At-GAIN - Howacelliswired Environment DNA Small molecules...

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DNA mRNA Protein Small  molecules Environment Regulatory RNA How a cell is wired How a cell is wired The dynamics of such interactions emerge as cellular  processes and functions
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How do the genes and their products interact to  collectively perform a function? A B Gene G 35 RPM Inhibitor U2AF Gene G Molecular interaction networks Molecular interaction networks
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Molecular interaction networks Molecular interaction networks A network containing genes connected to each other  whenever they physically or functionally interact Proteins that interact/co-complex (ribosomal, polymerase,  etc.) Transcription factors and their target Enzymes catalyzing different steps in the same metabolic  pathway Genes with correlation in expression Genes with similar phylogenetic profiles Functional ^
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Arabidopsis is the primary model  Arabidopsis is the primary model  organism for plants organism for plants Complex organization from molecular to whole organism  level. A key challenge … Understanding the cellular machinery that sustains this  complexity. In the current post-genomic times, a main aspect of this  challenge is ‘ gene function prediction ’: Identification of functions of all the (~30, 000) genes in the  genome.
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Total of ~30,000 genes in the genome Extent of gene annotations in  Extent of gene annotations in  Arabidopsis Arabidopsis ~15% with  some   experimental  annotation ~8% with ‘expert’  annotation ~13% with  annotations based on  manually curated  computational  analysis ~14% with electronic  annotations Leaving  ~50%  of  the genome without  any  annotation Ashburner et al, (2000)  Nat. Gen. Swarbreck et al (2008)  Nuc. Acids. 
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Exploit high-throughput data Exploit high-throughput data Integrating functional genomic data could lead to Network models of gene interactions that resemble the  underlying cellular map. Typically these networks contain gene  functional interactions Connecting pairs of genes that participate in the same  biological processes. In such a network, the very place of a gene establishes the  functional context that gene. ‘Guilt-by-association’ – genes of unknown functions can also  be imputed with the function of their annotated neighbors.
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Functional interaction networks Functional interaction networks Functional interaction network models have been developed  for Arabidopsis. Lee et al. (2010) Rational association of genes with traits 
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This note was uploaded on 01/23/2012 for the course CS 3824 taught by Professor Staff during the Fall '08 term at Virginia Tech.

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At-GAIN - Howacelliswired Environment DNA Small molecules...

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