Comparison of the transcriptional landscapes between human and mouse tissues

Shin Lin, Yiing Lin, Joseph R. Nery, Mark A. Urich, Alessra Breschi, Carrie A. Davis, Alexer Dobin, Christopher Zaleski, Michael A. Beer, William C. Chapman, Thomas R. Gingeras, Joseph R. Ecker, Michael P. Snyder

Research output: Contribution to journalArticlepeer-review

250 Scopus citations


Although the similarities between humans and mice are typically highlighted, morphologically and genetically, there are many differences. To better understand these two species on a molecular level, we performed a comparison of the expression profiles of 15 tissues by deep RNA sequencing and examined the similarities and differences in the transcriptome for both protein-coding and -noncoding transcripts. Although commonalities are evident in the expression of tissue-specific genes between the two species, the expression for many sets of genes was found to be more similar in different tissues within the same species than between species. These findings were further corroborated by associated epigenetic histone mark analyses. We also find that many noncoding transcripts are expressed at a low level and are not detectable at appreciable levels across individuals. Moreover, the majority lack obvious sequence homologs between species, evenwhen we restrict our attention to thosewhich aremost highly reproducible across biological replicates. Overall, our results indicate that there is considerable RNA expression diversity between humans and mice,well beyond what was described previously, likely reflecting the fundamental physiological differences between these two organisms.

Original languageEnglish
Pages (from-to)17224-17229
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Issue number48
StatePublished - Dec 2 2014


  • Epigenome
  • Noncoding transcripts
  • Species comparison
  • Transcriptome


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