Journal ArticleDOI
Noise-robust soft clustering of gene expression time-course data
TLDR
To overcome the limitations of hard clustering, this work applied soft clustering which offers several advantages for researchers, including more noise robust and a priori pre-filtering of genes can be avoided.Abstract:
Clustering is an important tool in microarray data analysis. This unsupervised learning technique is commonly used to reveal structures hidden in large gene expression data sets. The vast majority of clustering algorithms applied so far produce hard partitions of the data, i.e. each gene is assigned exactly to one cluster. Hard clustering is favourable if clusters are well separated. However, this is generally not the case for microarray time-course data, where gene clusters frequently overlap. Additionally, hard clustering algorithms are often highly sensitive to noise. To overcome the limitations of hard clustering, we applied soft clustering which offers several advantages for researchers. First, it generates accessible internal cluster structures, i.e. it indicates how well corresponding clusters represent genes. This can be used for the more targeted search for regulatory elements. Second, the overall relation between clusters, and thus a global clustering structure, can be defined. Additionally, soft clustering is more noise robust and a priori pre-filtering of genes can be avoided. This prevents the exclusion of biologically relevant genes from the data analysis. Soft clustering was implemented here using the fuzzy c-means algorithm. Procedures to find optimal clustering parameters were developed. A software package for soft clustering has been developed based on the open-source statistical language R. The package called Mfuzz is freely available.read more
Citations
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Journal ArticleDOI
Diet-rich in wheat bran modulates tryptophan metabolism and AhR/IL-22 signalling mediated metabolic health and gut dysbacteriosis: A novel prebiotic-like activity of wheat bran.
Tao Yan,Lin Shi,Tianqi Liu,Xiangnan Zhang,Minmin Yang,Wen Peng,Xiaomin Sun,Lijing Yan,Xiaoshuang Dai,Xinbing Yang +9 more
TL;DR: In this paper , a 6-week high-fat diet (HFD) disturbed tryptophan metabolism accompanied with gut dysbacteriosis, also influenced the dietary tryphan induced changes in cecum microbiome and serum metabolome in mice.
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Transcriptome analysis of the binucleate ciliate <i>Tetrahymena thermophila</i> with asynchronous nuclear cell cycles
Pyoung Jik Lee,Mohit Kumar Jolly +1 more
TL;DR: In this paper , the first RNA-seq analysis across the cell cycle of a binucleated organism was performed, where RNA was isolated at 30 min intervals across 1.5 vegetative cell cycles, starting with a macronuclear G1 population synchronized by centrifugal elutriation.
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Integrative lipidomic features identify plasma lipid signatures in chronic urticaria
Jie Li,Liqiao Li,Runqiu Liu,Lei Zhu,Bing Zhou,Yi Xiao,Guixue Hou,Liang Lin,Xin Chen,Cong Peng +9 more
TL;DR: It is found that supplementation with PC could attenuate IgE-induced immune responses in mast cells, and the landscape of plasma lipid alterations in CU patients is described and novel insights are provided into the role of PC inmast cells.
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The consequences of surviving infection across the metamorphic boundary : tradeoff insights from RNAseq and life history measures
TL;DR: The long-term effects of injury and infection using two bacteria in the butterfly Pieris napi is investigated, revealing that the negative consequences of bacterial infection carry across the metamorphic boundary.
References
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Journal ArticleDOI
Cluster analysis and display of genome-wide expression patterns
TL;DR: A system of cluster analysis for genome-wide expression data from DNA microarray hybridization is described that uses standard statistical algorithms to arrange genes according to similarity in pattern of gene expression, finding in the budding yeast Saccharomyces cerevisiae that clustering gene expression data groups together efficiently genes of known similar function.
Book
Pattern Recognition with Fuzzy Objective Function Algorithms
TL;DR: Books, as a source that may involve the facts, opinion, literature, religion, and many others are the great friends to join with, becomes what you need to get.
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