A biclustering procedure using BicBin algorithm for HIV-1 human protein interaction database in NCBI
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 growin...
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| creator | Tampubolon, Patuan Pangihutan Bustamam, Alhadi Lestari, Dian Mangunwardoyo, Wibowo |
| description | 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 p1 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, p1 = 1, and I = 600 in our procedure. |
| doi_str_mv | 10.1063/1.5094272 |
| format | Conference Proceeding |
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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 p1 is used to control the density of the biclusters. 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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 p1 is used to control the density of the biclusters. 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| subjects | Algorithms Bioinformatics Data mining Graph theory Parameters Proteins Scientific papers |
| title | A biclustering procedure using BicBin algorithm for HIV-1 human protein interaction database in NCBI |
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