A biclustering procedure using BicBin algorithm for HIV-1 human protein interaction database in NCBI

Patuan Pangihutan Tampubolon, Alhadi Bustamam, Dian Lestari, Wibowo Mangunwardoyo

Research output: Chapter in Book/Report/Conference proceedingConference contributionResearchpeer-review

Abstract

The objective of establishing the HIV-1 Human Interaction Database (HHPID) in the NCBI that is to encourage the scientists to produce more publications. The database collates two types of interactions from the published reports - protein in- teractions and replication interactions. One of the growing up data mining technique is bioinformatics is biclustering. The BicBin algorithm is one of the biclustering method to a binary matrix. We propose a systematic procedure to make biclusters to the HHPID using BicBin algorithm. First, we select the HIV-1 proteins, the human proteins, and the interaction keywords from HHPID to model the interaction as a bipartite graph. The Keywords are divided into three classes based on the direction of the interactions and then separated them into two binary matrices, i.e., positive and negative matrix. The binary matrices then become the input to the BicBin algorithm. The algorithm outputs many biclusters. The user sets the input parameter α and β to control the search area in each binary matrix. The parameter p 1 is used to control the density of the biclusters. Then, the algorithm is iterated by parameter I. We set α = 0.5, β = 0.5, p 1 = 1, and I = 600 in our procedure.

Original languageEnglish
Title of host publicationProceedings of the Symposium on BioMathematics, SYMOMATH 2018
EditorsBevina Desjwiandra Handari, Hiromi Seno, Hengki Tasman
PublisherAmerican Institute of Physics Inc.
ISBN (Electronic)9780735418141
DOIs
Publication statusPublished - 22 Mar 2019
EventInternational Symposium on BioMathematics 2018, SYMOMATH 2018 - Depok, Indonesia
Duration: 31 Aug 20182 Sep 2018

Publication series

NameAIP Conference Proceedings
Volume2084
ISSN (Print)0094-243X
ISSN (Electronic)1551-7616

Conference

ConferenceInternational Symposium on BioMathematics 2018, SYMOMATH 2018
CountryIndonesia
CityDepok
Period31/08/182/09/18

Fingerprint

human immunodeficiency virus
proteins
matrices
interactions
data mining
output

Cite this

Tampubolon, P. P., Bustamam, A., Lestari, D., & Mangunwardoyo, W. (2019). A biclustering procedure using BicBin algorithm for HIV-1 human protein interaction database in NCBI. In B. D. Handari, H. Seno, & H. Tasman (Eds.), Proceedings of the Symposium on BioMathematics, SYMOMATH 2018 [020008] (AIP Conference Proceedings; Vol. 2084). American Institute of Physics Inc.. https://doi.org/10.1063/1.5094272
Tampubolon, Patuan Pangihutan ; Bustamam, Alhadi ; Lestari, Dian ; Mangunwardoyo, Wibowo. / A biclustering procedure using BicBin algorithm for HIV-1 human protein interaction database in NCBI. Proceedings of the Symposium on BioMathematics, SYMOMATH 2018. editor / Bevina Desjwiandra Handari ; Hiromi Seno ; Hengki Tasman. American Institute of Physics Inc., 2019. (AIP Conference Proceedings).
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abstract = "The objective of establishing the HIV-1 Human Interaction Database (HHPID) in the NCBI that is to encourage the scientists to produce more publications. The database collates two types of interactions from the published reports - protein in- teractions and replication interactions. One of the growing up data mining technique is bioinformatics is biclustering. The BicBin algorithm is one of the biclustering method to a binary matrix. We propose a systematic procedure to make biclusters to the HHPID using BicBin algorithm. First, we select the HIV-1 proteins, the human proteins, and the interaction keywords from HHPID to model the interaction as a bipartite graph. The Keywords are divided into three classes based on the direction of the interactions and then separated them into two binary matrices, i.e., positive and negative matrix. The binary matrices then become the input to the BicBin algorithm. The algorithm outputs many biclusters. The user sets the input parameter α and β to control the search area in each binary matrix. The parameter p 1 is used to control the density of the biclusters. Then, the algorithm is iterated by parameter I. We set α = 0.5, β = 0.5, p 1 = 1, and I = 600 in our procedure.",
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Tampubolon, PP, Bustamam, A, Lestari, D & Mangunwardoyo, W 2019, A biclustering procedure using BicBin algorithm for HIV-1 human protein interaction database in NCBI. in BD Handari, H Seno & H Tasman (eds), Proceedings of the Symposium on BioMathematics, SYMOMATH 2018., 020008, AIP Conference Proceedings, vol. 2084, American Institute of Physics Inc., International Symposium on BioMathematics 2018, SYMOMATH 2018, Depok, Indonesia, 31/08/18. https://doi.org/10.1063/1.5094272

A biclustering procedure using BicBin algorithm for HIV-1 human protein interaction database in NCBI. / Tampubolon, Patuan Pangihutan; Bustamam, Alhadi; Lestari, Dian; Mangunwardoyo, Wibowo.

Proceedings of the Symposium on BioMathematics, SYMOMATH 2018. ed. / Bevina Desjwiandra Handari; Hiromi Seno; Hengki Tasman. American Institute of Physics Inc., 2019. 020008 (AIP Conference Proceedings; Vol. 2084).

Research output: Chapter in Book/Report/Conference proceedingConference contributionResearchpeer-review

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Tampubolon PP, Bustamam A, Lestari D, Mangunwardoyo W. A biclustering procedure using BicBin algorithm for HIV-1 human protein interaction database in NCBI. In Handari BD, Seno H, Tasman H, editors, Proceedings of the Symposium on BioMathematics, SYMOMATH 2018. American Institute of Physics Inc. 2019. 020008. (AIP Conference Proceedings). https://doi.org/10.1063/1.5094272