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LongHorn predicts
modulation of canonical regulators (or effectors), including miRNA, RBP, and
TF, by lncRNAs. Leveraging large-scale cancer genomics datasets from TCGA,
LongHorn identifies four models for lncRNA regulation: 1)
Decoy: binds and inhibits the
activity of effectors by affecting their availability to regulate their
protein-coding targets 2)
Co-factor: binds proximal
promoters of protein-coding genes and alter their regulation by TFs 3)
Guide: facilitates
regulation of protein-coding genes by TFs 4)
Switch: alters the activity
of TFs and RBPs across multiple targets LongHorn has been implemented in
MATLAB. Please download it from here. |
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News: 04/26/2018:
LongHorn is
covered by BCM’s From
The Labs. 04/09/2018:
LongHorn is covered by lncRNA
Blog. 04/08/2018:
LongHorn v1.0
is now released. 04/05/2018:
LongHorn is covered by BCM
news. 04/05/2018:
LongHorn predictions in the study of pan-gynecologic and breast cancers
published in Cancer Cell
are covered by lncRNA
Blog. 04/05/2018:
TCGA Pan-Cancer Atlas is now released at Cell.
It is a collection of 27 studies, including LongHorn, based
on pan-cancer analysis using TCGA datasets. 04/03/2018:
TCGA Pan-Cancer Atlas’s studies published in the journal Cell
Reports are covered by GenomeWeb. 04/03/2018:
TCGA Pan-Cancer Atlas is featured as the
cover story in the journal Cell
Reports. |
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References: §
Chiu HS*,
Somvanshi S* et al. 2018. Pan-Cancer Analysis
of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor
Context. Cell Rep 23: 297-312 e212. (LongHorn main paper) §
Berger AC et al. 2018. A Comprehensive
Pan-Cancer Molecular Study of Gynecologic and Breast Cancers. Cancer
Cell 33: 1-16. (LongHorn
predictions were used to generate Figure 5) §
Decoy-related
papers: o
Sumazin P*,
Yang X*, Chiu HS* et al. 2011. An extensive
microRNA-mediated network of RNA-RNA interactions regulates established
oncogenic pathways in glioblastoma. Cell 147: 370-381. o
Chiu HS*, Llobet-Navas D* et
al. 2015. Cupid:
simultaneous reconstruction of microRNA-target and ceRNA networks. Genome
Res 25: 257-267. o
Chiu HS et al. 2017. High-throughput
validation of ceRNA regulatory networks. BMC Genomics 18:
418. o
Chiu HS*,
Martinez MR* et al. 2018. The number of titrated
microRNA species dictates ceRNA regulation. Nucleic Acids Res 46(9): 4354-4369. We thank the EU funded PrECISE,
HORIZON-2020 #668858, for partially supporting the development of LongHorn. |
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Regulatory
Circuits Lab @ Texas Children’s
Hospital (affiliated with Baylor College
of Medicine) 1102 Bates Ave (Feigin
Center), Houston, Texas 77030 |
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