Functional genomics

Résumé

Functional genomics is a field of molecular biology that attempts to describe gene (and protein) functions and interactions. Functional genomics make use of the vast data generated by genomic and transcriptomic projects (such as genome sequencing projects and RNA sequencing). Functional genomics focuses on the dynamic aspects such as gene transcription, translation, regulation of gene expression and protein–protein interactions, as opposed to the static aspects of the genomic information such as DNA sequence or structures. A key characteristic of functional genomics studies is their genome-wide approach to these questions, generally involving high-throughput methods rather than a more traditional "candidate-gene" approach. Definition and goals of functional genomics In order to understand functional genomics it is important to first define function. In their paper Graur et al. define function in two possible ways. These are "selected effect" and "causal role". The "select

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https://en.wikipedia.org/wiki/Functional_genomics

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Development and Characterization of a Microfluidic Chip to Capture Circulating Prostate Cancer Cells

Colette Bichsel

The analysis of circulating tumor cells (CTCs) from the blood of cancer patients promises a better understanding of metastasis formation and tumor phenotypes. CTCs are rare (there is 1 CTC in 1 billion of circulating blood cells) and therefore challenging to isolate. Recently developed highly sensitive microfluidic platforms made a leap forward in trapping these cells efficiently. This work focused on the development of a microfluidic platform that specifically captures prostate cancer cells from a whole blood sample. The versatility of the system was exploited by tethering different capturing antibodies on the microchip surface. Circulating prostate tumor cells were successfully recognized with the microfluidic chip. Furthermore, the platform was enhanced to carry out proliferation assays of captured cells directly on the chip, using hydrogel as a three-dimensional cell culture matrix. Although further improvements regarding the on-chip proliferation assay need to be done, the potential benefit of a functional readout promises new insights in cancer progression that can be translated to advanced cancer staging or prognostic tools.

2011

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Plasmodium falciparum is an obligate intracellular parasite and the leading cause of severe malaria responsible for tremendous morbidity and mortality particularly in sub-Saharan Africa. Successful completion of the P. falciparum genome sequencing project in 2002 provided a comprehensive foundation for functional genomic studies on this pathogen in the following decade. Over this period, a large spectrum of experimental approaches has been deployed to improve and expand the scope of functionally annotated genes. Meanwhile, rapidly evolving methods of systems biology have also begun to contribute to a more global understanding of various aspects of the biology and pathogenesis of malaria. Herein we provide an overview on metabolic modelling, which has the capability to integrate information from functional genomics studies in P. falciparum and guide future malaria research efforts towards the identification of novel candidate drug targets.

Oxford Univ Press2013

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The Eukaryotic Promoter Database (EPD), available online at https://epd.epfl.ch, provides accurate transcription start site (TSS) information for promoters of 15 model organisms plus corresponding functional genomics data that can be viewed in a genome browser, queried or analyzed via web interfaces, or exported in standard formats (FASTA, BED, CSV) for subsequent analysis with other tools. Recent work has focused on the improvement of the EPD promoter viewers, which use the UCSC Genome Browser as visualization platform. Thousands of high-resolution tracks for CAGE, ChIP-seq and similar data have been generated and organized into public track hubs. Customized, reproducible promoter views, combining EPD-supplied tracks with native UCSC Genome Browser tracks, can be accessed from the organism summary pages or from individual promoter entries. Moreover, thanks to recent improvements and stabilization of ncRNA gene catalogs, we were able to release promoter collections for certain classes of ncRNAs from human and mouse. Furthermore, we developed automatic computational protocols to assign orphan TSS peaks to downstream genes based on paired-end (RAMPAGE) TSS mapping data, which enabled us to add nearly 9000 new entries to the human promoter collection. Since our last article in this journal, EPD was extended to five more model organisms: rhesusmonkey, rat, dog, chicken and Plasmodium falciparum.

2020

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