Identification of transcription factors and single nucleotide polymorphisms of Lrh1 and its homologous genes in Lrh1-knockout pancreas of mice.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:24735206", "kind": "science-record", "revision": 5, "content_hash": "sha256:65f44a6bd10557cccb60acaeedd1fa1ca743e407b250f41a0bd9a8243671d5a5", "created_at": "2026-11-01T15:40:05Z", "updated_at": "2026-11-01T21:19:48Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of transcription factors and single nucleotide polymorphisms of Lrh1 and its homologous genes in Lrh1-knockout pancreas of mice.", "doi": "10.1186/1471-2350-15-43", "pmid": "24735206", "authors": ["Maochun Tang", "Li Cheng", "Rongrong Jia", "Lei Qiu", "Hua Liu", "Shu Zhou", "Xiuying Ma", "Guoyong Hu", "Xingpeng Wang", "Yan Zhao"], "journal": "BMC medical genetics", "year": 2014, "abstract": "BACKGROUND: To identify transcription factors (TFs) and single nucleotide polymorphisms (SNPs) of Lrh1 (also named Nr5a2) and its homologous genes in Lrh1-knockout pancreas of mice.\nMETHODS: The RNA-Seq data GSE34030 were downloaded from Gene Expression Omnibus (GEO) database, including 2 Lrh1 pancreas knockout samples and 2 wild type samples. All reads were processed through TopHat and Cufflinks package to calculate gene-expression level. Then, the differentially expressed genes (DEGs) were identified via non-parametric algorithm (NOISeq) methods in R package, of which the homology genes of Lrh1 were identified via BLASTN analysis. Furthermore, the TFs of Lrh1 and its homologous genes were selected based on TRANSFAC database. Additionally, the SNPs were analyzed via SAM tool to record the locations of mutant sites.\nRESULTS: Total 15683 DEGs were identified, of which 23 was Lrh1 homology genes (3 up-regulated and 20 down-regulated). Fetoprotein TF (FTF) was the only TF of Lrh1 identified and the promoter-binding factor of FTF was CYP7A. The SNP annotations of Lrh1 homologous genes showed that 92% of the mutation sites were occurred in intron and upstream. Three SNPs of Lrh1 were located in intron, while 1819 SNPs of Phkb were located in intron and 1343 SNPs were located in the upstream region.\nCONCLUSION: FTF combined with CYP7A might play an important role in Lrh1 regulated pancreas-specific transcriptional network. Furthermore, the SNPs analysis of Lrh1 and its homology genes provided the candidate mutant sites that might affect the Lrh1-related production and secretion of pancreatic fluid.", "claims": [{"id": "claim-method", "statement": "The DEGs were identified via non-parametric algorithm (NOISeq) methods in R package [12].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:24735206", "locator": "sections[4] \"Data pre-processing, gene expression and homology gene of Lrh1\" paragraph 2", "quote": "The DEGs were identified via non-parametric algorithm (NOISeq) methods in R package [12]."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The RNA-seq data was downloaded from NCBI (http://www.ncbi.nlm.nih.gov/) Gene Expression Omnibus (GEO) database (GEO accession: GSE34030 [9]), including 2 Lrh1 pancreas knockout samples and 2 wild type samples.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:24735206", "locator": "sections[3] \"RNA-seq data acquisition\" paragraph 2", "quote": "The RNA-seq data was downloaded from NCBI (http://www.ncbi.nlm.nih.gov/) Gene Expression Omnibus (GEO) database (GEO accession: GSE34030 [9]), including 2 Lrh1 pancreas knockout samples and 2 wild type samples."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Using the GEO RNA-Seq dataset GSE34030, which contained 2 Lrh1 pancreas knockout samples and 2 wild-type samples, the authors identified 15,683 differentially expressed genes with NOISeq at FDR < 0.001; among them, 23 were Lrh1 homologous genes (3 up-regulated and 20 down-regulated).", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:24735206", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "The RNA-Seq data GSE34030 were downloaded from Gene Expression Omnibus (GEO) database, including 2 Lrh1 pancreas knockout samples and 2 wild type samples."}, {"asset": "source:pmid:24735206", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "Then, the differentially expressed genes (DEGs) were identified via non-parametric algorithm (NOISeq) methods in R package, of which the homology genes of Lrh1 were identified via BLASTN analysis."}, {"asset": "source:pmid:24735206", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Total 15683 DEGs were identified, of which 23 was Lrh1 homology genes (3 up-regulated and 20 down-regulated)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Using the GEO RNA-Seq dataset GSE34030, which contained 2 Lrh1 pancreas knockout samples and 2 wild-type samples, the authors identified 15,683 differentially expressed genes with NOISeq at FDR < 0.001; among them, 23 were Lrh1 homologous genes (3 up-regulated and 20 down-regulated).", "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:24735206"], "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. 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