A pathogenesis-based transcript signature in donor-specific antibody-positive kidney transplant patients with normal biopsies.

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Biopsy and whole-blood profiles for these DSA-positive, AMR-negative (DSA +/AMR-) patients were compared to both DSA-positive, AMR-positive (DSA +/AMR +) patients as well as DSA-negative (DSA -) controls. While individual gene expression changes across sample groups were relatively subtle, gene-set enrichment analysis using previously identified pathogenesis-based transcripts (PBTs) identified a clear molecular signature involving increased rejection-associated transcripts in AMR - patients. Results from this study have been published in Kidney International (Hayde et al., 2014 [1]) and the associated data have been deposited in the GEO archive and are accessible via the following link: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE50084.", "claims": [{"id": "claim-method", "statement": "The enrichment analysis was carried out using the limma romer function which implements a parametric re-sampling approach to gene-set enrichment analysis suitable for use with linear models.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26484130", "locator": "sections[6] \"Gene ontology and gene-set enrichment analysis\" paragraph 3", "quote": "The enrichment analysis was carried out using the limma romer function which implements a parametric re-sampling approach to gene-set enrichment analysis suitable for use with linear models."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Deposited data can be found here: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE50084.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26484130", "locator": "sections[2] \"Direct link to deposited data\" paragraph 2", "quote": "Deposited data can be found here: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE50084."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The paper used gene-set enrichment analysis of previously identified pathogenesis-based transcripts to identify increased rejection-associated transcripts in AMR-negative patients, with the associated data deposited in GEO under accession GSE50084.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:26484130", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "gene-set enrichment analysis using previously identified pathogenesis-based transcripts (PBTs) identified a clear molecular signature involving increased rejection-associated transcripts in AMR − patients."}, {"asset": "source:pmid:26484130", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "the associated data have been deposited in the GEO archive and are accessible via the following link: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE50084"}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The paper used gene-set enrichment analysis of previously identified pathogenesis-based transcripts to identify increased rejection-associated transcripts in AMR-negative patients, with the associated data deposited in GEO under accession GSE50084.", "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:26484130"], "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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