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Bioinformatics-Department-C-BIG / mofa_tutorial

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Mir-gene-tf-gene network signatures #12

Open eathieniti opened 7 months ago

eathieniti commented 7 months ago

MIR-GENE TARGET NETWORK

  1. Interactions between DE mirs to DE genes
  2. Colour by up and down
  3. check for de mirs

Image

eathieniti commented 7 months ago

--> Look at specific pathways (eg. known pathways) and specific clusters --> regulatory information + mirnas --> https://genomebiology.biomedcentral.com/articles/10.1186/s13059-023-02877-1 network differentiation

Build networks

  1. add mirnas, add genes with a prior knowledge (signor, mirtar )
  2. filter by anticorelated
  3. filter/ color by MOFA

Compare with time

  1. run V06 and compare networks
eathieniti commented 7 months ago

Addition of gene-gene interactions to the mir-gene network

cluster 2

  1. mirnas-genes
  2. TOP 10 % of factor 8
  3. Added regulatoru information:
  4. added one edge --> BNIP3L-FOX03

with 20% there is still just one edge

Image

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8688453/

eathieniti commented 7 months ago

time comparison: could not add time to the results because mirs de are zero...:( TODO: could check the logfold changes if they are kept the same even if not DE

eathieniti commented 7 months ago

CLUSTER 1

image

CLUSTER 2 image

unique nodes: SNCA in blood

eathieniti commented 7 months ago

TODO:

  1. differential network analysis
  2. Comparison of Logfold2change in time
  3. Get the main molecules in signature in V8
  4. Then color by their fold change In V6?
  5. Colour by FC, add border by significant or not ?