Identification of genetic signatures is the main objective for many computational oncology studies. The signature usually consists of numerous genes that are differentially expressed between two clinically distinct gr...Identification of genetic signatures is the main objective for many computational oncology studies. The signature usually consists of numerous genes that are differentially expressed between two clinically distinct groups of samples, such as tumor subtypes. Prospectively, many signatures have been found to generalize poorly to other datasets and, thus, have rarely been accepted into clinical use. Recognizing the limited success of traditionally generated signatures, we developed a systems biology-based framework for robust identification of key transcription factors and their genomic regulatory neighborhoods. Application of the framework to study the differences between gastrointestinal stromal tumor (GIST) and leiomyosarcoma (LMS) resulted in the identification of nine transcription factors (SRF, NKX2-5, CCDC6, LEF1, VDR, ZNF250, TRIM63, MAF, and MYC). Functional annotations of the obtained neighborhoods identified the biological processes which the key transcription factors regulate differently between the tumor types. Analyzing the differences in the expression patterns using our approach resulted in a more robust genetic signature and more biological insight into the diseases compared to a traditional genetic signature.展开更多
In this editorial we introduce the research paradigms of signal processing in the era of systems biology.Signal processing is a field of science traditionally focused on modeling electronic and communications systems,...In this editorial we introduce the research paradigms of signal processing in the era of systems biology.Signal processing is a field of science traditionally focused on modeling electronic and communications systems,but recently it has turned to biological applications with astounding results.The essence of signal processing is to describe the natural world by mathematical models and then,based on these models,develop efficient computational tools for solving engineering problems.Here,we underline,with examples,the endless possibilities which arise when the battle-hardened tools of engineering are applied to solve the problems that have tormented cancer researchers.Based on this approach,a new field has emerged,called cancer systems biology.Despite its short history,cancer systems biology has already produced several success stories tackling previously impracticable problems.Perhaps most importantly,it has been accepted as an integral part of the major endeavors of cancer research,such as analyzing the genomic and epigenomic data produced by The Cancer Genome Atlas(TCGA) project.Finally,we show that signal processing and cancer research,two fields that are seemingly distant from each other,have merged into a field that is indeed more than the sum of its parts.展开更多
基金supported by Project for the Biological Information and Information Processing Properties of Biological Systems from the Academy of Finland(No.122973)Project for the Structure-dynamics Relationships in Biological Network from the Academy of Finland(No.132877)Finnish Funding Agency for Technology and Innovation Finland Distinguished Professor program(No.1480/31/09)
文摘Identification of genetic signatures is the main objective for many computational oncology studies. The signature usually consists of numerous genes that are differentially expressed between two clinically distinct groups of samples, such as tumor subtypes. Prospectively, many signatures have been found to generalize poorly to other datasets and, thus, have rarely been accepted into clinical use. Recognizing the limited success of traditionally generated signatures, we developed a systems biology-based framework for robust identification of key transcription factors and their genomic regulatory neighborhoods. Application of the framework to study the differences between gastrointestinal stromal tumor (GIST) and leiomyosarcoma (LMS) resulted in the identification of nine transcription factors (SRF, NKX2-5, CCDC6, LEF1, VDR, ZNF250, TRIM63, MAF, and MYC). Functional annotations of the obtained neighborhoods identified the biological processes which the key transcription factors regulate differently between the tumor types. Analyzing the differences in the expression patterns using our approach resulted in a more robust genetic signature and more biological insight into the diseases compared to a traditional genetic signature.
文摘In this editorial we introduce the research paradigms of signal processing in the era of systems biology.Signal processing is a field of science traditionally focused on modeling electronic and communications systems,but recently it has turned to biological applications with astounding results.The essence of signal processing is to describe the natural world by mathematical models and then,based on these models,develop efficient computational tools for solving engineering problems.Here,we underline,with examples,the endless possibilities which arise when the battle-hardened tools of engineering are applied to solve the problems that have tormented cancer researchers.Based on this approach,a new field has emerged,called cancer systems biology.Despite its short history,cancer systems biology has already produced several success stories tackling previously impracticable problems.Perhaps most importantly,it has been accepted as an integral part of the major endeavors of cancer research,such as analyzing the genomic and epigenomic data produced by The Cancer Genome Atlas(TCGA) project.Finally,we show that signal processing and cancer research,two fields that are seemingly distant from each other,have merged into a field that is indeed more than the sum of its parts.
