Data from: Positive selection of the TRIM family regulatory region in primate genomes

He D, Lu Y, Gittelman R, Jin Y, Ling F, Akey J

Date Published: September 14, 2016

DOI: http://dx.doi.org/10.5061/dryad.f3bd1

 

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Title The motifs identified in TRIM haDHSs
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Description Using the FIMO software to identified the putative transcription binding site motifs in TRIM haDHSs. And the corresponding six-primates sequences of these motifs were downloaed from Ensembl.
Download The motif identified in TRIM haDHSs.rar (6.975 Mb)
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Title Selection analysis of TRIM DHS
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Description The TRIM DHS data was generated from 145 cell types DHS data in ENCODE. And the methodology of DHS selection analysis was based on our previous DHS research(Comprehensive identification and analysis of human accelerated regulatory DNA, Rachel et al.Genome Research).
Download Selection analysis of TRIM DHS.bed (2.832 Mb)
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Title Transposable elements within TRIM DHS
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Description This files showed the transposable elements that overlapped with TRIM haDHSs and conversed DHSs and their detailed information. The first three columns represented the position of DHS, the fourth to sixth columns represented the position of transposable elements. The annotation file of transposable elements came from ReapeatsMasker output file in UCSC.
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Title SNP_in_haDHS(from 1000 human genome project)
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Description This file showed all the SNPs(data from 1000 human genome project) that located in TRIM haDHSs, with their information such as the positions of SNPs and allele frequencies.
Download SNP_in_haDHS(from 1000 human genome project).rar (143.0 Kb)
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When using this data, please cite the original publication:

He D, Lu Y, Gittelman R, Jin Y, Ling F, Akey J (2016) Positive selection of the TRIM family regulatory region in primate genomes. Proceedings of the Royal Society B 283(1840): 20161602. http://dx.doi.org/10.1098/rspb.2016.1602

Additionally, please cite the Dryad data package:

He D, Lu Y, Gittelman R, Jin Y, Ling F, Akey J (2016) Data from: Positive selection of the TRIM family regulatory region in primate genomes. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.f3bd1
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