Identifying direct targets of transcription factor Rfx2 that coordinate ciliogenesis and cell movement.

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To our knowledge, it was the first paper to utilize the genomic resources, including genome sequences and interim gene annotations, from the ongoing Xenopus laevis genome project. For researchers who are interested in the application of genomics and systems biology approaches in Xenopus studies, here we provide additional details about our dataset (NCBI GEO accession number GSE50593) and describe how we analyzed RNA-seq and ChIP-seq data to identify direct targets of Rfx2.", "claims": [{"id": "claim-method", "statement": "Then we used edgeR [6] to identify differentially expressed genes, focusing on genes with greater than 2-fold difference and a false discovery rate less than 0.05.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:25419512", "locator": "sections[5] \"RNA-seq analysis\" paragraph 2", "quote": "Then we used edgeR [6] to identify differentially expressed genes, focusing on genes with greater than 2-fold difference and a false discovery rate less than 0.05."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All raw sequencing data are free to use. Genome and gene annotation data is free to use for high-throughput experiment data analysis, such as RNA-seq, ChIP-seq, or proteomics. Otherwise, please contact us (Edward Marcotte marcotte@icmb.utexas.edu) or a member of the International Xenopus Genome Consortium (Daniel Rokhsar dsrokhsar@lbl.gov or Masanori Taira m_taira@biol.s.u-tokyo.ac.jp).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:25419512", "locator": "sections[1] \"p\" paragraph 1", "quote": "All raw sequencing data are free to use. Genome and gene annotation data is free to use for high-throughput experiment data analysis, such as RNA-seq, ChIP-seq, or proteomics. Otherwise, please contact us (Edward Marcotte marcotte@icmb.utexas.edu) or a member of the International Xenopus Genome Consortium (Daniel Rokhsar dsrokhsar@lbl.gov or Masanori Taira m_taira@biol.s.u-tokyo.ac.jp)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The paper identified differentially expressed genes with edgeR using a greater-than-twofold change and a false-discovery-rate threshold below 0.05, and the source dataset is available through GEO accession GSE50593 at http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE50593.", "kind": "quantitative", "target": {"value": 2.0, "unit": "fold change", "tolerance": null, "source": "Then we used edgeR [6] to identify differentially expressed genes, focusing on genes with greater than 2-fold difference and a false discovery rate less than 0.05."}, "evidence": [{"asset": "source:pmid:25419512", "locator": "sections[5] \"RNA-seq analysis\" paragraph 2", "quote": "Then we used edgeR [6] to identify differentially expressed genes, focusing on genes with greater than 2-fold difference and a false discovery rate less than 0.05."}, {"asset": "source:pmid:25419512", "locator": "sections[7] \"ChIP-seq analysis\" paragraph 4", "quote": "Out of 29,448 peaks identified in total, 6646 peaks were selected for further study that exhibited either an FDR < 5% or a fold-enrichment > 20, and 5024 of those peaks were assigned to their neighboring genes."}, {"asset": "source:pmid:25419512", "locator": "sections[7] \"ChIP-seq analysis\" paragraph 4", "quote": "This analysis resulted in a final set of 911 putative directly bound Rfx2 target genes that also showed significantly differential gene expression after Rfx2 knockdown [1]."}, {"asset": "source:pmid:25419512", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "NCBI GEO accession number GSE50593"}, {"asset": "source:pmid:25419512", "locator": "sections[2] \"Direct link to deposited data\" paragraph 2", "quote": "http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE50593."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The paper identified differentially expressed genes with edgeR using a greater-than-twofold change and a false-discovery-rate threshold below 0.05, and the source dataset is available through GEO accession GSE50593 at http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE50593.", "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:25419512"], "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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