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: | Â | Â | Â |
 | • 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: | Â | Â | Â |
 | • 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: | Â | Â | Â |
 | • 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 |