Make networks for the Apweiler data from our own database

dondi / GRNsight

Web app and service for modeling and visualizing gene regulatory networks.

http://dondi.github.io/GRNsight

BSD 3-Clause "New" or "Revised" License

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Make networks for the Apweiler data from our own database #958

Closed dondi closed 2 years ago

dondi commented 2 years ago

@ahmad00m will partner with @Onariaginosa to do a query on the Postgres database to pull out networks with the same genes that were created for Yeastract

ahmad00m commented 2 years ago

@Onariaginosa and @ahmad00m recreated the networks using the SGD database. A PowerPoint is created to demonstrate the GRN for these matrices during the meeting later today.

dondi commented 2 years ago

As part of following up here, @Onariaginosa will check the existing expression gene table to see how many additional genes need to be entered in order for @ahmad00m to load the expression data into the database

kdahlquist commented 2 years ago

After review here are the next tasks:

add the number of edges to the powerpoint and post it on this issue
remove the three genes from the YEASTRACT network where the SGD version had 3 disconnected connected nodes
for the other network that had a lot of disconnected genes in the SGD version, we will just run the Yeastract version.
Focus on the networks from profile 2. Manually make the GRNmap input workbook for the two networks for profile 2
Work with @Onariaginosa after she gets the expression data into the Postgres database to do an automatic export and compare the two
Then we will run GRNmap on the input workbooks

ahmad00m commented 2 years ago

Here is the PowerPoint demonstrated during the meeting --> GRN matrices.pptx

ahmad00m commented 2 years ago

I started created the input workbooks and I'm nearly finished. The only problem I have is that I cannot open Microsoft Access file to access the degradation rates and production rates.

dondi commented 2 years ago

Degradation and production rates are currently in our database; @Onariaginosa can show @ahmad00m the script(s) for accessing these

dondi commented 2 years ago

For this @kdahlquist can pre-run a prototype workbook for some quick feedback. The goal is to have run GRNmap before WCBSURC on April 9

ahmad00m commented 2 years ago

I have finished the input workbooks for profile 2 and attached them below. But just to clarify the only difference between the input workbooks of SGD and YEASTRACT database would be the network matrices correct?

inputWorkbook_SGD_profile2.xlsx inputWorkbook_YEASTRACT_profile2.xlsx

kdahlquist commented 2 years ago

@ahmad00m, you are correct, the only difference is the network matrices. I will run these and let you know what happened.

ahmad00m commented 2 years ago

Alright, thank you so much!

dondi commented 2 years ago

@ahmad00m will continue to work with @bengfitzpatrick in order to refine the way the Apweiler data are copied into the workbooks