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Welcome to Horse Genome Net


The Horse Transcriptome Data before and after exercise.

 BMC Genomics publication of the horse transcriptomes

Introduction of horse Transcriptome(RNA-Seq) data
  • Our research is for analyzing large amount of horse RNA-Seq sequences related to exercise. We generated 1.3 billion short reads (90bp pair-end sequences) from 24 samples (six horse individuals). Through our in-house bioinformatics pipelines, we identified 32,361 unigenes among which 20,428 unigenes were not matched to the current Ensembl annotation. Moreover, 189,873 SNVs were also identified, most of which were not overlapped with around 1.1 SNPs identified till now. Via DEG analysis, we identified 62 up- and 80 down-regulated genes in blood and 878 up- and 285 down-regulated genes in the muscle. In addition, several examples of different expression levels of alternative splicings were found.
  • BMC Genomics paper abstract 20120912


This web page provides the download pages for horse RNA-Seq sequences
  • Whole transcriptome analyses of six thoroughbred horses before and after exercising using RNA-seq
    - Raw data download



Some numbers of this large scale equine Transcriptome Study  (Illumina Hiseq2000)
  • Total reads generated: 1,300,000,000 fragments.
  • Base pair size: 90 bp Pair-end
  • Unigene cluster found:  32,361 unigene clusters 
  • Total length of transcript is:  51.83 Mb 
  • 20,428 UCs were not previously reported


Parameters used in the Horse transcriptome analysis
  • RNA-Seq Alignment against the horse reference genome

    TopHat 1.2.0 with two options: --mate-inner-dist=200, --allow-indels


    Reference genome : Horse genome (Ensembl 62)


    Identification of the unigenes from the RNA-Seq alignment results


    Cufflink 0.9.3 with default option


    * For the detailed procedures, please see the supplementary method section of the paper (in preparation).


Research Groups 
  • Busan National University, Korea.
  • Hankyung National University, Korea
  • Konkuk University, Korea
  • PGI (Personal Genomics Institute), Genome Research Foundation. Korea
  • TheragenEtex Inc. Korea.
  • Korean Bioinformation Center, KRIBB, Korea.


Research Articles

 BMC Genomics publication of the horse transcriptomes


See the horses


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