![cytoscape assign colors to different clusters cytoscape assign colors to different clusters](https://f1000researchdata.s3.amazonaws.com/manuscripts/7716/d9953e35-dff6-4431-a0c3-d9adea829334_figure4.gif)
- CYTOSCAPE ASSIGN COLORS TO DIFFERENT CLUSTERS HOW TO
- CYTOSCAPE ASSIGN COLORS TO DIFFERENT CLUSTERS UPDATE
- CYTOSCAPE ASSIGN COLORS TO DIFFERENT CLUSTERS LICENSE
Then the TF associated by motif similarity. Then, the motif2TF algorithm will give preference to the TF associated by orthology, The best transcriptionįactors are those that are directly annotated ("Direct") and a preference will be for the TF that areįrom the input. The TFs are ordered by the motif2TF algorithm by decreasing order of preference. That the motifs has a lot in common, and that is a good result.Ī motif can be associated to different transcription factors, which one has the So the motif of this transcription factor is clustered in the same cluster as the top motif. The transcription factor or motif I'm looking for has a low ranking, but has The Transcription Factor view relies on the motif clustering which is performed only on the enrichedĪssigned to a cluster of motifs that are similar, but if such TF is annotated for a motif which variesĮnough to be clustered with other motifs, then you can find the same TF associated to another cluster How can the same transcription factor be detected in two different So this means when you click on the header this column will be sorted and checked rows will be
CYTOSCAPE ASSIGN COLORS TO DIFFERENT CLUSTERS HOW TO
How to look for a specific motif (or TF) of interest in the results?Īll columns in the table are sortable, so also the search column (the one with the checks and theĬrosses). (2007) STAMP: a web tool for exploring DNA-binding motif similarities, Beware there is a limitedĪmount of colors used (so check the clustercode if you go at the bottom of the list).
![cytoscape assign colors to different clusters cytoscape assign colors to different clusters](http://www.rbvi.ucsf.edu/cytoscape/clusterMaker2/PCoAScatterPlot.png)
The color it's faster to recognize motifs that are part of the same cluster. The color of the background indicates the cluster in which the motif is (like the clustercode). What does the row background colors of TFs/motifs mean? I use Flybase numbers for the Drosophila and it doesn't work. I use MGI numbers for the Mus musculus and it doesn't work. This is because iRegulon uses the symbols and not the numbers. I use HGNC numbers for the homo sapiens and it doesn't work. HGNC symbols for human, MGI symbols for mouse, CG numbers and Flybase names for drosophila.
CYTOSCAPE ASSIGN COLORS TO DIFFERENT CLUSTERS UPDATE
Is this a good result? A motif has different transcription factors, which one has the highest rank? A transcription factor has orthologous and the motif below that (same cluster) has a perfect match, is the second transcription factor better? Is it possible to color all edges from the same motif in the same color? How to compare the predicted targets for a given TF to its metatargetome? Can I export the results? Can iRegulon be run automatically on several clusters? Who developed iRegulon? When was the last update of the help? How to contact us? What does the row background colors of TFs/motifs mean? How to look for a specific motif (or TF) of interest in the results? How can the same transcription factor be detected in two different clusters? The transcription factor or motif I'm looking for has a low ranking, but has clustercode 1.
![cytoscape assign colors to different clusters cytoscape assign colors to different clusters](http://web.stanford.edu/group/orphan_pks/img/Fig6_New-01.png)
CYTOSCAPE ASSIGN COLORS TO DIFFERENT CLUSTERS LICENSE
How to cite iRegulon? How to get a license for Transfac Pro? What are the supported organisms? What are the supported gene ids? I use HGNC numbers for the homo sapiens and it doesn't work.