Screening of differentially expressed genes in children with cerebral palsy and the construction of a network of the effective components of traditional Chinese medicine.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35685065", "kind": "science-record", "revision": 3, "content_hash": "sha256:3ca5b01f82935a869b3de3b9cb771b1ec9ba0f23ac7976d7d331c9da5c87dfc1", "created_at": "2026-11-01T18:14:38Z", "updated_at": "2026-11-01T21:28:04Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Screening of differentially expressed genes in children with cerebral palsy and the construction of a network of the effective components of traditional Chinese medicine.", "doi": "10.21037/tp-22-171", "pmid": "35685065", "authors": ["Yueping Che", "Yan Shi"], "journal": "Translational pediatrics", "year": 2022, "abstract": "Background: The study sought to construct a network of the effective components of traditional Chinese medicine (TCM) and potential therapeutic target genes of cerebral palsy based on data sets from high-throughput sequencing and the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP).\nMethods: A transcriptome sequencing data set (GSE183021) of blood samples from children with cerebral palsy was downloaded from the Gene Expression Omnibus (GEO) database. The differentially expressed genes (DEGs) between the cerebral palsy blood samples and control blood samples were screened. The TCM active components and target genes were identified from the TCMSP. We constructed a network of the active ingredients of TCM and the cerebral palsy DEGs.\nResults: Using a |log2 fold change| ≥1 and a false discovery rate <0.05 as the screening criteria for the blood samples of 5 children with cerebral palsy and 5 control participants, 399 DEGs were identified. In the cerebral palsy blood samples, 209 genes were upregulated, and 190 genes were downregulated. The effective components of Angelica sinensis, Shenjincao, and Achyranthes bidentata, targeted 158 genes, and 49 genes crossed with the cerebral palsy DEGs. A network was constructed with the active ingredients of Angelica sinensis, Shenjincao, and Achyranthes bidentata and the DEGs of the cerebral palsy as nodes. Interleukin (IL)-1β, IL-6, prostaglandin-endoperoxide synthase 1, tumor necrosis factor, estrogen receptor 1, and nitric oxide synthase 2 had a wide range of effects on the effective components of Angelica sinensis, Shenjincao, and Achyranthes bidentata.\nConclusions: The effective components of Angelica sinensis, Shenjincao, Achyranthes sinensis, and interact closely with the cerebral palsy DEGs. Based on the interaction network, the pharmacological mechanism of TCM in the treatment of cerebral palsy can be elucidated and new therapeutic targets discovered.", "claims": [{"id": "claim-method", "statement": "The differential genes were screened using the rank-sum test.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35685065", "locator": "sections[4] \"Differential gene screening\" paragraph 2", "quote": "The differential genes were screened using the rank-sum test."}], "state": "complete"}, {"id": "claim-data-access", "statement": "In this study, a whole transcriptome sequencing data set (GSE183021) of the blood samples of children with cerebral palsy was downloaded from the Gene Expression Omnibus (GEO) database. The data set included blood samples from 5 children with cerebral palsy and 5 control subjects.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35685065", "locator": "sections[3] \"Data download\" paragraph 2", "quote": "In this study, a whole transcriptome sequencing data set (GSE183021) of the blood samples of children with cerebral palsy was downloaded from the Gene Expression Omnibus (GEO) database. The data set included blood samples from 5 children with cerebral palsy and 5 control subjects."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Using a |log2 fold change| ≥1 and a false discovery rate <0.05 as the screening criteria for the blood samples of 5 children with cerebral palsy and 5 control participants, 399 DEGs were identified.", "kind": "quantitative", "target": {"value": 2.0, "unit": "fold change", "tolerance": null, "source": "Using a |log2 fold change| ≥1 and a false discovery rate <0.05 as the screening criteria for the blood samples of 5 children with cerebral palsy and 5 control participants, 399 DEGs were identified."}, "evidence": [{"asset": "source:pmid:35685065", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Using a |log2 fold change| ≥1 and a false discovery rate <0.05 as the screening criteria for the blood samples of 5 children with cerebral palsy and 5 control participants, 399 DEGs were identified."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Using a |log2 fold change| ≥1 and a false discovery rate <0.05 as the screening criteria for the blood samples of 5 children with cerebral palsy and 5 control participants, 399 DEGs were identified.", "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:35685065"], "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:GSE183021"], "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:GSE183021"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:35685065", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.21037/tp-22-171", "sha256": "sha256:bb81ca351787e490dd8e7a4d1d8441e65d8e45ab015341ca31652f325f6bb037", "bytes": 22917, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.21037/tp-22-171", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9173875", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE183021", "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=GSE183021", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE183021", "version": null, "note": "In this study, a whole transcriptome sequencing data set (GSE183021) of the blood samples of children with cerebral palsy was downloaded from the Gene Expression Omnibus (GEO) database. 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