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Helsinki, Finland

Kallio H.,University of Tampere | Tolvanen M.,University of Tampere | Janis J.,University of Eastern Finland | Pan P.-w.,University of Tampere | And 9 more authors.
PLoS ONE | Year: 2011

Our previous microarray study showed that the non-specific cytotoxic cell receptor protein 1 (Nccrp1) transcript is significantly upregulated in the gastric mucosa of carbonic anhydrase IX (CA IX)-deficient (Car9 -/-) mice. In this paper, we aimed to characterize human NCCRP1 and to elucidate its relationship to CA IX. Recombinant NCCRP1 protein was expressed in Escherichia coli, and a novel polyclonal antiserum was raised against the purified full-length protein. Immunocytochemistry showed that NCCRP1 is expressed intracellularly, even though it has previously been described as a transmembrane protein. Using bioinformatic analyses, we identified orthologs of NCCRP1 in 35 vertebrate genomes, and up to five paralogs per genome. These paralogs are FBXO genes whose protein products are components of the E3 ubiquitin ligase complexes. NCCRP1 proteins have no signal peptides or transmembrane domains. NCCRP1 has mainly been studied in fish and was thought to be responsible for the cytolytic function of nonspecific cytotoxic cells (NCCs). Our analyses showed that in humans, NCCRP1 mRNA is expressed in tissues containing squamous epithelium, whereas it shows a more ubiquitous tissue expression pattern in mice. Neither human nor mouse NCCRP1 expression is specific to immune tissues. Silencing CA9 using siRNAs did not affect NCCRP1 levels, indicating that its expression is not directly regulated by CA9. Interestingly, silencing NCCRP1 caused a statistically significant decrease in the growth of HeLa cells. These studies provide ample evidence that the current name, "non-specific cytotoxic cell receptor protein 1," is not appropriate. We therefore propose that the gene name be changed to FBXO50. © 2011 Kallio et al. Source


Alternative splicing is a widespread process contributing to structural transcript variation and proteome diversity. In cancer, the splicing process is commonly disrupted, resulting in both functional and non-functional end-products. Cancer-specific splicing events are known to contribute to disease progression; however, the dysregulated splicing patterns found on a genome-wide scale have until recently been less well-studied. In this review, we provide an overview of aberrant RNA splicing and its regulation in cancer. We then focus on the executors of the splicing process. Based on a comprehensive catalog of splicing factor encoding genes and analyses of available gene expression and somatic mutation data, we identify cancer-associated patterns of dysregulation. Splicing factor genes are shown to be significantly differentially expressed between cancer and corresponding normal samples, and to have reduced inter-individual expression variation in cancer. Furthermore, we identify enrichment of predicted cancer-critical genes among the splicing factors. In addition to previously described oncogenic splicing factor genes, we propose 24 novel cancer-critical splicing factors predicted from somatic mutations.Oncogene advance online publication, 24 August 2015; doi:10.1038/onc.2015.318. © 2015 Macmillan Publishers Limited Source


An aspect of the present invention is a computer executable method for characterizing, e.g. for diagnostic purposes, utilizing a reference database, a query sample tissue based on the gene expression data of the tissue. The method is characterized in that it comprises the steps of calculating an expression match score (EM-score) indicating the likelihood of having the gene expression level observed in the query sample in each of the tissue categories of the reference database, calculating for the genes of the sample tissue, using e.g. the EM-score, tissue specificity score (TS-score), that expresses how uniquely a gene identifies the query sample as belonging to a certain tissue category, calculating, utilizing e.g. the TS-score, overall similarity of the sample tissue in relation to a tissue category of the reference database, and storing at least some resulting characterization data to a memory device or outputting the data to an output device of a computer. An arrangement and a computer program product are also disclosed.


Trademark
MediSapiens | Date: 2012-03-20

Software for research and personalized treatment of cancer and other diseases; software for research on the human genome; software for drug development. Scientific and technological services, namely, research and design in the field of bioinformatics, genomics and gene expression research and development; Design and development of computer hardware and software; Design and development of computer hardware and software, namely, application service provider hosting services, namely, hosting, managing, developing, analyzing, and maintaining applications, software and websites of others in the fields of genomics and gene expression; Design and development of computer hardware and software, namely, programming and updating of genomics and gene expression databases. Medical services for the diagnosis and treatment of the human body.


Trademark
MediSapiens | Date: 2012-07-24

Software for research and personalized treatment of cancer and other diseases; software for research on the human genome; software for drug development. Scientific and technological services, namely, research and design in the field of bioinformatics, genomics and gene expression research and development; Design and development of computer hardware and software; Design and development of computer hardware and software, namely, application service provider hosting services, namely, hosting, managing, developing, analyzing, and maintaining applications, software and websites of others in the fields of genomics and gene expression; Design and development of computer hardware and software, namely, programming and updating of genomics and gene expression databases. Medical services for the diagnosis and treatment of the human body.

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