Description
This track shows the genome-wide expression map of monkeypox virus. ORFs
are selectively expressed at early, intermediate, or late times of infection.
This is due to stage-specific viral promoters and transcription factors
associated with the viral DNA-dependent RNA polymerase. ORFs are named
according to the official nomenclature of orthopoxviruses.
Display Conventions and Configuration
ORFS are colored according to the time of their transcription: green for early genes, blue for intermediate genes, and red for late genes.
Methods
Expression data were obtained from ribosome profiling data from the Vacinia
virus study: Deciphering poxvirus gene expression by RNA sequencing and
ribosome profiling. The monkexpox data were annotated for similarity. The
monkexpox genome is very similar to the vaccinia virus genome, and all
orthopoxviruses share the same expression pattern and replication cycle.
The gene names follow the universal OPGXXX (OrthoPoxvirus Gene number XXX) convention published in Ancient Gene Capture and Recent Gene Loss Shape the Evolution of Orthopoxvirus-Host Interaction Genes.
Data Access
The raw data can be explored interactively with the
Table Browser or combined with other datasets in the
Data Integrator tool.
For automated analysis, the genome annotation is stored in
a bigBed file that can be downloaded from
the download server.
Annotations can
be converted from binary to ASCII text by our command-line tool bigBedToBed.
Instructions for downloading this command can be found on our
utilities page.
The tool can also be used to obtain features within a given range without downloading the file,
for example:
bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/mpxvRivers/viralzoneGenes/viralzone.bb -chrom=NC_063383.1 -start=0 -end=100000 stdout
Please refer to our
mailing list archives
for questions, or our
Data Access FAQ
for more information.
Credits
Many thanks to Philippe Mercier from Viralzone for providing these annotations.
References
Zhilong Yang, Shuai Cao, Craig A Martens, Stephen F Porcella, Zhi Xie, Ming Ma, Ben Shen, Bernard Moss
Deciphering poxvirus gene expression by RNA sequencing and ribosome profiling
J Virol 2015 Jul;89(13):6874-86.
Tatiana G Senkevich, Natalya Yutin, Yuri I Wolf, Eugene V Koonin, Bernard Moss
Ancient Gene Capture and Recent Gene Loss Shape the Evolution of Orthopoxvirus-Host Interaction Genes
mBio 2021 Aug 31;12(4):e0149521
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