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HotNet specifications

Information


Unique identifier OMICS_08335
Name HotNet
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Documentation


Maintainers


  • person_outline Fabio Vandin
  • person_outline Benjamin Raphael

Additional information


http://bio.cs.brown.edu/projects/hotnet/ Previous version: https://github.com/raphael-group/hotnet

Information


Unique identifier OMICS_08335
Name HotNet
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


Maintainers


  • person_outline Fabio Vandin
  • person_outline Benjamin Raphael

Additional information


http://bio.cs.brown.edu/projects/hotnet/ Previous version: https://github.com/raphael-group/hotnet

Publications for HotNet

HotNet citations

 (51)
library_books

Identification and characterization of functional modules reflecting transcriptome transition during human neuron maturation

2018
BMC Genomics
PMCID: 5905132
PMID: 29665773
DOI: 10.1186/s12864-018-4649-2

[…] f mature and immature neurons, and p is the P-value of ANOVA with neuron maturity state as the independent variable.A heat-diffusion-based network smoothing procedure, as described and implemented in HotNet2 [], was then applied to the obtained PPI network where the above expression alteration scores were assigned to corresponding nodes. In brief, a diffusion matrix, which describes the amount of […]

library_books

Applying Expression Profile Similarity for Discovery of Patient Specific Functional Mutations

2018
PMCID: 5876532
PMID: 29485617
DOI: 10.3390/ht7010006

[…] ikely to be mutated []. Using mutual exclusivity, members of signalling pathways are investigated for their coverage across a large number of patients while not co-mutated in the same patients [,,,]. HotNet2, a network approach is applied to identify significantly mutated groups of interacting genes across pathways and protein complexes []. Besides of functional annotations, expression information […]

library_books

Network modules uncover mechanisms of skeletal muscle dysfunction in COPD patients

2018
J Transl Med
PMCID: 5819708
PMID: 29463285
DOI: 10.1186/s12967-018-1405-y

[…] ion network represents, whose topology already encodes basic biological functions [, ] and provides high performance in predicting biologically meaningful pathways []. Additionally, the model used in HotNet2, simulating the spread of influence of protein activity, enables the identification of key proteins with less significant changes but with high biological meaning due to surrounding expression […]

library_books

Integrative genomic and transcriptomic analysis of leiomyosarcoma

2018
Nat Commun
PMCID: 5762758
PMID: 29321523
DOI: 10.1038/s41467-017-02602-0

[…] Network analysis was performed using HotNet2 (version 1.0.1), and the global interaction network (HINT+HI2012) was retrieved from the HotNet2 website (http://compbio-research.cs.brown.edu/pancancer/hotnet2). For each node (gene) in the g […]

library_books

Exploring the pathogenesis of canine epilepsy using a systems genetics method and implications for anti epilepsy drug discovery

2017
Oncotarget
PMCID: 5862570
PMID: 29568349
DOI: 10.18632/oncotarget.23719

[…] imilar to those of humans []. In this study, the genotype and epilepsy phenotype data of Hayward et al. [] were used to explore the pathogenesis of canine epilepsy in a combined method using GWAS and HotNet2.Using the combination of GWAS and HotNet2, we ultimately identified 26 subnetworks associated with canine epilepsy. Through GO enrichment analysis and a literature review, we focused on the re […]

library_books

Graph theoretical comparison of normal and tumor networks in identifying BRCA genes

2017
BMC Syst Biol
PMCID: 5700672
PMID: 29166896
DOI: 10.1186/s12918-017-0495-0

[…] or in diseased individuals []. Rather than identifying a set of cancer-related genes, the goal of the integrative computational approaches usually is to extract modules deemed central to the cancer. HotNet2 employs a random-walk on the PPI network distributing the mutation frequencies of genes throughout the network, giving rise to a directed graph where the strongly connected components represen […]

Citations

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HotNet institution(s)
Department of Computer Science, Brown University, Providence, RI, USA; Center for Computational Molecular Biology, Brown University, Providence, RI, USA; Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, USA; The Genome Institute, Washington University in St. Louis, MO, USA; The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Research Unit on Biomedical Informatics, Department of Experimental and Health Sciences, University Pompeu Fabra, Barcelona, Spain; Program of Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Biostatistics, Yale School of Public Health, New Haven, CT, USA; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain; Massachusetts General Hospital, Boston, MA, USA; Department of Medicine, Washington University in St. Louis, MO, USA; Siteman Cancer Center, Washington University in St. Louis, MO, USA
HotNet funding source(s)
Supported by NSF grant IIS-1016648 and NIH grants R01HG005690, 1R01HG007069, and 1R01CA180776, and National Human Genome Research Institute grant U01HG006517; by a Career Award at the Scientific Interface from the Burroughs Wellcome Fund, an Alfred P. Sloan Research Fellowship, and an NSF CAREER Award (CCF-1053753); by NSF GRFP DGE 0228243.

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