HumanNet v2

Human gene networks for disease research

Sohyun Hwang, Chan Yeong Kim, Sunmo Yang, Eiru Kim, Traver Hart, Edward M. Marcotte, In suk Lee

Research output: Contribution to journalArticle

5 Citations (Scopus)

Abstract

Human gene networks have proven useful in many aspects of disease research, with numerous network-based strategies developed for generating hypotheses about gene-disease-drug associations. The ability to predict and organize genes most relevant to a specific disease has proven especially important. We previously developed a human functional gene network, HumanNet, by integrating diverse types of omics data using Bayesian statistics framework and demonstrated its ability to retrieve disease genes. Here, we present HumanNet v2 (http://www.inetbio.org/humannet), a database of human gene networks, which was updated by incorporating new data types, extending data sources and improving network inference algorithms. HumanNet now comprises a hierarchy of human gene networks, allowing for more flexible incorporation of network information into studies. HumanNet performs well in ranking disease-linked gene sets with minimal literature-dependent biases. We observe that incorporating model organisms- protein-protein interactions does not markedly improve disease gene predictions, suggesting that many of the disease gene associations are now captured directly in human-derived datasets. With an improved interactive user interface for disease network analysis, we expect HumanNet will be a useful resource for network medicine.

Original languageEnglish
Pages (from-to)D573-D580
JournalNucleic acids research
Volume47
Issue numberD1
DOIs
Publication statusPublished - 2019 Jan 8

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Gene Regulatory Networks
Research
Genes
Information Services
Information Storage and Retrieval
Proteins
Medicine
Databases
Pharmaceutical Preparations

All Science Journal Classification (ASJC) codes

  • Genetics

Cite this

Hwang, S., Kim, C. Y., Yang, S., Kim, E., Hart, T., Marcotte, E. M., & Lee, I. S. (2019). HumanNet v2: Human gene networks for disease research. Nucleic acids research, 47(D1), D573-D580. https://doi.org/10.1093/nar/gky1126
Hwang, Sohyun ; Kim, Chan Yeong ; Yang, Sunmo ; Kim, Eiru ; Hart, Traver ; Marcotte, Edward M. ; Lee, In suk. / HumanNet v2 : Human gene networks for disease research. In: Nucleic acids research. 2019 ; Vol. 47, No. D1. pp. D573-D580.
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Hwang, S, Kim, CY, Yang, S, Kim, E, Hart, T, Marcotte, EM & Lee, IS 2019, 'HumanNet v2: Human gene networks for disease research', Nucleic acids research, vol. 47, no. D1, pp. D573-D580. https://doi.org/10.1093/nar/gky1126

HumanNet v2 : Human gene networks for disease research. / Hwang, Sohyun; Kim, Chan Yeong; Yang, Sunmo; Kim, Eiru; Hart, Traver; Marcotte, Edward M.; Lee, In suk.

In: Nucleic acids research, Vol. 47, No. D1, 08.01.2019, p. D573-D580.

Research output: Contribution to journalArticle

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Hwang S, Kim CY, Yang S, Kim E, Hart T, Marcotte EM et al. HumanNet v2: Human gene networks for disease research. Nucleic acids research. 2019 Jan 8;47(D1):D573-D580. https://doi.org/10.1093/nar/gky1126