3, PRAM1, CYBRD1, KPNA5, CMIP, ITGAL, CRTC2, MOB4, TRIM13, MAP 4 K1, PRRC2A, CIC, POLR2A, TMED2, CD69, ITGAV, HECTD3, LIMD2, CD4, MTMR6, TRAM1, CHD3, EDA2R, RPS9, ZNF26, SKI, FEM1C, MRFAP1L1, HNRNPUL1, UCP2, UBA1, FYTTD1, SP4, BEX5, NCOR2, SPTAN1", "0.0000906709830702394"], ["GO:0098641 ~ cadherin binding involved in cell-cell adhesion", "6", "PKM, TLN1, BAG3, VASP, GOLGA2, SPTAN1", "0.014824041"], ["GO:0004888 ~ transmembrane signaling receptor activity", "5", "KLRB1, P2RX5, CD69, CD4, KLRF1", "0.02204474"], ["GO:0044822 ~ poly(A) RNA binding", "12", "PKM, HNRNPUL1, UBA1, FYTTD1, SRRM2, IFIT5, SF1, RPS9, PRRC2A, ZYX, CHD3, POLR2A", "0.023879125"], ["GO:0032393 ~ MHC class I receptor activity", "2", "CD160, KLRF1", "0.02949141"], ["GO:0005522 ~ profilin binding", "2", "FMNL1, VASP", "0.043913166"]], "row_count": 31, "column_count": 4, "numeric_cells": 89, "header_rows": 1, "locator": "section[11]/table-wrap[1]#Tab1"}}, {"id": "asset:table:pmid:32938406:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:43d086adb5d2fc1b60902a88230a1090bb094436b7bff7ae5ec2b0f620745f42", "bytes": 3752, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[1]#Tab2", "version": null, "note": "Summary of the function of 10 hub genes", "structure": {"pmcid": "PMC7493348", "section_index": 12, "section_title": "PPI network and hub genes analysis", "row_count": 11, "column_count": 3}, "table": {"label": "Table 2", "caption": "Summary of the function of 10 hub genes", "rows": [["Symbol", "Full name", "Function"], ["ITGAL", "Integrin Subunit Alpha L", "Involved in a variety of immune phenomena including leukocyte-endothelial cell interaction, cytotoxic T-cell mediated killing, and antibody dependent killing by granulocytes and monocytes. Contributes to natural killer cell cytotoxicity. Involved in leukocyte adhesion and transmigration of leukocytes including T-cells and neutrophils.contributes to apoptotic neutrophil phagocytosis by macrophages."], ["TLN1", "Talin 1", "Probably involved in connections of major cytoskeletal structures to the plasma membrane. High molecular weight cytoskeletal protein concentrated at regions of cell-substratum contact and, in lymphocytes, at cell-cell contacts"], ["POLR2A", "RNA Polymerase II Subunit A", "DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Largest and catalytic component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Forms the polymerase active center together with the second largest subunit. Pol II is the central component of the basal RNA polymerase II transcription machinery."], ["CD69", "CD69 Molecule", "Involved in lymphocyte proliferation and functions as a signal transmitting receptor in lymphocytes, natural killer (NK) cells, and platelets. By antigens, mitogens or activators of PKC on the surface of T and B-lymphocytes. By interaction of IL-2 with the p75 IL-2R on the surface of NK cells."], ["GZMA", "Granzyme A", "activates caspase-independent cell death with morphological features of apoptosis when delivered into the target cell through the immunological synapse. It cleaves after Lys or Arg. Cleaves APEX1 after ‘Lys-31’ and destroys its oxidative repair activity. Cleaves the nucleosome assembly protein SET after ‘Lys-189’, which disrupts its nucleosome assembly activity and allows the SET complex to translocate into the nucleus to nick and degrade the DNA."], ["VASP", "Vasodilator Stimulated Phosphoprotein", "Ena/VASP proteins are actin-associated proteins involved in a range of processes dependent on cytoskeleton remodeling and cell polarity such as axon guidance, lamellipodial and filopodial dynamics, platelet activation and cell migration. VASP promotes actin filament elongation. Plays a role in actin-based mobility of Listeria monocytogenes in host cells. Regulates actin dynamics in platelets and plays an important role in regulating platelet aggregation."], ["HNRNPUL1", "Heterogeneous Nuclear Ribonucleoprotein U Like 1", "Acts as a basic transcriptional regulator. Represses basic transcription driven by several virus and cellular promoters. When associated with BRD7, activates transcription of glucocorticoid-responsive promoter in the absence of ligand-stimulation. Plays also a role in mRNA processing and transport. Binds avidly to poly(G) and poly(C) RNA homopolymers in vitro."], ["SF1", "Splicing Factor 1", "Necessary for the ATP-dependent first step of spliceosome assembly. Binds to the intron branch point sequence (BPS) 5′-UACUAAC-3′ of the pre-mRNA. May act as transcription repressor."], ["SRRM2", "Serine/Arginine Repetitive Matrix 2", "Required for pre-mRNA splicing as component of the spliceosome."], ["ITGAV", "Integrin Subunit Alpha V", "The alpha-V (ITGAV) integrins are receptors for vitronectin, cytotactin, fibronectin, fibrinogen, laminin, matrix metalloproteinase-2, osteopontin, osteomodulin, prothrombin, thrombospondin and vWF. They recognize the sequence R-G-D in a wide array of ligands."]], "row_count": 11, "column_count": 3, "numeric_cells": 10, "header_rows": 1, "locator": "section[12]/table-wrap[1]#Tab2"}}], "gaps": ["asset:data:geo:GSE13985 not downloaded", "asset:data:geo:GSE13985 licence not read", "asset:data:geo:GSE6054 not downloaded", "asset:data:geo:GSE6054 licence not read"]}, "analysis": {"state": "complete", "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": "DEGs between FH patients and those of matched controls of the two expression profile data sets were screened out respectively using the Linear Models for Microarray (LIMMA; Version: 3.30.3) affy in R package12 [19]."}}, {"id": "method-2", "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": "PPI"}}, {"id": "method-3", "family": "network_analysis", "specific": "pathway_enrichment", "label": "Network / pathway analysis", "dsl_operations": ["pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.8, "band": "high", "quote": "pathway enrichment"}}], "targets": [], "gaps": []}, "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": ["GSE13985", "GSE6054"], "resolved_accessions": ["GSE13985", "GSE6054"], "statements": ["Availability of data and materialsThe gene expression profiles of GSE13985 and GSE6054 were downloaded from Gene Expression Omnibus (GEO) (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE13985 and https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6054)."], "basis": "The paper names GSE13985, GSE6054 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. 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Then,"], "order_basis": "paper_text_order:770", "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": 1.0, "evidence": ["DEGs between FH patients and those of matched controls of the two expression profile data sets were screened out respectively using the Linear Models for Microarray (LIMMA; Version: 3.30.3) affy in R package12 [19]."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}