Expresso: A database and web server for exploring the interaction of transcription factors and their target genes in Arabidopsis thaliana using ChIP-Seq peak data.

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Even though in vivo transcriptional regulation often involves the concerted action of more than one transcription factor, the format of each individual ChIP-Seq dataset usually represents the action of a single transcription factor. Therefore, a relational database in which available ChIP-Seq datasets are curated is essential. Results: We present Expresso (database and webserver) as a tool for the collection and integration of available Arabidopsis ChIP-Seq peak data, which in turn can be linked to a user's gene expression data. Known target genes of transcription factors were identified by motif analysis of publicly available GEO ChIP-Seq data sets. Expresso currently provides three services: 1) Identification of target genes of a given transcription factor; 2) Identification of transcription factors that regulate a gene of interest; 3) Computation of correlation between the gene expression of transcription factors and their target genes. Availability: Expresso is freely available at http://bioinformatics.cs.vt.edu/expresso/.", "claims": [{"id": "claim-method", "statement": "Users can upload gene expression data and Expresso finds genes and transcription factor pairs present in Expresso database and performs Pearson correlation analysis on their corresponding expression data.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:28529706", "locator": "sections[3] \"Results\" paragraph 5", "quote": "Users can upload gene expression data and Expresso finds genes and transcription factor pairs present in Expresso database and performs Pearson correlation analysis on their corresponding expression data."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Expresso is freely available online: http://bioinformatics.cs.vt.edu/expresso/\nSource code available at: https://github.com/doaa-altarawy/Expresso/tree/2.0.0\nArchived source code as at time of publication: doi, 10.5281/zenodo.399501 ( Altarawy, 2017).\nLicense: MIT\nAll datasets were publicly available and were downloaded from GEO DataSets. The list of ChIP-Seq datasets available in Expresso is available at ‘Experiments’ section on Expresso. The list of transcription factors and target genes can be downloaded in the text format.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:28529706", "locator": "sections[5] \"Software and data availability\" paragraphs 1-6", "quote": "Expresso is freely available online: http://bioinformatics.cs.vt.edu/expresso/\nSource code available at: https://github.com/doaa-altarawy/Expresso/tree/2.0.0\nArchived source code as at time of publication: doi, 10.5281/zenodo.399501 ( Altarawy, 2017).\nLicense: MIT\nAll datasets were publicly available and were downloaded from GEO DataSets. The list of ChIP-Seq datasets available in Expresso is available at ‘Experiments’ section on Expresso. The list of transcription factors and target genes can be downloaded in the text format."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Expresso used Pearson correlation on user-uploaded gene-expression data to analyze transcription-factor–target-gene pairs, demonstrating the method with an RNA-Seq dataset from Segaran (2007); three of four PIF3 target genes showed high positive correlation with PIF3 expression, while one showed a negative correlation (R=-0.92).", "kind": "quantitative", "target": {"value": -0.92, "unit": "correlation coefficient", "tolerance": null, "source": "For example, three out of four target genes of PIF3 show high correlation with the expression of PIF3, although one gene was found to have a negative correlation (R=-0.92)."}, "evidence": [{"asset": "source:pmid:28529706", "locator": "sections[3] \"Results\" paragraph 5", "quote": "Users can upload gene expression data and Expresso finds genes and transcription factor pairs present in Expresso database and performs Pearson correlation analysis on their corresponding expression data."}, {"asset": "source:pmid:28529706", "locator": "sections[3] \"Results\" paragraph 5", "quote": "To demonstrate the application of correlation analysis on finding potential TF-target gene pairs, a RNA-Seq dataset ( Segaran, 2007) has been added to Expresso as a demo (see “Gene Expression” on the Expresso website: http://bioinformatics.cs.vt.edu/expresso/?q=node/5)."}, {"asset": "source:pmid:28529706", "locator": "sections[3] \"Results\" paragraph 5", "quote": "For example, three out of four target genes of PIF3 show high correlation with the expression of PIF3, although one gene was found to have a negative correlation (R=-0.92)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "Expresso used Pearson correlation on user-uploaded gene-expression data to analyze transcription-factor–target-gene pairs, demonstrating the method with an RNA-Seq dataset from Segaran (2007); three of four PIF3 target genes showed high positive correlation with PIF3 expression, while one showed a negative correlation (R=-0.92).", "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:28529706"], "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": "blocked", "blocked_on": "data:accession_absent", "description": "The GEO series accession resolves and its sample accessions are listed. 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