Biology subjects

Bhattacharyya, D. K.

Publications and source records attributed to Bhattacharyya, D. K..

3 recordsLinked to original sources

bioRxiv2025

D-CoMEx: A Unified Approach to Identify Phenotype-specific miRNA Biomarkers Related to Diseases

Profiling of miRNAs is important to understand how they regulate biological pathways and contribute to diseases. With current technological advancements leading to capture of voluminous biological data, it is interesting and challenging to explore new methods that can discover disease-data associations and provide better insights into the underlying mechanisms of diseases. Such understanding may also help prevent severe pathogenesis of the disease and contribute to knowledge required for effective drug development. This paper proposes a unified approach, D-CoMEx, to mine miRNA biomarkers from dysregulated pathways associated with Parkinsons disease (PD) and Breast Cancer (BC). The approach integrates a co-expression network (CEN) module extraction technique with a differential analysis method to capture interactions between miRNAs and dysregulated pathways. Our method identifies more statistically and biologically significant dysregulated pathways compared to DCGL, MODA, and DiffCoEx. We present three evidence-backed recommendations supporting strong associations between miRNAs and dysregulated pathways, demonstrating that D-CoMEx extracts biologically relevant miRNA biomarkers linked to disease progression.

bioinformatics↗

bioRxiv2021

Integrative analysis identified common and unique molecular signatures in hepatobiliary cancers

Hepatobiliary cancers (HBCs) are the most aggressive and sixth most diagnosed cancers globally. Biomarkers for timely diagnosis and targeted therapy in HBCs are still limited. Considering the gap, our objective is to identify unique and overlapping molecular signatures associated with HBCs. We analyzed publicly available transcriptomic datasets on Gallbladder cancer (GBC), Hepatocellular carcinoma (HCC), and Intrahepatic cholangiocarcinoma (ICC) to identify potential biomarkers using integrative systems approaches. An effective Common and Unique Molecular Signature Identification (CUMSI) approach has been developed, which contains analysis of differential gene expression (DEG), gene co-expression networks (GCN), and protein-protein interactions (PPIs) networks. Functional analysis of the DEGs unique for GBC, HCC, and ICC indicated that GBC is associated with cellular processes, HCC is associated with immune signaling pathways, and ICC is associated with lipid metabolic pathways. Our findings shows that the hub genes and pathways identified for each individual cancer type of the HBS are related with the primary function of each organ and each cancer exhibit unique expression patterns despite being part of the same organ system.

systems biology↗

bioRxiv2021

Integrative systems biology approach identified crucial genes and transcription factors associated with gallbladder cancer pathogenesis

Gallbladder cancer (GBC) has a lower incidence rate among the population relative to other cancer types but majorly contributes to the total cancer cases of the biliary tract system. GBC is distinguished from other malignancies due to its high mortality, marked geographical variation and poor prognosis. To date no systemic targeted therapy is available for GBC. The main objective of this study is to determine the molecular signatures correlated with GBC development using integrative system level approaches. We performed analysis of publicly available transcriptomic data to identify differentially regulated genes and pathways. Co-expression network analysis and differential regulatory network analysis identified hub genes and hub transcription factors (TFs) associated with GBC pathogenesis and progression. We then assessed the epithelial-mesenchymal transition (EMT) status of the hub genes using a combination of three scoring methods. The hub genes such as; CDC6, MAPK15, CCNB2, BIRC7, L3MBTL1 identified are regulators of cell cycle components which suggests that cell cycle regulatory genes are significantly linked to GBC pathogenesis and progression.

systems biology↗