CLIC: clustering analysis of large microarray datasets with individual dimension-based clustering

Large microarray data sets have recently become common. However, most available clustering methods do not easily handle large microarray data sets due to their very large computational complexity and memory requirements. Furthermore, typical clustering methods construct oversimplified clusters that ignore subtle but meaningful changes in the expression patterns present in large microarray data sets. It is necessary to develop an efficient clustering method that identifies both absolute expression differences and expression profile patterns in different expression levels for large microarray data sets. This study presents CLIC, which meets the requirements of clustering analysis particularly but not limited to large microarray data sets. CLIC is based on a novel concept in which genes are clustered in individual dimensions first and in which the ordinal labels of clusters in each dimension are then used for further full dimension-wide clustering. CLIC enables iterative sub-clustering into more homogeneous groups and the identification of common expression patterns among the genes separated in different groups due to the large difference in the expression levels. In addition, the computation of clustering is parallelized, the number of clusters is automatically detected, and the functional enrichment for each cluster and pattern is provided. CLIC is freely available at http://gexp2.kaist.ac.kr/clic

Disease association and inter-connectivity analysis of human brain specific co-expressed functional modules

BACKGROUND: In the recent studies, it is suggested that the analysis of transcriptomic change of functional modules instead of individual genes would be more effective for system-wide identification of cellular functions. This could also provide a new possibility for the better understanding of difference between human and chimpanzee RESULTS: In this study, we analyzed to find molecular characteristics of human brain functions from the difference of transcriptome between human and chimpanzee's brain using the functional module-centric co-expression analysis. We performed analysis of brain disease association and systems-level connectivity of species-specific co-expressed functional modules CONCLUSIONS: Throughout the analyses, we found human-specific functional modules and significant overlap between their genes in known brain disease genes, suggesting that human brain disorder could be mediated by the perturbation of modular activities emerged in human brain specialization. In addition, the human-specific modules having neurobiological functions exhibited higher networking than other functional modules. This finding suggests that the expression of neural functions are more connected than other functions, and the resulting high-order brain functions could be identified as a result of consolidated inter-modular gene activities. Our result also showed that the functional module based transcriptome analysis has a potential to expand molecular understanding of high-order complex functions like cognitive abilities and brain disorder

Additional file 1: Table S1. of Discovering gene expression signatures responding to tyrosine kinase inhibitor treatment in chronic myeloid leukemia

Lists of differentially expressed genes of each dataset (GSE1467, GSE2535, and GSE33224). (XLS 115 kb

A chemically stable fluorescent marker of the ureter.

Surgical methods guided by exogenous fluorescent markers have the potential to define tissue types in real time. Small molecule dyes with efficient and selective renal clearance could enable visualization of the ureter during surgical procedures involving the abdomen and pelvis. These studies report the design and synthesis of a water soluble, net neutral C4\u27-O-alkyl heptamethine cyanine, Ureter-Label (UL)-766, with excellent properties for ureter visualization. This compound is accessed through a concise synthetic sequence involving an N- to O-transposition reaction that provides other inaccessible C4\u27-O-alkyl heptamethine cyanines. Unlike molecules containing a C4\u27-O-aryl substituent, which have also been used for ureter visualization, UL-766 is not reactive towards glutathione and the cellular proteome. In addition, rat models of abdominal surgery reveal that UL-766 undergoes efficient and nearly exclusive renal clearance in vivo. In total, this molecule represents a promising candidate for visualizing the ureter during a variety of surgical interventions