文档介绍：Pathway Bioinformatics ---Database, Software, and Discovery
Y. Tom Tang, .
Bioinformatics R & D
Hyseq Pharmaceuticals, Inc.
Sunnyvale, CA, USA
Outline of the Talk
Introduction to Pathway Bioinformatics
Overview Pathmetrics Technology and Products
Data Representation and SLIPR Format
parison and Pathway Database Searches
Pathway Predictions and Beyond
A Broad Definition of Bioinformatics
Informatics
Its carrier is a set of digital codes and a language.
In its manifestation in the space-time continuum, it has utility (. to decrease entropy of an open system).
Bioinformatics
The essence of life is information (. from digital code to emerging properties of biosystems.)
Bioinformatics is the study of information content of life
Pathways
It can be defined ad a modular unit of interacting molecules to fulfill a cellular function.
It is usually represented by a 2-D diagram with characteristic symbols linking the protein and non-protein entities.
A circle indicates a protein or a non-protein biomolecule. An symbol in between
indicates the nature of molecule-molecule interaction.
An Example of a Pathway ---EPO (erythropoeitin) pathways
Pathway Database --Increasing Level plexity
The genome
4 bases
3 billion bp total
3 billion bp/cell, identical
The proteome
20 amino acids
~60K genes, ~200K proteins
~10K proteins/cell; different cells/conditions, different expressions
The pathome
~200K reactions
~20K pathways
~1K pathways/cell; different cells/conditions, different expressions
Evolutionary Theory of Pathways --A New Field of Theoretical Studies
The most important assumption for sequence informatics is evolution
Evolution principle also applies to pathway informatics
From simple plex
Duplication, diversifying, and modular re-use
Will provide new view toward fundamental questions toward a unified informatics theory of life
What is life?
How does new function arise?
How does evolution work? (pathway is the bridge between digital signal a