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History[edit]
The idea of a "tree of life" arose from ancient notions of a ladder-like progression from lower to
higher forms of life (such as in the Great Chain of Being). Early representations of "branching"
phylogenetic trees include a "paleontological chart" showing the geological relationships among
plants and animals in the book Elementary Geology, by Edward Hitchcock (first edition: 1840).
Charles Darwin (1859) also produced one of the first illustrations and crucially popularized the
notion of an evolutionary "tree" in his seminal book The Origin of Species. Over a century
later, evolutionary biologists still use tree diagrams to depict evolution because such diagrams
effectively convey the concept that speciation occurs through the adaptive and
semirandom splitting of lineages. Over time, species classification has become less static and
more dynamic.
Functional genomics
Functional genomics is a field of molecular biology that attempts to make use of the vast wealth
of data produced by genomic and transcriptomic projects (such as genome sequencing
projects and RNA-seq) to describe gene (and protein) functions and interactions.
Unlike genomics, functional genomics focuses on the dynamic aspects such as
genetranscription, translation, regulation of gene expression and proteinprotein interactions, as
opposed to the static aspects of the genomic information such as DNA sequence or structures.
Functional genomics attempts to answer questions about the function of DNA at the levels of
genes, RNA transcripts, and protein products. 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 gene-by-gene approach.
SAGE
SAGE (serial analysis of gene expression) is an alternate method of gene expression analysis
based on RNA sequencing rather than hybridization. SAGE relies on the sequencing of 1017
base pair tags which are unique to each gene. These tags are produced from poly-A mRNA and
ligated end-to-end before sequencing. SAGE gives an unbiased measurement of the number of
transcripts per cell, since it does not depend on prior knowledge of what transcripts to study (as
microarrays do).
Small RNA sequencing
Small RNAs are a class of non-coding RNA molecules that are key regulators of transcriptional
and post-transcriptional gene silencing, or RNA silencing. Next generation sequencing is the gold
standard tool for non-coding RNA discovery, profiling and expression analysis.