SpliceNet: recovering splicing isoform-specific differential gene networks from RNA-Seq data of normal and diseased samples

@inproceedings{Yalamanchili2014SpliceNetRS,
  title={SpliceNet: recovering splicing isoform-specific differential gene networks from RNA-Seq data of normal and diseased samples},
  author={Hari Krishna Yalamanchili and Zhaoyuan Li and Panwen Wang and Maria Pik Wong and Jian-Feng Yao and Junwen Wang},
  booktitle={Nucleic acids research},
  year={2014}
}
Conventionally, overall gene expressions from microarrays are used to infer gene networks, but it is challenging to account splicing isoforms. High-throughput RNA Sequencing has made splice variant profiling practical. However, its true merit in quantifying splicing isoforms and isoform-specific exon expressions is not well explored in inferring gene networks. This study demonstrates SpliceNet, a method to infer isoform-specific co-expression networks from exon-level RNA-Seq data, using large… CONTINUE READING
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VIEW 6 EXCERPTS
CITES BACKGROUND & METHODS
HIGHLY INFLUENCED

References

Publications referenced by this paper.
SHOWING 1-10 OF 45 REFERENCES

Siva-1 binds to and inhibits BCL-X(L)-mediated protection against UV radiation-induced apoptosis.

  • Proceedings of the National Academy of Sciences of the United States of America
  • 2002
VIEW 16 EXCERPTS
HIGHLY INFLUENTIAL

C-CAM1, a candidate tumor suppressor gene, is abnormally expressed in primary lung cancers.

  • Clinical cancer research : an official journal of the American Association for Cancer Research
  • 2000
VIEW 4 EXCERPTS
HIGHLY INFLUENTIAL

Inhibition of death receptor signals by cellular FLIP

  • Nature
  • 1997
VIEW 16 EXCERPTS
HIGHLY INFLUENTIAL