Implementation χ -sim co-similarity and agglomerative hierarchical to cluster gene expression data of lymphoma by gene and condition

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Abstract

Application chi-sim co-similarity and agglomerative hierarchical clustering in this study are used to clustering gene expression data of Lymphoma by gene and condition. The process begins by taking the gene expression data of Lymphoma, after that microarray gene expression data of Lymphoma will be standardized by using standardized rows and columns. Then, the concept of chi-sim co-similarity applied to create the matrix similarity row (SR) and similarity column (SC). The matrix elements of SR and SC are normalized by using a pseudo normalization. Finally, we use three approaches in agglomerative hierarchical clustering to cluster the data by gene and condition. Three approaches in agglomerative hierarchical clustering are single linkage, average linkage, and complete linkage. The result of clustering by column and gene in this study, give us the best outcome when complete linkage in agglomerative hierarchical clustering is combined with chi-sim co-similarity compared with single linkage and average linkage in agglomerative hierarchical clustering combined with chi-sim co-similarity.

Original languageEnglish
Title of host publicationProceedings of the 3rd International Symposium on Current Progress in Mathematics and Sciences 2017, ISCPMS 2017
EditorsRatna Yuniati, Terry Mart, Ivandini T. Anggraningrum, Djoko Triyono, Kiki A. Sugeng
PublisherAmerican Institute of Physics Inc.
ISBN (Electronic)9780735417410
DOIs
Publication statusPublished - 22 Oct 2018
Event3rd International Symposium on Current Progress in Mathematics and Sciences 2017, ISCPMS 2017 - Bali, Indonesia
Duration: 26 Jul 201727 Jul 2017

Publication series

NameAIP Conference Proceedings
Volume2023
ISSN (Print)0094-243X
ISSN (Electronic)1551-7616

Conference

Conference3rd International Symposium on Current Progress in Mathematics and Sciences 2017, ISCPMS 2017
Country/TerritoryIndonesia
CityBali
Period26/07/1727/07/17

Keywords

  • Agglomerative Hierarchical Clustering
  • Chi-Sim Co-Similarity
  • cluster
  • silhouette

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