Today we will take a look at a study on Rheumatoid Arthritis (RA) published in 2017 on Arthritis Research & Therapy using our Omics Playground Platform. In this study, the authors sequenced the transcriptome of 24 patients (12 healthy individuals, 5 patients with untreated RA and 7 patients undergoing treatment for RA) and proposed three novel candidate genes (namely ERBB2, TP53 and THOP1) as being involved in the pathogenesis of RA. …

Credit: UnityPoint Health

Today’s post was inspired by the following online blog post on the benefits of high intravenous vitamin C (aka ascorbate) doses in cancer therapy. This has been a rather controversial topic that attracted the attention of none other than two times Nobel prize winning scientist Linus Pauling, who ended up co-authoring a series of studies on the efficacy of vitamin C in treating cancer in the 70s. …

For Malaria day, we decided to re-analyse the data (GSE97158) from a published article. The data is currently available on the public ARCHS4-omics Playground.

In their study, the authors performed controlled infection with Plasmodium falciparum in volunteers who had been previously exposed to malaria and followed gene expression from liver to blood stages at three different time points post-inoculation (day 5, 9 and 28).

There was no observable clustering by time point in the dataset, because of large differences between individuals, as noted in the original paper (Figure 1).

Using the “Enrichment” tab on the Viromics platform, we consulted the Drug Connectivity Map database to identify potentially inhibitory drug profiles against both SARS-CoV-2 infected cell lines from the Blanco et al dataset. Analysis revealed that in the profiles obtained from both cell lines, several Drug Modes of Actions were shared (Figure 1A and 1B). In particular the following inhibitors for the following pathways were in common between the two infected samples: PI3K, MEK and mTOR. This is consistent with previous results based on SARS- and MERS-coronavirus infections (here and here).

Figure 1.​ ​A​) Modes of action of potential inhibitors against A549 cells infected with SARS-CoV-2. ​B​) Modes of action of potential inhibitors against NHBE cells infected with SARS-CoV-2.

On an individual drugs level, it was interesting to…

The first public SARS-CoV-2 transcriptome is now available and we took the opportunity to upload it onto our platform for analysis. The datasets consists of transformed lung alveolar (A459) and primary human lung epithelium (NHBE) infected with different Multiplicity of Infections (MOI) of SARS-CoV-2 (collected after 24h), as well as transformed lung alveolar (A459) cells infected with either respiratory syncytial virus (RSV) (collected after 24h) or Influenza A virus (IAV) (collected after 9h).

In order to replicate the main findings from this dataset, we first generated a wordcloud of the most significantly enriched gene sets in both SARS-CoV-2 infected cell…

The first proteome of a SARS-CoV-2 in vitro infection has recently been published. The data set consists of a time series between 2h-24h post-infection. It is now available in our open access Viromics platform for analysis. In their article, the authors describe several cellular pathways that are differentially expressed following infection and proceed to test potential antivirals based on the infection proteome profile.

We used our platform to re-analyse the data. To fully replicate the authors’ results we also included viral proteins in the analysis.

First of all we generated a PCA plot, which showed that only the 24h infected…

Final conclusions of Axel Martinelli’s analysis.

Credit: NIAID

In my previous post, I analysed an in vitro infection with a Middle Eastern coronavirus using our special edition of the Omics Playground platform. In my analysis I identified the SSX2 gene as a potential marker of early infection and trametinib as a potential antiviral drug.

In order to extend such findings to other coronavirus species, I looked at publicly available MERS and SARS datasets stored in our platform. Starting with MERS, I chose two datasets. The first dataset is from a more recent published study on the role of accessory ORFs in MERS infections. My main reason for picking…

Credit: NIAID

Our company, Bigomics Analytics, recently launched the Viromics Playground, an open access online version of the Omics Playground platform that includes over 200 viral infection transcriptomes. I thought it might be a good idea to give it a spin with some of the publicly available coronavirus datasets that have been pre-loaded. In particular, I wanted to see if I could quickly gain some insights via the platform on potential biomarkers of early infection and also a list of drugs with therapeutic potential.

I started by looking at a Middle Eastern coronavirus dataset from a published study, mainly due to the…

Credit: NIAID-RML.
Credit: NIAID-RML.

The current Coronavirus epidemic (COVID-19) has been causing widespread panic and has been a major health concern in the past months. Efforts from both governments, pharmaceutical companies and the scientific community have been focused on developing a vaccine and identifying therapies to contain its spread and treat patients. …

BigOmics Analytics

BigOmics is a Swiss Start-Up, focused on helping life scientists see and understand their omics data by providing them with smart tools for advanced analyses.

Get the Medium app

A button that says 'Download on the App Store', and if clicked it will lead you to the iOS App store
A button that says 'Get it on, Google Play', and if clicked it will lead you to the Google Play store