Leading edge analysis of transcriptomic changes during pseudorabies virus infection.

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The RNA was processed into fastq files for each library prior to being analyzed using Illumina Digital Gene Expression Tag Profiling sequences (DGETP) which were used as the downstream measure of differential expression. Analyzed tags consisted of 21 base pair sequences taken from time points 1, 3, 6, and 14 days' post infection (dpi) that generated 1,927,547 unique tag sequences. Tag sequences were analyzed for differential transcript expression and gene set enrichment analysis (GSEA) to uncover transcriptomic changes related to PRV pathology progression. In conjunction with the DGETP and GSEA, the study also incorporated use of leading edge analysis to help link the TBLN transcriptome data to clinical progression of PRV at each of the sampled time points. The purpose of this manuscript is to provide useful background on applying the leading edge analysis to GSEA and expression data to help identify genes considered to be of high biological interest. The data in the form of fastq files has been uploaded to the NCBI Gene Expression Omnibus (GEO) (GSE74473) database.", "claims": [{"id": "claim-method", "statement": "Step 2 computed the transcript abundances for infected and non-infected samples quantification using the Audic-Claverie algorithm [2] that allows for calculation of the nominal p-values between infected and control groups based upon Bayesian averaging to infer the Poisson distribution of the tags.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:27766207", "locator": "sections[5] \"Transcriptome analysis\" paragraph 2", "quote": "Step 2 computed the transcript abundances for infected and non-infected samples quantification using the Audic-Claverie algorithm [2] that allows for calculation of the nominal p-values between infected and control groups based upon Bayesian averaging to infer the Poisson distribution of the tags."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Raw sequence data for this study is available at: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE74473.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:27766207", "locator": "sections[1] \"Direct link to deposited data\" paragraph 2", "quote": "Raw sequence data for this study is available at: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE74473."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study used the Audic-Claverie algorithm for differential transcript abundance, with raw sequence data available through GEO accession GSE74473.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:27766207", "locator": "sections[5] \"Transcriptome analysis\" paragraph 2", "quote": "Step 2 computed the transcript abundances for infected and non-infected samples quantification using the Audic-Claverie algorithm [2] that allows for calculation of the nominal p-values between infected and control groups based upon Bayesian averaging to infer the Poisson distribution of the tags."}, {"asset": "source:pmid:27766207", "locator": "sections[1] \"Direct link to deposited data\" paragraph 2", "quote": "Raw sequence data for this study is available at: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE74473."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study used the Audic-Claverie algorithm for differential transcript abundance, with raw sequence data available through GEO accession GSE74473.", "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:27766207"], "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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