Cancer Datasets now available in DistilBio

We are in the process of adding disease http://www.awgolf.co.uk/ specific datasets in DistilBio and we have started with integrating cancer datasets. As an initial step we have integrated gene mutation, cell-line, compound screening studies and methylation data. Continue reading

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Anti-arrhythmic drugs for cancer? – DistilBio use case

I had earlier illustrated an christian louboutin outlet uk  for drug repurposing using the drug Rabeprazole. Recently, I came across an interesting paper that discussed repurposing of drugs for cancer and thought it would be interesting to see if some of these results could be reproduced using DistilBio (1).

Two of the drugs,  and , from the paper are used here to illustrate the use of DistilBio as an initial tool for drug repurposing. Losartan is an anti-hypertensive and  here  anti-arrhythmic agent while Procainamide is an anti-arrhythmic agent with different targets.

Let’s look at Losartan first.

The query I ran is as follows christian louboutin sale uk to find the  protein targets of Losartan and the biological processes.http://www.theblc.co.uk/

 

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 Query: losartan > protein > Go-biological process

The results are as follows:

The details tab for Losartan shows that this is a drug targeting the Angiotensin receptor II. I filtered the protein targets by the source and selected the source as DrugBank. Generally, DrugBank data gives us the primary targets of drugs.  is the target for losartan and I had a look at the biological processes associated with the protein. Calcium mediated signalling, Cell growth, Cell  proliferation, Inflammatory response are some of the biological processes associated with AGTR1. These are known processes that play a role in cancer. I further extended the query by selecting AGTR1_Human to find the proteins interacting with AGTR1 and their biological processes.

The query reads as:

 Query: AGTR1_Human > protein > Go-biological process

The results are as follows:

Again, you can see that proteins like interact with AGTR1. These are proteins that have been in implicated in cancer. (2-4). Also, looked at the biological processes and some of them are epidermal growth factor receptor signaling pathway, fibroblast growth factor receptor signaling pathway, positive regulation of ERK1 and ERK2 cascade, positive regulation of angiogenesis, positive regulation of endothelial cell migration, positive regulation of epithelial cell migration, processes that may play a role in cancer.

The other drug is procainamide. I ran a query similar to the query for Losartan.

 Query: Procainamide > protein > Go-biological process

The result is below.

Again, filtered the results by DrugBank. Procainamide is a sodium channel blocker and the primary target is sodium channel  The drug also targets . The processes associated with DNMT1 are DNA methylation, Positive expression of gene expression, Transcription, DNA dependant, Chromatin modification. These again may play a role in development of cancer.

I further extended the query to find the drugs targeting DNMT1 and also the diseases related to these drugs.

 Query: DNMT1_Human > drug > disease (related)

The diseases associated with the drugs targeting DNMT1 are Neoplasms of the Breast, Prostate, Colon, Colorectum, Head and Neck, Lung, Pancreas, Stomach, Carcinoma and Leukemia like Myeloid, Acute, CML.

The results again are interesting that the drugs targeting DNMT1 are anti-cancer drugs which indicate that DNMT1 may play a role in cancer.

Therefore the question that arises is “Can these drugs be repurposed as anti-cancer drugs?” Further studies could perhaps reveal the anti-cancer properties of these drugs.

The above examples look at 2 different concepts in drug repurposing –

  • Primary target of a drug that may play a role in cancer apart from its role in disease for which the drug has been approved and
  • Off-target of a drug that may play a role in cancer.

Hence using DistilBio as an initial tool, a researcher can find novel interactions between drugs, diseases and targets.

References:

  1. The prince and the pauper. A tale of anticancer targeted agents.
  2. Jak2 tyrosine kinase and cancer: how good cells get HiJAKed.
  3. Phospholipase Cgamma1 is required for metastasis development and progression.
  4. The tyrosine phosphatase Shp2 (PTPN11) in cancer.

 

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New Feature: Upload your list of terms on DistilBio and discover connections

Do you have a long list of terms and want to find all connections available for them? There are times when you have a list of hereterms and finding connections for each of them, co-relating and analyzing the data can be a huge task. You can now upload  Abercrombie Outlet your list on DistilBio using the Upload terms feature. We are excited to introduce this new feature to make your searching experience easier Abercrombie uk on DistilBio. Continue reading

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Metaome releases the “DistilBio Terms Bookmarklet”

Metaome has released the DistilBio Terms Burberry Wallets bookmarklet which detects and lists biomedical concepts such as genes, proteins, drugs, compounds and pathway mentioned in a webpage. This is similar to the app released by Metaome for Elsevier’s ScienceDirect. Now the app can be used on any webpage. The user has to install the bookmarklet in their browser’s bookmark bar once and has to only push the button to highlight all recognized terms in a page. Continue reading

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DistilBio – New features and Data

Over the past few weeks we have been cheap beats ukadding new features and data to enhance the user experience. Some of the new features are detailed below. Continue reading

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DistilBio Terms App now available in Elsevier’s ScienceDirect

The DistilBio Terms application detects Cheap Burberry Outlet UK and lists biomedical concepts such as genes, proteins, drugs, compounds and pathway mentioned in the article. Once the user has installed the app, it is visible when viewing ScienceDirect articles and detects the terms using relevant life-science ontologies and synonyms. Continue reading

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Improved Autosuggest

The DistilBio team has been louboutin outlet uk working at improving the “autosuggest” to make querying easier and to display more relevant options to Cheap Burberry Outlet UK the user. Based on user feedback new features have been added to the autosuggest some of which are listed below. Continue reading

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DistilBio: Tell us what you think

It has been two months since we launched DistilBio, our semantic search engine for the life sciences. We have had quite a bit of traction: so a big Cheap Burberry Outlet UK thanks to all those that visited. To those haven’t been there yet, we would be thrilled if you checked it out.

As we add new features and data to DistilBio, we would like this process to be user driven. This means that we would like you to tell us what you want. Searches across public data will remain free.

Input that we are specifically looking for:

  1. Are there specific databases you would like us to add?
  2. Are there specific types of data you would like us to add? Fore.g. gene expression data, clinical data etc.?
  3. Are there specific analysis tools that you would like us to add e.g. Blast, Clustalw etc.?
  4. Would a chemistry structure search be useful?
  5. How could we make the UI better to enhance the user experience?
  6. Could you we enhance the tool so it would suit specific communities centered on a model organism, a target or a disease?
  7. Would the tool be useful to search across private data?
  8. Anything else you can think of?

Any inputs would be welcome. You can respond Burberry Dresses on this blog, or write to me at kalpana@metaome.com

Thanks,
Kalpana Krishnaswami,
CEO and Founder
Metaome Science Informatics

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Autosuggest ranking in DistilBio – New feature

A new feature enhancement in DistilBio is Cheap Burberry Outlet UK ranking of terms in the autosuggest drop-down according to their relevance. Previously, for instance, while querying for a drug, the autosuggest would suggest properties of drugs according to alphabetical order.

This has been enhanced in the new version to rank “connections” related to the query higher over “properties”. The suggestions are also ranked in terms of the number of connections available for the particular query. For instance, when you query for a drug, the autosuggest now prompts the connections <interacts with> and <targets> as terms 1 and 2. Similarly for a disease, highest numbers of connections are available for <reference> and <related>. This is for “reference publications” and “related drugs” for the disease. This feature should make querying easier for Burberry Shirts a user to build complex queries by showing the connections/properties available for each type.

Do give us your feedback!

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Compound searches and their bio-activities in DistilBio

In my previous posts, I had focused on queries for drugs, diseases and proteins using DistilBio. Apart from this, DistilBio also contains data on bioactive chemical compounds from databases like ChEMBL and ChEBI. Experimental data properties, assays, cell line information for a compound are displayed in a simple and easily searchable faceted view.

I chose the compound “Letrozole” as an example to illustrate this. Letrozole is an approved drug used as an adjuvant treatment for hormonally-responsive breast cancer. Make sure the type “compound” is selected.  (Watch Demo Video)

Continue reading

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