Prediction of Differentially Expressed Genes and a Diagnostic Signature of Preeclampsia via Integrated Bioinformatics Analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35711567", "kind": "science-record", "revision": 5, "content_hash": "sha256:5a6fa14c88d814a734a487a88b452b474d262cb3aadb5a755661a4feaafde03c", "created_at": "2026-11-01T18:14:41Z", "updated_at": "2026-11-01T22:49:18Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Prediction of Differentially Expressed Genes and a Diagnostic Signature of Preeclampsia via Integrated Bioinformatics Analysis.", "doi": "10.1155/2022/5782637", "pmid": "35711567", "authors": ["Shan Huang", "Shuangming Cai", "Huibin Li", "Wenni Zhang", "Huanshun Xiao", "Danfeng Yu", "Xuan Zhong", "Pei Tao", "Yiping Luo"], "journal": "Disease markers", "year": 2022, "abstract": "Background: Preeclampsia (PE), which has a high incidence rate worldwide, is a potentially dangerous syndrome to pregnant women and newborns. However, the exact mechanism of its pathogenesis is still unclear. In this study, we used bioinformatics analysis to identify hub genes, establish a logistic model, and study immune cell infiltration to clarify the physiopathogenesis of PE.\nMethods: We downloaded the GSE75010 and GSE10588 datasets from the GEO database and performed weighted gene coexpression network analysis (WGCNA) as well as Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses. The online search tool for the retrieval of interacting genes and Cytoscape software were used to identify hub genes, which were then used to establish a logistic model. We also analyzed immune cell infiltration. Finally, we verified the expression of the genes included in the predictive model via RT-PCR.\nResults: A total of 100 and 212 differently expressed genes were identified in the GSE75010 and GSE10588 datasets, respectively, and after overlapping with WGCNA results, 17 genes were identified. KEGG and GO analyses further indicated the involvement of these genes in bioprocesses, such as gonadotropin secretion, immune cell infiltration, and the SMAD and MAPK pathways. Additionally, protein-protein interaction network analysis identified 10 hub genes, six (FLT1, FLNB, FSTL3, INHA, TREM1, and SLCO4A1) of which were used to establish a logistic model for PE. RT-PCR analysis also confirmed that, except FSTL3, these genes were upregulated in PE. Our results also indicated that macrophages played the most important role in immune cell infiltration in PE.\nConclusion: This study identified 10 hub genes in PE and used 6 of them to establish a logistic model and also analyzed immune cell infiltration. These findings may enhance the understanding of PE and enable the identification of potential therapeutic targets for PE.", "claims": [{"id": "claim-method", "statement": "To identify DEGs between placenta tissue samples from normal pregnant women and women with PE in both datasets, we used the “limma” R software package.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35711567", "locator": "sections[4] \"2.2. Identification of DEGs\" paragraph 2", "quote": "To identify DEGs between placenta tissue samples from normal pregnant women and women with PE in both datasets, we used the “limma” R software package."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The GSE75010 and GSE10588 placental mRNA profiles were downloaded from the GEO database (https://www.ncbi.nlm.nih.gov/geo/).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35711567", "locator": "sections[24] \"Data Availability\" paragraph 2", "quote": "The GSE75010 and GSE10588 placental mRNA profiles were downloaded from the GEO database (https://www.ncbi.nlm.nih.gov/geo/)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study identified 10 hub genes in preeclampsia and used 6 of them to establish a logistic model.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35711567", "locator": "sections[0] \"Abstract\" paragraph 4", "quote": "This study identified 10 hub genes in PE and used 6 of them to establish a logistic model and also analyzed immune cell infiltration."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study identified 10 hub genes in preeclampsia and used 6 of them to establish a logistic model.", "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:35711567"], "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:GSE10588"], "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:GSE10588"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:35711567", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1155/2022/5782637", "sha256": "sha256:79b61f4a1c8266fc3366ab8352d0381cee6bef69061238cf29c54c302ad1e0e3", "bytes": 34723, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1155/2022/5782637", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9197614", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE10588", "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=GSE10588", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE10588", "version": null, "note": "The GSE75010 and GSE10588 placental mRNA profiles were downloaded from the GEO database (https://www.ncbi.nlm.nih.gov/geo/).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The GSE75010 and GSE10588 placental mRNA profiles were downloaded from the GEO database (https://www.ncbi.nlm.nih.gov/geo/).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM225470", "GSM225471", "GSM225472", "GSM225473", "GSM225474", "GSM225475", "GSM225476", "GSM225477", "GSM225478", "GSM225479", "GSM225480", "GSM225481", "GSM225483", "GSM225484", "GSM225485", "GSM225486", "GSM225487", "GSM225488", "GSM225489", "GSM225490", "GSM225491", "GSM225492", "GSM225493", "GSM225494", "GSM225495", "GSM225496", "GSM225497", "GSM225498", "GSM225499", "GSM225500", "GSM225501", "GSM225502", "GSM225503", "GSM225504", "GSM225505", "GSM225506", "GSM225507", "GSM225508", "GSM225509", "GSM225510", "GSM225511", "GSM225512", "GSM225513"], "sample_count": 43, "group_sizes": null, "group_sizes_basis": null, "platform": "2986", "taxon": "Homo sapiens", "title": "Placental gene expression in severe preeclampsia.", "resolution_checked_at": "2026-11-01T18:06:43Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE75010", "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=GSE75010", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE75010", "version": null, "note": "The GSE75010 and GSE10588 placental mRNA profiles were downloaded from the GEO database (https://www.ncbi.nlm.nih.gov/geo/).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The GSE75010 and GSE10588 placental mRNA profiles were downloaded from the GEO database (https://www.ncbi.nlm.nih.gov/geo/).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1940492", "GSM1940493", "GSM1940494", "GSM1940495", "GSM1940496", "GSM1940497", "GSM1940498", "GSM1940499", "GSM1940500", "GSM1940501", "GSM1940502", "GSM1940503", "GSM1940504", "GSM1940505", "GSM1940506", "GSM1940507", "GSM1940508", "GSM1940509", "GSM1940510", "GSM1940511", "GSM1940512", "GSM1940513", "GSM1940514", "GSM1940515", "GSM1940516", "GSM1940517", "GSM1940518", "GSM1940519", "GSM1940520", "GSM1940521", "GSM1940522", "GSM1940523", "GSM1940524", "GSM1940525", "GSM1940526", "GSM1940527", "GSM1940528", "GSM1940529", "GSM1940530", "GSM1940531", "GSM1940532", "GSM1940533", "GSM1940534", "GSM1940535", "GSM1940536", "GSM1940537", "GSM1940538", "GSM1940539", "GSM1940540", "GSM1940541", "GSM1940542", "GSM1940543", "GSM1940544", "GSM1940545", "GSM1940546", "GSM1940547", "GSM1940548", "GSM1940549", "GSM1940550", "GSM1940551", "GSM1940552", "GSM1940553", "GSM1940554", "GSM1940555", "GSM1940556", "GSM1940557", "GSM1940558", "GSM1940559", "GSM1940560", "GSM1940561", "GSM1940562", "GSM1940563", "GSM1940564", "GSM1940565", "GSM1940566", "GSM1940567", "GSM1940568", "GSM1940569", "GSM1940570", "GSM1940571", "GSM1940572", "GSM1940573", "GSM1940574", "GSM1940575", "GSM1940576", "GSM1940577", "GSM1940578", "GSM1940579", "GSM1940580", "GSM1940581", "GSM1940582", "GSM1940583", "GSM1940584", "GSM1940585", "GSM1940586", "GSM1940587", "GSM1940588", "GSM1940589", "GSM1940590", "GSM1940591", "GSM1940592", "GSM1940593", "GSM1940594", "GSM1940595", "GSM1940596", "GSM1940597", "GSM1940598", "GSM1940599", "GSM1940600", "GSM1940601", "GSM1940602", "GSM1940603", "GSM1940604", "GSM1940605", "GSM1940606", "GSM1940607", "GSM1940608", "GSM1940609", "GSM1940610", "GSM1940611", "GSM1940612", "GSM1940613", "GSM1940614", "GSM1940615", "GSM1940616", "GSM1940617", "GSM1940618", "GSM1940619", "GSM1940620", "GSM1940621", "GSM1940622", "GSM1940623", "GSM1940624", "GSM1940625", "GSM1940626", "GSM1940627", "GSM1940628", "GSM1940629", "GSM1940630", "GSM1940631", "GSM1940632", "GSM1940633", "GSM1940634", "GSM1940635", "GSM1940636", "GSM1940637", "GSM1940638", "GSM1940639", "GSM1940640", "GSM1940641", "GSM1940642", "GSM1940643", "GSM1940644", "GSM1940645", "GSM1940646", "GSM1940647", "GSM1940648"], "sample_count": 157, "group_sizes": null, "group_sizes_basis": null, "platform": "6244", "taxon": "Homo sapiens", "title": "Placental gene expression profiling for the identification of clinically relevant subclasses of human preeclampsia", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE10588 not downloaded", "asset:data:geo:GSE10588 licence not read", "asset:data:geo:GSE75010 not downloaded", "asset:data:geo:GSE75010 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": "To identify DEGs between placenta tissue samples from normal pregnant women and women with PE in both datasets, we used the “limma” R software package."}}, {"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": "protein-protein interaction"}}, {"id": "method-3", "family": "epidemiological_modelling", "specific": "incidence_rate", "label": "Epidemiological rate modelling", "dsl_operations": ["incidence_rate_model", "offset_regression"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["event_counts_with_exposure_time"], "evidence": {"score": 0.7, "band": "medium", "quote": "incidence rate"}}], "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": ["GSE75010", "GSE10588"], "resolved_accessions": ["GSE75010", "GSE10588"], "statements": ["The GSE75010 and GSE10588 placental mRNA profiles were downloaded from the GEO database (https://www.ncbi.nlm.nih.gov/geo/)."], "basis": "The paper names GSE75010, GSE10588 in Gene Expression Omnibus (GEO) 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:35711567", "data:geo:GSE10588"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE10588"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T17:50:35Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 11127, "completion_tokens": 1070, "cached_tokens": 128}}, "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:35711567", "type": "paper", "label": "pmid:35711567"}, {"id": "source:pmid:35711567", "type": "manuscript", "label": "PMID 35711567 full text"}, {"id": "data:geo:GSE10588", "type": "dataset", "label": "GEO GSE10588"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:35711567", "type": "paper", "label": "pmid:35711567"}, {"id": "source:pmid:35711567", "type": "manuscript", "label": "PMID 35711567 full text"}, {"id": "data:geo:GSE10588", "type": "dataset", "label": "GEO GSE10588"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-35711567", "type": "extraction", "used": ["source:pmid:35711567"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE10588", "type": "accession_resolution", "used": ["data:geo:GSE10588"], "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:35711567", "parent_hash": "sha256:25b3f30133df1b5a77eb1f934cde7cce52fd2400144c051b8f2b5ec8e98f0459", "fork_of": null, "generation": 4}, "gaps": ["asset:data:geo:GSE10588 licence not read", "asset:data:geo:GSE10588 not downloaded", "asset:data:geo:GSE75010 licence not read", "asset:data:geo:GSE75010 not downloaded", "execution.not_run", "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": ["To identify DEGs between placenta tissue samples from normal pregnant women and women with PE in both datasets, we used the “limma” R software package."], "order_basis": "analysis_only", "id": "assay:1"}]}