ExplainBio is a network analysis tool that connects each gene (target) to source genes whose expressions predict the expression of the target.
The easiest way to start off is to put in a gene name in the Gene Search box and press enter. For example, if you put in "APP" (amyloid precursor) in the search box on top, it shows a circle corresponding to the APP gene with nine other genes (INSR, TCF4 etc.) and arrows going from those nine genes to APP. What that means is that the expressions of those 9 genes together predict the expression of APP in normal samples of various tissue types.
The thickness of the arrow indicates the strength of the relationship, i.e. the R^2 of the prediction of the target gene expression using the source gene expression. If you hover over the arrow, it will show the R value and the coefficient (beta). The color indicates the direction, green is positive (increase in source gene expression is related to increase in target gene expression) and pink is negative.
No, the fact that the source genes predict the expression of the target gene does not mean that the source genes are causing the expression of the target gene in any way. Although in some cases it is possible that source genes are upstream of the target gene and causally affect its expression, it is also possible that the reverse happens (i.e. target causes the expression of the source) or a third factor controls the expression of both. But it does give us an idea of which genes are transcriptionally connected to each other.
If you click on a gene node, you will get three icons. The first icon (magnifying glass) shows a scatterplot of the predicted vs. actual expression of the gene. The points that are shown are samples from the sample group selected on the left (NCI60 by default).
The second icon (inward pointing arrow) will add genes to the network that are the sources of the selected gene. So if you select the TCF4 gene and click on the inward pointing arrow, it will add 6 other genes that are source genes for TCF4. That is one way of building up a network of connected genes
The third icon (outward pointing arrow) will add genes to the network that are targets of the selected gene. That is another way of building a network.
If you click on a gene that already has all of its source genes added to the network, you will also see a fourth icon (cross). If you click on the cross, that target gene gets deleted (as well as all of its source genes).
|Biospecimen id||Sample name||Sample title||Sample description||Channel||Biospecimen source||Characteristics||Tag name|
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