Mouse livers with mTORC1 activation

[cwyoo]

From the dataset GSE186783, analyze the following RNAseq raw counts for the eight mice by adding the genes of interest posted in Mouse Liver Experiments using the RNAseq raw data cleaning steps described in Human knock down a nuclear Zn transporter, ZIP11.

GSM5660960 WT-1_S1
GSM5660961 WT-2_S2
GSM5660962 WT-3_S3
GSM5660963 WT-4_S4
GSM5660964 AKO-1_S5
GSM5660965 AKO-2_S6
GSM5660966 AKO-3_S7
GSM5660967 AKO-4_S8

[samanthagonzales]

Here is the sub network for the mTORC1 activation mouse liver dataset.

Currently, no genes of interest were found to be within 3 generations of the experimental node, however this may be due to a coding error I am still investigating.
I will update this post with new results once any possible issues are resolved.


Update: Fixed the error and have replaced the network graphic with the correct one.

[cwyoo]

Here is the sub network for the mTORC1 activation mouse liver dataset.

Currently, no genes of interest were found to be within 3 generations of the experimental node, however this may be due to a coding error I am still investigating.
I will update this post with new results once any possible issues are resolved.


Update: Fixed the error and have replaced the network graphic with the correct one.

Thanks, could you post the normalized data here?

[samanthagonzales]

Below is the normalized, standardized, and discretized subset of mtorc1 gene expression data used for the banjo analysis.

[jliuzzi]

Thank you for your help.

Could you use this list of genes and run a new separate analysis Only with these genes ?
TFEB, TFE3, Becn1, RB1CC1, Lamp1, Lamp2, MAP1LC3B, MCOLN1 and ATP6V0E1
MTF1, MT1, MT2, MT3, MT4
Slc30a1, slc30a4, slc30a5, slc30a6, slc30a7,slc30a9,Slc30a10
Slc39a1, slc39a2, slc39a3, slc39a4,slc39a5,slc39a6, slc39a7,slc39a8,slc39a9,
Slc39a10, slc39a13 and slc39a14.

[cwyoo]

Thank you for your help.

Could you use this list of genes and run a new separate analysis Only with these genes ?
TFEB, TFE3, Becn1, RB1CC1, Lamp1, Lamp2, MAP1LC3B, MCOLN1 and ATP6V0E1
MTF1, MT1, MT2, MT3, MT4
Slc30a1, slc30a4, slc30a5, slc30a6, slc30a7,slc30a9,Slc30a10
Slc39a1, slc39a2, slc39a3, slc39a4,slc39a5,slc39a6, slc39a7,slc39a8,slc39a9,
Slc39a10, slc39a13 and slc39a14.

To clarify, proceed by identifying genes that have shown significant fold changes first, and then include the aforementioned genes as genes of interest.

[samanthagonzales]

Here is the normalized data subsets with the new list of genes included.

I will post the network results as soon as they are ready.

[samanthagonzales]

Here is the resulting network with the new list of genes of interest.

Steps to generate:
- qc/preprocessing
- differential expression (de) analysis via DESEq2
- normalization via DESeq2 Median of Ratios
- standardization into Z-scores and discretization
- ran Banjo for 32h on the union(genes of interest, top 200 de genes) for a total of 231 genes (2 of the genes of interest, Mt3, Mt4, were not present in the data)
- extracted the subnetwork which includes the MB of node AKO_Mutant, genes of interest within 3 generations of the node AKO_Mutant, and and parents/children between AKO_Mutant and the genes of interest.

Color coding:
yellow: markov blanket of AKO_Mutant
green: genes of interest
purple: parents of AKO_Mutant's children nodes
red: children of AKO_Mutant
blue: parents of AKO_Mutant