Genome-wide gene expression profiling of homeodomain-interacting protein kinase 2 deficient medullary thymic epithelial cells.

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The antigens are presented to developing thymocytes in the thymus to select for non-self reactive T-cell receptors in order to prevent autoimmune reactions in the periphery. However the molecular regulation of tissue-restricted antigen expression is still poorly understood. The only regulator known to play a role in the transcriptional regulation so far is the autoimmune regulator (AIRE). AIRE is thought to act in a multi-protein complex, promoting transcription, elongation and splicing of target genes. Yet the full composition of this Aire-associated multi-protein complex and its mode of action remain to be elucidated. Here we describe the experimental details and controls of the gene array analysis on the impact of the homeodomain-interacting protein kinase 2 (Hipk2) on promiscuous gene expression in medullary thymic epithelial cells based on the analysis of newly generated TEC-specific Hipk2 conditional knockout mice. The changes in gene expression are presumably mediated through a regulatory effect of Hipk2 on AIRE as published in the study by Rattay and colleagues in the Journal of Immunology [1]. The gene array data reported in this paper have been deposited in the Gene Expression Omnibus (GEO) database, www.ncbi.nlm.nih.gov/geo (accession no. GSE63432).", "claims": [{"id": "claim-method", "statement": "Statistical T-test calculation was performed in R, Benjamini-Hochberg correction is applied over all p-values of the differential expression analysis.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26697330", "locator": "sections[11] \"Normalization and analysis details\" paragraph 2", "quote": "Statistical T-test calculation was performed in R, Benjamini-Hochberg correction is applied over all p-values of the differential expression analysis."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The gene array data reported in this paper have been deposited in the Gene Expression Omnibus (GEO) database, www.ncbi.nlm.nih.gov/geo (accession no. GSE63432).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26697330", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The gene array data reported in this paper have been deposited in the Gene Expression Omnibus (GEO) database, www.ncbi.nlm.nih.gov/geo (accession no. GSE63432)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study provides the first description of the effect of Hipk2 deficiency on promiscuous gene expression in mTECs; statistical testing used an R T-test with Benjamini-Hochberg correction, and the source microarray data were deposited in GEO under accession number GSE63432.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:26697330", "locator": "sections[12] \"Discussion\" paragraph 2", "quote": "These data provide the first description of the effect of Hipk2 deficiency on promiscuous gene expression in mTECs."}, {"asset": "source:pmid:26697330", "locator": "sections[11] \"Normalization and analysis details\" paragraph 2", "quote": "Statistical T-test calculation was performed in R, Benjamini-Hochberg correction is applied over all p-values of the differential expression analysis."}, {"asset": "source:pmid:26697330", "locator": "sections[11] \"Normalization and analysis details\" paragraph 2", "quote": "The microarray data were deposited in GEO under accession number GSE63432."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study provides the first description of the effect of Hipk2 deficiency on promiscuous gene expression in mTECs; statistical testing used an R T-test with Benjamini-Hochberg correction, and the source microarray data were deposited in GEO under accession number GSE63432.", "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:26697330"], "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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