Kwon T et al. (2014), Identifying direct targets of transcription fac...

XB-ART-49585

Genom Data 2014 Dec 01;2:192-194. doi: 10.1016/j.gdata.2014.06.015.

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

Kwon T , Chung MI , Gupta R , Baker JC , Wallingford JB , Marcotte EM .

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Recently, using the frog Xenopus laevis as a model system, we showed that transcription factor Rfx2 coordinates many genes involved in ciliogenesis and cell movement in multiciliated cells (Chung et al., 2014). 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.

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Species referenced: Xenopus laevis
Genes referenced: rfx2 tbx2

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References [+] :

Chung, Coordinated genomic control of ciliogenesis and cell movement by RFX2. 2014, Pubmed, Xenbase

	Fig. 1. Mapping results of RNA-seq reads on X. laevis homoeologs."Unique", "Shared", and "More than shared" indicate reads that map only once, twice, or more than twice to the set of X. laevis homoeologs, respectively.
	Fig. 2. Distribution of fold enrichment and false discovery rate (FDR) in ChIP-seq peak calling. Most peaks with greater than 20 fold enrichment exhibit an FDR less than 0.05. Based on this observation, we included peaks with FDR greater than 0.05 in successive analyses if they exhibited a fold enrichment greater than 20.
	Fig. 3. Distance between ChIP-seq-identified Rfx2 binding sites and nearby genes. “Direct + DE” represents genes that have an Rfx2 binding peak and a significantly differentially expressed pattern in the Rfx2 knockdown condition. “Direct” represents genes that have an Rfx2 binding peak but lack significant differential expression in Rfx2 knockdown. In both cases, however, most peaks are located less than 1000 bp away from annotated genes.