Browsing the FUBARome.

Genes evolve differently. We define the "evolutionary fingerprint" of a gene to be the distribution of synonymous and non-synonymous rates over all sites for that gene. Here we use a souped-up version of FUBAR (Murrell et al. 2012) to infer these distributions for 35,370 genes from 12 primate species. This scatterplot represents the first three principal components of the evolutionary fingerprints inferred by FUBAR: PC1 and PC2 spatial, and PC3 colors the points. You may select alternate variables to be plotted on the axes as well.

If you mouseover a point, the gene name and description will appear at the top of the plot, along with the first few GO annotations.

If you click on a point, the alignment will be displayed below.

Enter a search term in the field below and click on the button to highlight only points whose descriptions contain that term as a substring. Suggestions: "immun", "olfact", and "regul".

Alternatively search GO terms for matches. You may use numbers (eg. "0002769") or words (eg. "natural killer cell inhibitory signaling pathway"). As with the "description" search, sub-strings will also match.

   

X axis     Y axis     Color

Here are the 50 GO terms most associated with high values of PC1.

Avg PC1 GO term #GO matches
14.31 GO:0002769 [natural killer cell inhibitory signaling pathway] 27
13.20 GO:0002767 [immune response-inhibiting cell surface receptor signaling pathway] 46
12.72 GO:2001183 [negative regulation of interleukin-12 secretion] 25
12.60 GO:0002774 [Fc receptor mediated inhibitory signaling pathway] 46
12.16 GO:2001180 [negative regulation of interleukin-10 secretion] 26
12.15 GO:2001189 [negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell] 27
11.72 GO:0046629 [gamma-delta T cell activation] 47
11.58 GO:2001199 [negative regulation of dendritic cell differentiation] 30
11.48 GO:0045919 [positive regulation of cytolysis] 27
11.18 GO:0014063 [negative regulation of serotonin secretion] 27
10.92 GO:0045591 [positive regulation of regulatory T cell differentiation] 33
10.58 GO:2000669 [negative regulation of dendritic cell apoptotic process] 28
10.42 GO:0045953 [negative regulation of natural killer cell mediated cytotoxicity] 50
10.37 GO:0042267 [natural killer cell mediated cytotoxicity] 98
10.29 GO:0001913 [T cell mediated cytotoxicity] 56
10.27 GO:0002740 [negative regulation of cytokine secretion involved in immune response] 32
10.24 GO:0002309 [T cell proliferation involved in immune response] 32
10.23 GO:0050689 [negative regulation of defense response to virus by host] 30
10.18 GO:0001915 [negative regulation of T cell mediated cytotoxicity] 40
10.15 GO:0030101 [natural killer cell activation] 112
10.00 GO:2001186 [negative regulation of CD8-positive. alpha-beta T cell activation] 33
9.99 GO:0045077 [negative regulation of interferon-gamma biosynthetic process] 30
9.63 GO:0019835 [cytolysis] 66
9.56 GO:0042536 [negative regulation of tumor necrosis factor biosynthetic process] 33
9.36 GO:0050776 [regulation of immune response] 633
8.97 GO:2001205 [negative regulation of osteoclast development] 33
8.84 GO:0001580 [detection of chemical stimulus involved in sensory perception of bitter taste] 65
8.65 GO:0006968 [cellular defense response] 241
8.58 GO:0051926 [negative regulation of calcium ion transport] 61
8.09 GO:0072643 [interferon-gamma secretion] 42
7.80 GO:0032609 [interferon-gamma production] 41
7.66 GO:0019882 [antigen processing and presentation] 140
7.47 GO:2001202 [negative regulation of transforming growth factor-beta secretion] 34
7.12 GO:0045671 [negative regulation of osteoclast differentiation] 66
7.02 GO:0045806 [negative regulation of endocytosis] 39
7.00 GO:0097028 [dendritic cell differentiation] 42
6.95 GO:0050777 [negative regulation of immune response] 41
6.80 GO:0048387 [negative regulation of retinoic acid receptor signaling pathway] 56
6.61 GO:0033629 [negative regulation of cell adhesion mediated by integrin] 28
5.97 GO:0002480 [antigen processing and presentation of exogenous peptide antigen via MHC class I. TAP-independent] 45
5.93 GO:0042130 [negative regulation of T cell proliferation] 89
5.85 GO:0036003 [positive regulation of transcription from RNA polymerase II promoter in response to stress] 28
5.74 GO:0032689 [negative regulation of interferon-gamma production] 61
5.71 GO:0090240 [positive regulation of histone H4 acetylation] 27
5.59 GO:0002250 [adaptive immune response] 442
5.45 GO:0072488 [ammonium transmembrane transport] 26
5.33 GO:0015695 [organic cation transport] 32
5.29 GO:0048247 [lymphocyte chemotaxis] 34
5.27 GO:0050907 [detection of chemical stimulus involved in sensory perception] 87
5.22 GO:0050911 [detection of chemical stimulus involved in sensory perception of smell] 425

Here are the 50 GO terms most associated with low values of PC1.

Avg PC1 GO term #GO matches
-6.69 GO:0086027 [AV node cell to bundle of His cell signaling] 28
-6.69 GO:0086018 [SA node cell to atrial cardiac muscle cell signalling] 28
-6.65 GO:0035585 [calcium-mediated signaling using extracellular calcium source] 27
-6.47 GO:0061577 [calcium ion transmembrane transport via high voltage-gated calcium channel] 29
-6.43 GO:0010045 [response to nickel cation] 29
-6.40 GO:0086045 [membrane depolarization during AV node cell action potential] 66
-6.36 GO:0086046 [membrane depolarization during SA node cell action potential] 40
-6.32 GO:0098912 [membrane depolarization during atrial cardiac muscle cell action potential] 32
-6.15 GO:0086015 [SA node cell action potential] 40
-5.88 GO:0086016 [AV node cell action potential] 39
-5.80 GO:0002520 [immune system development] 33
-5.71 GO:0086012 [membrane depolarization during cardiac muscle cell action potential] 47
-5.69 GO:0060371 [regulation of atrial cardiac muscle cell membrane depolarization] 43
-5.69 GO:0098911 [regulation of ventricular cardiac muscle cell action potential] 36
-5.58 GO:0086064 [cell communication by electrical coupling involved in cardiac conduction] 47
-5.52 GO:0070509 [calcium ion import] 79
-5.35 GO:0045956 [positive regulation of calcium ion-dependent exocytosis] 50
-5.11 GO:0086002 [cardiac muscle cell action potential involved in contraction] 44
-5.07 GO:0035904 [aorta development] 38
-5.06 GO:0030048 [actin filament-based movement] 28
-4.97 GO:0035235 [ionotropic glutamate receptor signaling pathway] 64
-4.97 GO:0060402 [calcium ion transport into cytosol] 61
-4.96 GO:0090129 [positive regulation of synapse maturation] 27
-4.95 GO:0086091 [regulation of heart rate by cardiac conduction] 114
-4.91 GO:0090162 [establishment of epithelial cell polarity] 25
-4.88 GO:0060134 [prepulse inhibition] 29
-4.84 GO:0086010 [membrane depolarization during action potential] 86
-4.72 GO:0010952 [positive regulation of peptidase activity] 36
-4.70 GO:0001778 [plasma membrane repair] 26
-4.69 GO:0048596 [embryonic camera-type eye morphogenesis] 26
-4.65 GO:0071380 [cellular response to prostaglandin E stimulus] 37
-4.61 GO:0010518 [positive regulation of phospholipase activity] 26
-4.60 GO:0001967 [suckling behavior] 31
-4.58 GO:0060484 [lung-associated mesenchyme development] 29
-4.56 GO:0007043 [cell-cell junction assembly] 34
-4.56 GO:0071625 [vocalization behavior] 29
-4.54 GO:2000463 [positive regulation of excitatory postsynaptic potential] 48
-4.52 GO:0086005 [ventricular cardiac muscle cell action potential] 33
-4.52 GO:0051968 [positive regulation of synaptic transmission. glutamatergic] 29
-4.49 GO:0016180 [snRNA processing] 26
-4.49 GO:0030516 [regulation of axon extension] 29
-4.40 GO:0032012 [regulation of ARF protein signal transduction] 28
-4.40 GO:0061178 [regulation of insulin secretion involved in cellular response to glucose stimulus] 38
-4.37 GO:0003407 [neural retina development] 30
-4.36 GO:0001952 [regulation of cell-matrix adhesion] 38
-4.36 GO:0060044 [negative regulation of cardiac muscle cell proliferation] 25
-4.36 GO:0032811 [negative regulation of epinephrine secretion] 30
-4.36 GO:1903861 [positive regulation of dendrite extension] 44
-4.34 GO:0007158 [neuron cell-cell adhesion] 34
-4.34 GO:0060976 [coronary vasculature development] 55

The phylogeny.

The 12 taxa included 5 Great Apes, which includes you, one Lesser Ape, the Northern white-cheeked gibbon, and 6 Old World Monkeys. You can toggle between a cladogram and a phylogeny: (). Mouseover on a name and the root to tip path with be highlighted.