Pulmonary Arterial Hypertension - PAH

[Hamza]

I tried both forward Selection LR and Backward Elimination LR. The results are attached.

[Hamza]

This is the backward LR logistic regression with low removal probability as 0.01. I tried o.05 but it did not work too.

[Hamza]

Luis and I run the MB genes with predictors; and ROC curve results are attached.Also, predection datafile is attached.

Linear and logistic regression for the MB genes are attached.

MB GenIe network will be sent via email, since .xdsl doesn't upload in the forum.

[Hamza]

This table is for IPAH case control studies on Pubmed

[Hamza]

This is an updated version of PAH and IPAH case control studies table on Pubmed

[Hamza]

47 Case control studies were reported including PAH and IPAH "Healthy Controls".

[Hamza]

This is an updated version of the table.

[Hamza]

This is the last update of the table. it includes the search that was done earlier for PAH studies. The original search found 305 articles from pubmed search and 124 articles from other sources. Out of them, 271 studies were selected to review based on availability. 40 studies were selected based on HR or OR reporting. 18 studies were included based on reporting HR or OR for both age and sex variables.

The final result is 15 HR studies reported HR for age and sex & 3 studies reported OR for both age and sex.

In attachment is the excel file that include all information above+ PRISMA check-list which was followed for the 18 selected studies, and PRISMA diagram for the search was done.

[Hamza]

This mu update,
- Total of 6 datasets used from GEO (Descriptive table attached)
- 10716 Common among all datasets.
- 200 sample total (Table attached, sample description).
- Data were normalized by z-score and converted to descritized.
- independet T-test for (all samples, tissue, and blood sample- file attached).
- ID3 Correlation analysis (tissue, and blood sample- file attached).
- Quartile percentages were imcluded in the attachment far both independet T-test & ID3 Correlation analysis.

Now, I have :
1- Gene list provided from Dr. Felty (ID3 overexpressed genes).
2- ID3 target genes from literature (provided from Vincent).
3- my genelist from GEO datasets, combined, correlated with sample as well ID3.

What gene should I select from each of above lists, then I will find the common genes among them, to get focused gene list for further analysis?

[Hamza]

I used PAH associated genes pathways' from literature. Also, I used the list of genes I had earlier (ID3 correlated& PAH associated from GEO datasets) to find out pathways associated with the gene list. Then, I matched the genes in the common pathways both sides, and I got 30genes common in Blood samples, and 18 genes common on Tissue samples.

I run Bene with 18 genes and I got the network attached. However, with Blood samples 30 genes I didn't get any results so far. It is still running for 2 days now. I also run another terminals for 29, 28,27, and 26 genes to see if there is an issue with number of variables.

I run 25 variables and I gor the results as well.