edroaldo
commented
6 years ago Hi, No problem.
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Only top "transcriptional regulators" are shown. The ones with similar size/color are then predicted targets of the "trascriptional regulators".
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The derivative captures the changes that happen in the expression kinects along the trajectory. Is is the same concept of the derivative that people usually have in math/calculus classes. So, the derivative should be the highest or lowest where the changes are happening in the kinetic profile of a given gene. Let me know if that clarifies.
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Ater you create the gene regulatory network with functions available in CellRouter, and after you calculate the GRN scores, using, for example: transitions <- c('6.1','6.2', '6.7', '6.8') #transitions to be analyzed grn.scores <- grnscores(cellrouter, ggrn = grn.data$GRN, tfs = grn.data$tfs, transitions = transitions, direction='both', flip=TRUE, q.up=0.75, q.down=0.25, dir.targets='up', columns=2, width=5, height=7, filename='results/GRN_scores')
You can check the targets of the top regulators by doing (using transition
from cluster 6 to 1, as an example):
grn.scores$6.1$targets$Mxd1. Let me know if that clarifies. I am working
on some visualization functions for this, which will be available in a next
release of CellRouter.
No problem! Thanks for your using CellRouter =D!
2018-05-17 5:33 GMT-04:00 JianmeiZhong notifications@github.com:
Hi, sorry that i still have several questions to bother you.=.= 1.in the part of regulators network,labels of some genes are printed as picture below shows while other equal-sized ,equal-colored don't.what's meaning when a gene is labeled? [image: regulator_network] https://user-images.githubusercontent.com/37535747/40165700-3eca236e-59ef-11e8-9bdd-d5cc20634239.png
2.i'm a little confused about the definition of derivtive shown in heatmap of negtive and positive control.what's the difference and relationship with expression?
- your article mentioned that In the neutrophil trajectory, Mxd1 is upregulated in later stages of differentiation compared to Cebpe (Fig. 2c,d). According to GRN analyses, Mxd1 is predicted to regulate Mmp8, Mmp9, Retnlg, and Cd52 expression, all of which are known neutrophil markers (Fig. 2e, f).How to infer the predictive relationship of Mxd1 from the GRN results?
Thanks for your patience and your great work sincerely.
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-- Edroaldo
JianmeiZhong
Hi, sorry that i still have several questions to bother you.=.= 1.in the part of regulators network,labels of some genes are printed as picture below shows while other equal-sized ,equal-colored don't.what's meaning when a gene is labeled?
2.i'm a little confused about the definition of
derivtiveshown in heatmap of negtive and positive control.what's the difference and relationship withexpression?In the neutrophil trajectory, Mxd1 is upregulated in later stages of differentiation compared to Cebpe (Fig. 2c,d). According to GRN analyses, Mxd1 is predicted to regulate Mmp8, Mmp9, Retnlg, and Cd52 expression, all of which are known neutrophil markers (Fig. 2e, f).How to infer the predictive relationship of Mxd1 from the GRN results?Thanks for your patience and your great work sincerely.