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Table 1 BaseDiver distinguishes between evolutionary patterns associated with positive selection.

From: Patterns of evolutionary constraints on genes in humans

Evolutionary

constraints

and natural

selection

on functional

categories

BaseDiver

Nielsen et al.

PLoS Biology 2005

Bustamante et al.

Nature 2005

Voight et al.

PLoS Biology 2006

 

• 16, 223 human genes with orthologues in mammals

• 13,731 human genes with orthologs in chimpanzee.

• 11,624 human genes with orthologs in chimpanzee.

• Whole genome analysis covering all genes.

 

• Divergence-DAF distribution measuring change in constraints

• dN/dS ratio test for positive selection

• McDonald Kreitman test for positive selection

• iHS statistic estimating linkage disequilibrium

 

• 76 Biological processes and 146 Molecular functions-GO classification

• 133 Biological processes – PANTHER classification

• 133 Biological processes and 139 Molecular functions – classification

• 222 nested and overlapping PANTHER classes

Transcription

related

genes

Cluster I:

   
 

• Transcription factor activity.

 

• mRNA transcription

• mRNA transcription initiation

 

• Transcription factors DBD

 

• Transcription factor

• Chromatin packaging/remodeling

 

• Transcription

 

• Zinc finger transcription facto

 
 

• Regulation of transcription

 

• Nucleoside, nucleotide and nucleic acid metabolism

 
 

• Regulation of transcription nucleobase, nucleoside, nucleotide and nucleic acid metabolism.

 

• Homeotic transcription factor

 
   

• KRAB box transcription factor

 
   

• Nuclear hormone receptor

 

Immunity

related

genes

Cluster II:

   
 

• Inflammatory response

• Immunity and defense

• Natural killer cell mediated immunity

 
 

• Response to stress

• T-cell-mediated immunity

• Defence/immunity protein

• MHC-I-mediated Immunity

 

• Response to wounding

• Natural killer-cell- mediated immunity

• Immunoglobin receptor family member

• Peroxisome transport

 

• Immune response

• Interferon mediated immunity

  
 

• Defense Response

• B-cell and antibody mediated immunity

  
 

• Response to pest, pathogen or parasite.

   

Sensory

perception

related

genes

Cluster III:

   
 

• Perception of smell

• Chemosensory perception

• Sensory perception

• Chemosensory perception

  

• Olfaction

 

• Olfaction

    

• Other carbohydrate metabolism

    

• Electron transport

Other

categories

Cluster II:

  

• Steroid metabolism

 

• Response to biotic stimulus

• Inhibition of apoptosis

• Protein kinase

• Lipid and fatty acid binding

 

• Response to external biotic stimulus

 

• Receptor

• Protein modification

   

• Apoptosis

• Vitamin/cofactor transport

    

• Phosphate Metabolism