Category: Uncategorized

RANKED NOT SELECTED. “The first functional enrichment analysis methods identified pathways that were overrepresented within a list of differentially expressed genes and were rapidly followed by the gene set enrichment approach where a ranked, rather than a selected, list of genes was used to find associations between phenotypes and cellular functions.” https://bmcsystbiol.biomedcentral.com/articles/10.1186/1752-0509-8-S2-S1 View in LinkedIn

STARTING WITH TEASERS on a variety of different time perspectives. When we slip into a different time lens, we see the world completely differently. There are ancient beings on earth who appear to have this perspective, such as viruses, who seem at ease waiting millennia for the right time to animate. View in LinkedIn

THE ASSUMPTION. “These functional assessment methodologies rely on the premise that the expressed components of cellular systems are likely to be functionally coordinated and that genes belonging to the same functional unit should show similar expression profiles.” https://bmcsystbiol.biomedcentral.com/articles/10.1186/1752-0509-8-S2-S1 View in LinkedIn

SPACE AND TIME, are the two variables that dominate physics. So with biology: dimensional scales and time scales are of considerable importance. The quantum scale is ruled by different forces than the classical scale. Time for a bacteria is on a different scale than for a human. View in LinkedIn

BIOLOGICAL MEANING. “Functional enrichment analysis methods (also referred to as pathway or gene set enrichment) are methodologies that allow us to analyze gene expression data for the biological meaning of particular expression patterns in order to gain additional insight into the actual biology of the system.” https://bmcsystbiol.biomedcentral.com/articles/10.1186/1752-0509-8-S2-S1 View in LinkedIn

FRAGMENT FROM NATURE deals with a scant explored subject, namely biological time scales. With ranges of biological time from nanoseconds for some biochemical reactions to millennia for some types of evolution, and the likelihood that time scale shifts may be subject to some type of emergence, it is curious that we have so ignored this topic. View in LinkedIn

GENE NETWORKS. “The inference of gene and molecular networks is focused on mapping the mechanistic and structural properties of the system. Genome-wide gene network analyses typically produce large networks that involve hundreds of gene interactions. Such networks might have interesting topological properties that are biologically meaningful, but are normally difficult to interpret in terms of cellular functionality.” https://bmcsystbiol.biomedcentral.com/articles/10.1186/1752-0509-8-S2-S1 View in LinkedIn

THE BIGGER HOPE. “More generally, systems biology holds the promise of helping to decrease the time and costs of developing new drugs and also helping to provide more targeted and safe candidate drugs by leveraging pathway analysis.” https://bmcsystbiol.biomedcentral.com/articles/10.1186/1752-0509-8-S2-S1 View in LinkedIn

THE HOPE. “If systems biology can rise to the challenge of predicting the mutations that are most likely to allow a cancer to relapse, we may be able to design multi-drug treatments that will prevent cancers from evading conventional drug treatments.” https://bmcsystbiol.biomedcentral.com/articles/10.1186/1752-0509-8-S2-S1 View in LinkedIn

“ONE POSSIBLE SOLUTION is the use of network concepts to identify groups of genes that when perturbed give the same phenotype and hence form a disease module.” https://bmcsystbiol.biomedcentral.com/articles/10.1186/1752-0509-8-S2-S1 View in LinkedIn