Skip to main content

Results from Classification Analysis

As discussed in the previous post, Vitamin K appears to be one of the important topics according to the Network Analysis that has been performed. I wanted to see whether this would be the case using Classification Algorithms.

Below is a sample run with several algorithms being applied using Scikit-Learn (some topics found are not disclosed).




We see that TYRO3, GAS6, GRB2 are among Topics that are considered highly relevant to this Research. Recall that these are Vitamin K related Genes as discussed in the previous post. However we see more new Topics coming up and these are :

1) Liver Disease
2) Mitochondria
3) Norepinephrine
4) ROS (Reactive Oxygen Species)

See below Dr Ron Davis, discussing latest findings of  Research done at Stanford regarding Chronic Fatigue Syndrome. He mentions TCA Cycle :

https://www.youtube.com/watch?v=sGBXXlQO49g&feature=youtu.be&t=463


From wikipedia, regarding TCA Cycle we read :


The citric acid cycle is a key metabolic pathway that connects carbohydrate, fat, and protein metabolism. The reactions of the cycle are carried out by eight enzymes that completely oxidize acetate, in the form of acetyl-CoA, into two molecules each of carbon dioxide and water. Through catabolism of sugars, fats, and proteins, the two-carbon organic product acetyl-CoA (a form of acetate) is produced which enters the citric acid cycle. The reactions of the cycle also convert three equivalents of nicotinamide adenine dinucleotide (NAD+) into three equivalents of reduced NAD+ (NADH), one equivalent of flavin adenine dinucleotide (FAD) into one equivalent of FADH2, and one equivalent each of guanosine diphosphate (GDP) and inorganic phosphate (Pi) into one equivalent of guanosine triphosphate (GTP). The NADH and FADH2 generated by the citric acid cycle are, in turn, used by the oxidative phosphorylation pathway to generate energy-rich ATP.

Please note that CoA appears (top of the snapshot) at the Network Analysis as seen on the previous post . Take also note of "oxidative phosphorylation" being mentioned to the Wikipedia entry.


In the following video, Dr Davis discusses about Mitochondria, Lactate and Pyruvate :


https://www.youtube.com/watch?v=jXL2xzxCXBw


After a bit of searching i found a US Patent that uses Vitamin K for Mitochondrial Diseases from which i copy two sections :



[0023]
The ability to adjust biological production of energy has applications beyond the diseases described above. Various other disorders can result in suboptimal levels of energy biomarkers (sometimes also referred to as indicators of energetic function), such as ATP levels

Treatments for these disorders are also needed, in order to modulate one or more energy biomarkers to improve the health of the patient. 

In other applications, it can be desirable to modulate certain energy biomarkers away from their normal values in an individual that is not suffering from disease. For example, if an individual is undergoing an extremely strenuous undertaking, it can be desirable to raise the level of ATP in that individual.


[0084]
Several metabolic biomarkers have already been used to evaluate efficacy of CoQ10, and these metabolic biomarkers can be monitored as energy biomarkers for use in the methods of the current invention. 

Pyruvate, a product of the anaerobic metabolism of glucose, is removed by reduction to lactic acid in an anaerobic setting or by oxidative metabolism, which is dependent on a functional mitochondrial respiratory chain


Dysfunction of the respiratory chain may lead to inadequate removal of lactate and pyruvate from the circulation and elevated lactate/pyruvate ratios are observed in mitochondrial cytopathies (see Scriver C R, The metabolic and molecular bases of inherited disease, 7th ed., New York: McGraw-Hill, Health Professions Division, 1995; and Munnich et al., J. Inherit. Metab. Dis. 15(4):448-55 (1992)). 


Yet one more interesting finding is that MERTK (also discussed in the previous post) appears to be related to Pyruvate Metabolism and Acetyl-CoA carboxylase activity according to an Association Analysis tool called String-DB :

https://string-db.org/cgi/network.pl?taskId=jvtSkLCGQfx2




Of course, it is not suggested/claimed here in any way that Vitamin K supplementation can treat Chronic Fatigue Syndrome or any other Syndrome discussed.

However at this point we should take note that several Algorithms identify Liver Disease and Mitochondria appearing to be important Topics relevant to this Research. This Algorithmic Output are readily reproducible to any interested Researcher.

Comments

Popular posts from this blog

New findings : Myosin, D3, Actins, Autophagy/Phagocytosis

It is time to look at some new findings as these were identified by Machine Learning and Network Analysis.
Before continuing please note that in previous posts we discussed the importance of Endoplasmic Reticulum Stress, the Unfolded Protein Response and Genes AXL, GRB2, MGP, TYRO3, MERTK, GGCX, GAS6, SH2B3.
Recall also that Sulfation has been also selected as important.

The latest findings suggest the following Topics as being relevant to the Research presented in this Blog :
CYP27A1 and VDBP LXR (Liver X Receptor ) Actins (G-Actin, F-Actin) Myosin Phagocytosis / Autophagy

On the following algorithmic run, Machine Learning identifies relevant Topics to this Research :



Machine Learning, NLP and Network Analysis-Guided Medical Research : A Case Study

Can Machine Learning help us in identifying the origin of several Medical Syndromes?

In previous posts we have seen how approximately 8 Million PubMed abstracts were collected and analyzed using Natural Language Processing (NLP) techniques. This NLP Processing is the basis for generating Data that may then be used as Input to several Machine Learning algorithms.

In this Case Study our Goal is to identify relevant Medical Topics (Topics include Genes, Biological Pathways, etc) that are most likely to direct Medical Researchers towards the origin(s) of the following Syndromes :

-Post-Finasteride Syndrome
-Post-Accutane Syndrome
-Chronic Fatigue Syndrome
-Fibromyalgia
-Gulf-War Syndrome
-Post-Treatment Lyme disease Syndrome

Before continuing, please read the following post for important disclaimershere


Note that the results shown below originate strictly from output of Machine Learning Algorithms / Network Analysis. No Human intervention has been made apart from the fact that Candidate T…

Welcome to Algo-genomics

I decided to start this Blog because i wanted to document my 4-year effort on identifying what is behind several syndromes that have no known treatment such as the Post-Finasteride Syndrome (known as PFS) and also Chronic Fatigue Syndrome (also known as CFS).
I would also like to draw attention from Researchers that could potentially use/validate the hypotheses that will be discussed in this Blog.
My first effort has focused to  "Post-Finasteride Syndrome", a syndrome with a debilitating set of symptoms that persist for a small percentage of people that have taken the drug Finasteride. The problems that are associated with Post-Finasteride Syndrome  can be found  on the Post-Finasteride Foundation Website :

http://pfsfoundation.org

As Research progressed, i began realizing that there were several syndromes that had very similar/overlapping symptoms. According to the hypothesis being discussed here, these potentially associated Syndromes of unknown origin are the following :