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Protocols

HumanNet specifications

Information


Unique identifier OMICS_12794
Name HumanNet
Alternative name Human gene functional interaction Network
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Allowed
Version 1.0
Maintained Yes

Taxon


  • Primates
    • Homo sapiens

Documentation


Maintainer


  • person_outline Insuk Lee

Publications for Human gene functional interaction Network

HumanNet citations

 (19)
library_books

Identifying noncoding risk variants using disease relevant gene regulatory networks

2018
Nat Commun
PMCID: 5816022
PMID: 29453388
DOI: 10.1038/s41467-018-03133-y

[…] of ARVIN can be affected by the quality of GRN. In this study, we addressed this issue by weighting the edges and nodes in the network. To further examine the robustness of our method, we substituted HumanNet with the functional gene interaction network annotated in the STRING database. Using the same set of gold-standard promoter and enhancer SNPs, we found that ARVIN achieves similar performance […]

library_books

InfAcrOnt: calculating cross ontology term similarities using information flow by a random walk

2018
BMC Genomics
PMCID: 5780854
PMID: 29363423
DOI: 10.1186/s12864-017-4338-6

[…] y score and TF-IDF similarity score to evaluate the performance of InfAcrOnt.A WTGGN for DO-HPO terms and their annotated genes was built by DO, HPO, DO Annotations (DOA), HPO Annotations (HPOA), and HumanNet (Table ). Then the similarities of pair-wise DO-HPO terms were calculated by InfAcrOnt based on the WTGGN. DO [] and HPO [] were downloaded from open source repositories (Table ) which provid […]

library_books

Transcriptomic signatures of cellular and humoral immune responses in older adults after seasonal influenza vaccination identified by data driven clustering

2018
Sci Rep
PMCID: 5768803
PMID: 29335477
DOI: 10.1038/s41598-017-17735-x

[…] tween the individual genes found in the WGCNA gene clusters. Interactions from the Pathway Interaction Database, Transcription Factor Encyclopedia, a directed protein interaction network, HPRD, CCSB, HumanNet (minimum score ≥ 0.0), and STRING(minimum score ≥700) were accessed using RITAN. This integrated network resource provided a comprehensive summary of known interactions across the human prote […]

library_books

The integration of weighted gene association networks based on information entropy

2017
PLoS One
PMCID: 5741255
PMID: 29272314
DOI: 10.1371/journal.pone.0190029

[…] bability likelihood ratio scoring, and the other is based on Bayesian method. Lee et al used a log likelihood scoring (LLS) scheme to construct a genome-scale functional network of human genes called HumanNet, which incorporated diverse data sources, such as gene expression, protein interaction, genetic interaction, sequence, literature, and comparative genomics data. This network includes data di […]

library_books

Incorporating networks in a probabilistic graphical model to find drivers for complex human diseases

2017
PLoS Comput Biol
PMCID: 5638204
PMID: 29023450
DOI: 10.1371/journal.pcbi.1005580

[…] we use the iRefIndex network. It is one of the networks that were previously processed and used by Hotnet2 with a defined hyper-parameter beta proposed for their method. We also tried the Biogrid and HumanNet networks with no observed change in Conflux performance. The choice of network should not affect our results as long as it provides evidence for the underlying disease mechanism. If the given […]

library_books

DisSetSim: an online system for calculating similarity between disease sets

2017
J Biomed Semantics
PMCID: 5763469
PMID: 29297411
DOI: 10.1186/s13326-017-0140-2

[…] are manually curated databases of disease-related genes. All of diseases in these databases are mapped to terms in DO based on SIDD []. GO annotation (GOA) [] includes functional annotation of genes. HumanNet is the gene functional network of human. In addition, HMDD v2.0 [] contains disease-related miRNAs, diseases of which were manually mapped to terms in DO by OAHG []. […]

Citations

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HumanNet institution(s)
Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, Korea; Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, University of Texas, Austin, TX, USA; Department of Biomedical Science, College of Life Science, CHA University, Seongnam-si, Korea; Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Department of Molecular Biosciences, University of Texas at Austin, TX, USA
HumanNet funding source(s)
Supported by National Research Foundation of Korea (NRF) grant funded by the Korean Government (MSIT) [NRF2018M3C9A5064709, NRF-2018R1A5A2025079, NRF-2018R1C1B5032617]; Brain Korea 21 (BK21) PLUS Program; NIH; NSF; Welch Foundation (F-1515); CPRIT Grant [RR160032]; NIH Grants [R35GM130119, P30 CA016672].

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