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.

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.

 

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 (accepted).

 

 

We thank the EU funded PrECISE, HORIZON-2020 #668858, for partially supporting the development of LongHorn.

Regulatory Circuits Lab @ Texas Children’s Hospital (affiliated with Baylor College of Medicine)

1102 Bates Ave (Feigin Center), Houston, Texas 77030
Contact: Dr. Pavel Sumazin or Dr. Hua-Sheng Chiu
Last update:
5/5/2018 8:35:22 AM

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