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
Clustering longitudinal profiles using P-splines and mixed effects models applied to time-course gene expression data
TL;DR: An alternative approach is proposed, which aims to alleviate some of the limitations to the techniques previously described, and exploits the connection between the linear mixed effects model and P-spline smoothing to simultaneously smooth the gene expression data to remove any measurement error/noise.
Journal ArticleDOI
Combined transcriptome and proteome profiling reveals specific molecular brain signatures for sex, maturation and circalunar clock phase
Sven Schenk,Sven Schenk,Stephanie C Bannister,Stephanie C Bannister,Fritz J. Sedlazeck,Dorothea Anrather,Bui Quang Minh,Andrea Bileck,Markus Hartl,Arndt von Haeseler,Arndt von Haeseler,Christopher Gerner,Florian Raible,Florian Raible,Kristin Tessmar-Raible +14 more
TL;DR: This study corroborates that circadian and circalunar clock effects are likely distinct and identifies key molecular brain signatures for reproduction, sex and circaling phase and examples include prepro-whitnin/proctolin and ependymin-related proteins as circalUNar clock targets.
Journal ArticleDOI
Phosphoproteome and drug-response effects mediated by the three protein phosphatase 2A inhibitor proteins CIP2A, SET, and PME-1
Otto Kauko,Otto Kauko,Susumu Y. Imanishi,Evgeny Kulesskiy,Laxman Yetukuri,Teemu D. Laajala,Teemu D. Laajala,Mukund Sharma,Mukund Sharma,Karolina Pavic,Anna Aakula,Christian Rupp,Mikael Jumppanen,Pekka Haapaniemi,Luyao Ruan,Bhagwan Yadav,Veronika Suni,Taru Varila,Garry L. Corthals,Jüri Reimand,Jüri Reimand,Krister Wennerberg,Tero Aittokallio,Tero Aittokallio,Jukka Westermarck,Jukka Westermarck +25 more
TL;DR: Consistent with global phosphoproteome effects, PP2A modulations broadly affect responses to more than 200 drugs inhibiting a broad spectrum of cancer-relevant targets and may enable the development of combination therapies.
Book ChapterDOI
Motif-Based Classification of Time Series with Bayesian Networks and SVMs
TL;DR: This paper introduces a new motif class, generalized semi-continuous motifs, to allow flexibility and noise robustness, and proposes an efficient algorithm for mining generalized sequential motifs.
Journal ArticleDOI
Temporal Profiling of the Chromatin Proteome Reveals System-wide Responses to Replication Inhibition
Guennadi A. Khoudoli,Peter J. Gillespie,Graeme Stewart,Jens S. Andersen,Jason R. Swedlow,J. Julian Blow +5 more
TL;DR: An analysis of the changing association of proteins with chromatin during progression through interphase of the cell cycle revealed an unexpectedly broad system-wide effect on the chromatin proteome, indicating that the response to replication inhibition extends to many other functional modules in addition to the replication machinery.
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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