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HMMPFAM search against several major signature databases- PFAM, TIGRFAM, SMART, and Superfamily PowerPoint Presentation
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HMMPFAM search against several major signature databases- PFAM, TIGRFAM, SMART, and Superfamily - PowerPoint PPT Presentation


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What makes species different? A study of Unique Genes. Our Definition of genes with unknown function.

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Presentation Transcript
slide1

What makes species different?A study of Unique Genes

Our Definition of genes with unknown function

Gene models and proteomes for Saccharomyces cerevisiae (Sc), Schizosaccharomyces pombe (Sp), Arabidopsis thaliana (At), Oryza sativa (Os), Drosophila melanogaster (Dm), Anopheles gambiae (Ag), Caenorhabditis elegans (Ce), Mus musculus (Mm), Rattus norvegicus (Rn), and Homo sapiens (Hs) were downloaded from the NCBI website (ftp.ncbi.nlm.nih.gov).

HMMPFAM search against several major signature databases- PFAM, TIGRFAM, SMART, and Superfamily

match to one or more of the models in any one of the databases

“Known (PDF)”

no matches to any one of the models in any database

“Unknown(POF)”

slide3

“Unknowns” are not as conserved as “knowns”, even between related organisms!

Yeast

% hits at each e-value

BLAST e-value

slide4

Known Unknown

Sc

Sp

At

Os

Dm

Ag

Rn

Mm

Hs

Ce

Outl.

Relationship tree among the 10 different genomes reveals a high degree of evolutionary divergence among “unknowns” from different species

“Unknowns” have a different rate of evolution?

“Unknowns” are new genes?

slide5

5955

1197

Known

Unknown

19157

882

% Unique genes

2919

5601

3384

3173

5694

1440

836

5832

528

487

1908

2041

792

133

196

20

“Unknowns” are mainly species-specific.

Representation of “unknowns” in the “unique-ome” of different species.

“Unique-ome” was defined by a BLAST cut off of 10-6.

Between the 10 different genomes!

slide6

Known

Unknown

Compared to “knowns”, “Unknowns” are more disordered, less hydrophobic and shorter.

unknown conclusions
“Unknown” Conclusions
  • Unknown genes are typically species-specific and might provide some of the keys that define species-specific differences.
  • Unraveling the function of “unknowns” would improve our understanding of species-specific functions.
  • Disordered protein functions are thought to include the formation and regulation of large multi-molecular assemblies that participate in important regulatory functions. Disordered regions on proteins have been reported to evolve significantly more rapidly than ordered regions.
  • “Unknowns” are likely to be the result of greater evolutionary divergence among species leading to the establishment of new, species-specific regulatory networks.