Case Studies

First Ever Mutant Gain of Function (gof) Analysis P152L of P53

About

First ever deciphering GOF (Gain of Function) mechanisms and associated pathways of P152L mutant of P53 in Human Oral Cancer using our customized mutant analysis framework. (BioCOS equal contribution)

Specificity of Our Analysis

When the laboratory engaged in this research could not understand and decipher for more than a year in spite of desperate efforts with other data analysis companies and its data analysis R&D collaborators as why and by which mechanisms and pathways the mutant P152L of P53 proliferates and does involve in metastasis, BioCOS problem specific computational strengths and mutant analysis pipelines customized for the mutant GOF function could very accurately and quickly found the GOF function mechanisms and pathways. -- 100% lab validated

Our Findings

Our cancer mutant specific computational framework could pinpoint the exact metastasis pathways and underlying genes involved in the GOF function where others failed. Refer to the paper.

Reference

Activation of Multiple Signalling Pathways by P152Lp53 Mutant Reveals New Gain-of-function Implicating Tumorigenesis. [ under revision in JBC]

First Ever Nucleolin role in Lipids and Cholesterol Metabolism

Pathways, genes and interaction mechanism demonstrating the first ever role of nucleolin (NCL) in cholesterol and fatty acid metabolism with 100% lab validations

Interaction mechanism and networks demonstrating the first ever role of nucleolin (NCL) and involved miRNA in cholesterol and fatty acid metabolism.

Computationaly found Enzymes mainly in metabolism involved and perfact cholesterol down regulation validation

Computational analysis pin points the fatty acid regulation on down regulation of NCL.

Deciphering the miRNA and genes interactions

About

The study, a deep drive demonstration of strengths of our computational methods and unique pipelines in data analysis (Transcriptome/miRNA), unique Pathway enrichment, functional correlation between mRNA and miRNA, mRNA-miRNA-Pathway interaction network and many other related novel models and frameworks, first ever decipheres from data analysis the NCL role in lipids and cholesterol metabolism. As metabolism being hallmark of cancer and NCL being expressed on cell surface and implicated in many other ways in cancers, its important correlation of NCL to metabolism. (First and corresponding author)

Specificity of our analysis

This data and work was first tried for almost 10 years by our client research lab and could not be analyzed by them to any conclusive mechanisms. At first when we demonstrated computationally the role of NCL in metabolism, none on the board believed us and refused to validate our findings and hence the first version of the paper was submitted without any lab validations. As usual being a novel first ever finding, paper got rejected but then our team again re-analyzed the findings and claimed its absolute correctness which was then reluctantly got validated by our collaborators in France. What the accuracy we got in lab validation, demonstrates the best in class analysis correctness and uniqueness of our methods and pipelines.

Our Findings

Bioinformatic analysis strongly points to a role of nucleolin in lipid metabolism, and in many signaling pathways. Down regulation of nucleolin is associated with lower level of cholesterol while the amount of fatty acids is increased. This could be explained by the decreased and mis-localized expression of the transcription factor SREBP1 and the down-regulation of enzymes involved in the beta-oxidation and degradation of fatty acids. Functional classification of the miRNA-mRNA target genes revealed that deregulated miRNAs target genes involved in apoptosis, proliferation and signaling pathways.

Reference

Integrated analysis of mRNA and miRNA expression in HeLa cells expressing low levels of Nucleolin.

Novel RNA-seq and Chip-Seq Analysis & Algorithms

A novel and very accurate customized Chip-seq NGS data analysis Algorithm developed in house.

Perfection of analysis - Almost 100% matching with theoretical and validated results.

Comparisions of accuracy - Perfect.

Computational findings 100% validated.

About

A novel and very accurate customized Chip-seq NGS data analysis Algorithm developed in house for Nucleolin Chip-seq analysis.

Specificity

While the existing methods and tools like MAC2 etc failed to accurately analyse the data and the research lab in France could not get the accurate analysis from many others they tried before reaching to us, BioCOS devised a customized chip-seq algorithm to analyse the rDNA binding for this specific case. The analysis outcome was 100% in concordance with the theortical calculations and later 100% validation in lab. A perfect customized algorithm and solution development for the customer to target a specific analysis.

Our Findings:

This is an example of very customized analysis for a very specific need of the customer and very accurately deciphering the biology in the chip-seq NGS data. Refer to the paper and fig 3 for perfect analysis and validations.

Reference:

Interaction of nucleolin with ribosomal RNA genes and its role in RNA polymerase I transcription.

Metabolic Syndrome and T2D Marker Analysis Frameworks

Indigenously developed analysis framework and analysis results and networks

Indigenously developed analysis framework and analysis results and networks.

Indigenously developed analysis framework and analysis results and networks.

Indigenously developed analysis framework and analysis results and networks.

ABout

This was a ICMR grant supported framework development for Identification of Transcriptionally altered and genetically associated multiple inflammatory biomarkers predicting cardiovascular events / acute coronary complications and type 2 Diabetes

Specificity

The aim of the study would be to determine the effect of inflammatory biomarkers in creating the genetic pre-disposition of the Indian population to diabetes and thrombosis. We are also exploring the roles of anti-inflammatory biomarkers in providing the protection against these diseases.

Our Findings:

Yet not published - Going on but some of the highlights of the analysis shown in figures

Related Reference ( Current study yet not published)

Expression-Based Network Biology Identifies Alteration in Key Regulatory Pathways of Type 2 Diabetes and Associated Risk/Complications.

Infectious Disease (P.Falciparum Exportome Analysis) in-vivo data from Indian population

Deciphering the Plasmodium Falciparum exportome from in-vivo high throughput data with custom build analysis.

Deciphering the Plasmodium Falciparum exportome from in-vivo high throughput data with custom build analysis.

Deciphering the Plasmodium Falciparum exportome from in-vivo high throughput data with custom build analysis.

Deciphering the Plasmodium Falciparum exportome from in-vivo high throughput data with custom build analysis.

ABout

Interactions of Plasmodium Falciparum ETRAMP14.1 with pfEMP1, translocon componenets and other ETRAMP members at the interface of host-parasite PVM.

Specificity

This is our several years of efforts in development of specific data analysis framework for analysing the in-vivo plasmodium Falciparum ( Cerebral Malaria) exportome mechanisms from the in-vivo data from Indian population.

Our Findings:

With help of very customized framework and data analysis specific to plasmodium falciparum ( 3D7) we have found first ever proteins involved in exportome and its interaction with PTEX channel proteins. ( Research under review)

Reference:

Interactions of Plasmodium Falciparum ETRAMP14.1 with pfEMP1, translocon componenets and other ETRAMP members at the interface of host-parasite PVM.[ under review]