Data panels
Several graphs are available, each one displaying specific data related to the genes.
This panel calculates if your current set of genes is conserved, divergent or neutral in comparison to the genome.
It uses a statistics method called Bootstrapping. See the glossary for more information.
This graph shows the value of dN/dS for each gene. Eight species can be compared:
- Homo sapiens: the reference human genome hg19.
- Altaï: a Neanderthal from the Altaï mountains (genome here).
- Denisovan: a new species discovered in 2010 at the Denisovan cave in the Altaï mountains (genome here).
- Pan troglodytes: the common chimpanzee (panTro4).
- Gorilla gorilla: the western gorilla (gorGor3).
- Pongo abelii: the Sumatran orangutan (ponAbe2).
- Macaca mulatta: the rhesus macaque (rheMac3).
- Callithrix jacchus: the common marmoset (calJac3).
This graph shows the relationship between the values of human dN/dS and pN/pS for each gene.
You can thus see if a gene is more or less variable through human evolution (dN/dS), human population (pN/pS) or both.
The 1σ and 2σ standard deviations are displayed as gray zones. The means are the gray lines, and the medians are the blue dotted lines.
This graph shows the relationship between dN and dS for all the species previously described.
For convenience, you can hide some species data by clicking on their name in the caption.
If you want to see only one species data, double click on its name.
This graph shows the Neanderthal introgression measures of each gene for the European (X axis) and Asian (Y axis) populations.
The X and Y axis correspond to the average probability of Neanderthal introgression across SNPs within the CCDS of the gene.
The 1σ and 2σ standard deviations are displayed as gray zones. The means are the gray lines, and the medians are the blue dotted lines.
This graph shows the expression specificity of the genes in different regions of the brain.
The 3D model was computed by French L. and Paus T. 2015 from the Allen Human Brain Atlas. The BrainBrowser library was used to generate the brain.
Click on the expression or specificty buttons to change the type of data you want to display.
The expression levels are represented by a scale of red to green, black being the zero.
- Red: the gene is highly expressed in this area.
- Black: the expression of this gene is in the mean.
- Green: the gene is little expressed in this area.
The specificty is represented by a scale of yellow to blue, black being the zero.
- Yellow: the gene is specifically expressed in this area.
- Black: no particular specificity for this gene.
- Green: the gene is specifically not expressed in this area.
The brain itself is fully movable by clicking and dragging with the mouse.
You can click on a region to highlight it and display its name in the drop-down menu on the left. Click again on the region to reset it. You can also select a region in the drop-down menu to highlight the corresponding area in the brain.
If you moved the brain too much and want to reset the view, just double click outside the brain to make it go back to its original position.
By default, the brain displays the median expression specificity of the current set of genes you requested. If you want to see the data for only one gene, go to the side menu, click on the gene, and then on the brain expression button. The name of the gene will be displayed in the caption on the left of the brain, with a button to reset to the default.
This graph shows the expression specificity of the genes in 4 different regions of the Homo sapiens fetal brain.
A positive value indicates that the gene is specifically expressed in the corresponding region of the brain, at the fetal stage.
A negative value indicates that the gene is specifically not expressed, which means it is expressed elsewhere but not in the corresponding region.
This graph shows the expression specificity of the genes in 4 different regions of the Homo sapiens adult brain.
A positive value indicates that the gene is specifically expressed in the corresponding region of the brain, at the adult stage.
A negative value indicates that the gene is specifically not expressed, which means it is expressed elsewhere but not in the corresponding region.
You can quickly compare the different regions with the color scale of the associated brain map.
IMPORTANT: even if this brain map reacts to all the other graphs, according to the interactivity logic of the interface, this brain shows only the expression for the adult brain.