Hello Austin,

Congratulations on the tool. The tool is accessible though.

Here are my thoughts-

1. Can not find " button under "Load File" to load this file". I can create this file and toy around, but to save time can you send a good example file here or by emailing: [email protected] ?

2. The tool looks convenient to use (R-based with GUI, right?).

3. Tool says "Omics Comparison" but deals with RNA-seq and micro-array (= both transcriptomics). How about proteomics (same IDs though), genomics and Q. 5 (metabolite are pretty different IDs) ?

4. How would those values normalize together? They come from different platforms/ instruments and different dynamic ranges (fold changes) and hence statistical significance would be different too. Does the tool take into consideration these factors as well (scaling, normalization)?

5. For metabolomics it would need KEGG IDs equivalence for GeneIDs which is quite a task given the co-shared metabolites among most metabolic pathways.

6. When will the tool be formerly published/ released? Any names yet ?

7. For time-course analysis, how would it be better than existing STEM or EDGE analysis tools ?

8. Plans to integrate "plant"-oriented or microbe oriented DBs soon ?

Loads of questions, and feel free to email me at : [email protected] in case if this is not appropriate for you to answer here.

All the best.

Thanks in advance,

Biswa

 Hi Biswapriya,

Thank you for your feedback! I will take all of it into consideration and try to answer all of your questions. Please let me know if you want any more information or have more questions.

1. When you click the "Choose File" button, it automatically uploads and should have a progress bar below it that tracks the progress of the upload. I will send you a test file as soon as possible!

2. Yes it is an R based GUI.

3. The tool is mainly used for the analysis of gene expression. Metabolomics is quite different in how the databases are usually set up so I think that would be a different project. If the proteomics databases have the same IDs, they should work if we get the correct database files for up/down regulation effects of proteins on their associated pathways and the dataset is of differentially expressed proteins.

4. Each file is meant to act as a stand-alone holistic view of the particular experiment. There should not be any differences in methods used within a single data file. If you want to compare multiple datafiles using different tools and platforms it may produce large differences in dynamic ranges, especially in the impact, which is a log-adjusted value based on proportion, fold change, and p-values of the differentially expressed gene/protein (which is more liable to change between instruments). In this case however, the z-score analysis could be used to compare between pathways/datasets since it shows significance of time-points rather than magnitude of the impacts.

5. The tool does do some KEGG metabolism pathway analysis with genes that have a known negative impact having an opposite effect on the pathway (if expression increased the function or pathway is more inhibited). I am not sure if that is useful for you or not but I think there are some tools that could convert the Kegg Ids into Gene Ids. You can try this one here. https://biodbnet-abcc.ncifcrf.gov/db/db2db.php.

6. We are applying for a grant for funding for this tool actually so the formal release date is unknown at this time. The name will be DIA (dynamic impact approach) Analysis Tool although it is subject to change.

7. Both STEM and EDGE use clustering methods, which reduces the dataset or gene lists. This is good for finding co-regulated genes. However, this reduction and separation of datasets into smaller gene lists make it difficult for them to give a holistic view of dynamism of the functions and pathways through time. The DIA better captures biological impact and gives 3 different ways to interpret it: impact, direction of impact (flux), and z-score significance.

8. If there is a demand for plant/microbe based databases, we will definitely add it! The lab is primarily working on bovines/mouse right now so it is not the top priority but is something we are looking at.

Thank you again for your feedback!

Austin

Hi Zofia,

Here is a sample data set you can try. Let me know how it goes!

Thanks,

Austin

Hi, I can't open the url. My location is Bangalore, India.

Hi Zofia,

That would be great! Yes the tool is very useful for comparing time-course! Let me know if you find something interesting!

Austin

Hi Arpit,

Could it possibly be your internet server provider?  It seems to open in the United States and Europe. You might have to mark it as "safe" by your firewall if you have one. Let me know if you still have problems at [email protected]

Austin