SMLG (Statistical Machine Learning Group) Discussion Forum

cwyoo wrote:

samanthagonzales wrote:Reuploaded 2 net files fitted using different iss values:

mliver.fit.bayes <- bn.fit(final_subgraph, data = mliver_subset, method = "bayes", iss = 0.1)
mliver.fit.bayes <- bn.fit(final_subgraph, data = mliver_subset, method = "bayes", iss = 1)

Great. Moving forward, iss=1 will work. Please add MT1 and MT2 to the network, update the parameters, and upload the dot and net files.

Please add: TFEB, TFE3, Zkscan3, Lamp1, Lamp2, MAP1LC3B, MCOLN1 and ATP6V0E1 to the network. If any of them were not one of the genes that were selected as significant differential expression, please add them to the dataset and run banjo again.

Here is the updated network with additional genes of interest included. Since some of the new genes of interest were not included in the original banjo analysis, I reran banjo with the new genes of interest for 32h.

The sub network contains genes of interest and any connecting genes within 3 generations from the experimental node.
Color coding follows the same format as previous iterations, listed below in increasing priority:

yellow: experimental node
green: genes of interest
blue: parents of experimental node

Could you add this gene Slc30a10 to the network?

Thank you for your help

jliuzzi wrote:Could you add this gene Slc30a10 to the network?

Thank you for your help

Sure thing! Here is the network with Slc30a10 included.

Thanks!

Could you make a network with only these genes?
Acaa1a
Cyp2b10
Slc39a7
Aass
Hnf4a
Mtf1
Wdr34
Mt1
Slc30a1
Cyp2c50
Slc30a10
Slc39a1
Gpx4
Slc30a7
Cyb5
Thank you again.

jliuzzi wrote:Could you make a network with only these genes?
Acaa1a
Cyp2b10
Slc39a7
Aass
Hnf4a
Mtf1
Wdr34
Mt1
Slc30a1
Cyp2c50
Slc30a10
Slc39a1
Gpx4
Slc30a7
Cyb5
Thank you again.

Could you make the following two sub-networks from Mouse Liver Experiments?

For the first sub-network use the following genes:
Acaa1a
Cyp2b10
Slc39a7
Aass
Hnf4a
Mtf1
Wdr34
Mt1
Slc30a1
Cyp2c50
Slc30a10
Slc39a1
Gpx4
Slc30a7
Cyb5

For the second sub-network, use all the genes from the first sub-network and add Atg7KO.

Here are the sub networks including only the specific genes requested from the November 17th network analysis.

Genes Slc39a1 and Gpx4 were not directly connected to the network, and Acaa1a is connected only when "Atg7KO" is present.

Let me know if you have any questions or further requirements - Thanks!

samanthagonzales wrote:Here are the sub networks including only the specific genes requested from the November 17th network analysis.

Genes Slc39a1 and Gpx4 were not directly connected to the network, and Acaa1a is connected only when "Atg7KO" is present.

Let me know if you have any questions or further requirements - Thanks!

Thank you for the post. However, it seems some connections are not properly summarized. For example, Gpx4 is connected to Atg7ko.

Here are the updated summary networks using an updated algorithm.
Let me know if these make more sense!