Identification of potential new T cell activation molecules: a Bioinformatic Approach.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39333573", "kind": "science-record", "revision": 3, "content_hash": "sha256:1b825d8dbfe4f53929ac05928e4522723e0d89320c393b59cc6de97137bddbde", "created_at": "2026-11-01T20:29:31Z", "updated_at": "2026-11-01T22:12:47Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of potential new T cell activation molecules: a Bioinformatic Approach.", "doi": "10.1038/s41598-024-73003-9", "pmid": "39333573", "authors": ["Mario Morales-Martínez", "David Andón-García", "Karla Aimee Patiño-Santiago", "Jesús Miguel Parga-Ortega", "Abrahan Hernández-Hernández", "Guillermo Aquino-Jarquin", "Genaro Patino-Lopez"], "journal": "Scientific reports", "year": 2024, "abstract": "T-cell activation is central for the initiation of T cell mediated adaptive immune response and is the result of the close communication between the Antigen Presenting Cell (APC) and the T lymphocyte. Although T-cell activation is currently well understood, and many intracellular pathways are well characterized, nevertheless new players are constantly identified, and this complements the known protein interactome. In this work we aimed to identify new proteins involved in T cell activation. We reviewed and analyzed results of microarray gene expression datasets reported in the public database GEO-NCBI. Using data from GSE136625, GSE50971, GSE13887, GSE11989 and GSE902 we performed different comparisons using R and other bioinformatic tools including GEO2R and we report here upregulated genes that have no previous reports in immune related functions and with potential participation upon T-cell activation. Our results indicate that RND3, SYT10, IgSF6 and PIN1 are potential new T-cell activation molecules.", "claims": [{"id": "claim-method", "statement": "The analysis of the datasets was performed initially applying linear models for microarray data in R (limma_3.52.4 in R version 4.2.1) we used Log Fold Change (FC) > 1.5 and adj P < 0.05 this allowed us to identify an initial list of gene candidates to T-cell activation molecules.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39333573", "locator": "sections[8] \"Bioinformatic analysis\" paragraph 2", "quote": "The analysis of the datasets was performed initially applying linear models for microarray data in R (limma_3.52.4 in R version 4.2.1) we used Log Fold Change (FC) > 1.5 and adj P < 0.05 this allowed us to identify an initial list of gene candidates to T-cell activation molecules."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All data generated or analyzed during this study are included in this published article (and its Supplementary Information files).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39333573", "locator": "sections[20] \"notes\" paragraph 1", "quote": "All data generated or analyzed during this study are included in this published article (and its Supplementary Information files)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Our results indicate that RND3, SYT10, IgSF6 and PIN1 are potential new T-cell activation molecules.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:39333573", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Our results indicate that RND3, SYT10, IgSF6 and PIN1 are potential new T-cell activation molecules."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Our results indicate that RND3, SYT10, IgSF6 and PIN1 are potential new T-cell activation molecules.", "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:39333573"], "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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