Hubba: hub objects analyzer--a framework of interactome hubs identification for network biology.

Chung Yen Lin, Chia Hao Chin, Hsin Hung Wu, Shu Hwa Chen, Chin Wen Ho, Ming Tat Ko

Research output: Contribution to journalArticle

152 Citations (Scopus)

Abstract

One major task in the post-genome era is to reconstruct proteomic and genomic interacting networks using high-throughput experiment data. To identify essential nodes/hubs in these interactomes is a way to decipher the critical keys inside biochemical pathways or complex networks. These essential nodes/hubs may serve as potential drug-targets for developing novel therapy of human diseases, such as cancer or infectious disease caused by emerging pathogens. Hub Objects Analyzer (Hubba) is a web-based service for exploring important nodes in an interactome network generated from specific small- or large-scale experimental methods based on graph theory. Two characteristic analysis algorithms, Maximum Neighborhood Component (MNC) and Density of Maximum Neighborhood Component (DMNC) are developed for exploring and identifying hubs/essential nodes from interactome networks. Users can submit their own interaction data in PSI format (Proteomics Standards Initiative, version 2.5 and 1.0), tab format and tab with weight values. User will get an email notification of the calculation complete in minutes or hours, depending on the size of submitted dataset. Hubba result includes a rank given by a composite index, a manifest graph of network to show the relationship amid these hubs, and links for retrieving output files. This proposed method (DMNC || MNC) can be applied to discover some unrecognized hubs from previous dataset. For example, most of the Hubba high-ranked hubs (80% in top 10 hub list, and >70% in top 40 hub list) from the yeast protein interactome data (Y2H experiment) are reported as essential proteins. Since the analysis methods of Hubba are based on topology, it can also be used on other kinds of networks to explore the essential nodes, like networks in yeast, rat, mouse and human. The website of Hubba is freely available at http://hub.iis.sinica.edu.tw/Hubba.

Original languageEnglish
Pages (from-to)W438-443
JournalNucleic Acids Research
Volume36
Issue numberWeb Server issue
DOIs
Publication statusPublished - Jul 1 2008
Externally publishedYes

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Proteomics
Emerging Communicable Diseases
Fungal Proteins
Yeasts
Genome
Weights and Measures
Pharmaceutical Preparations
Neoplasms
Proteins
Datasets
Therapeutics

ASJC Scopus subject areas

  • Genetics

Cite this

Hubba : hub objects analyzer--a framework of interactome hubs identification for network biology. / Lin, Chung Yen; Chin, Chia Hao; Wu, Hsin Hung; Chen, Shu Hwa; Ho, Chin Wen; Ko, Ming Tat.

In: Nucleic Acids Research, Vol. 36, No. Web Server issue, 01.07.2008, p. W438-443.

Research output: Contribution to journalArticle

Lin, Chung Yen ; Chin, Chia Hao ; Wu, Hsin Hung ; Chen, Shu Hwa ; Ho, Chin Wen ; Ko, Ming Tat. / Hubba : hub objects analyzer--a framework of interactome hubs identification for network biology. In: Nucleic Acids Research. 2008 ; Vol. 36, No. Web Server issue. pp. W438-443.
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