System biology approaches identified novel biomarkers and their signaling pathways involved in renal cell carcinoma with different human diseases by Md. Saddam Hossen (18278698)

Subjects:

Network-based identification and prioritization of key transcriptional factors of diabetic kidney disease by Ikhlak Ahmed (150200)

“…Further, we recognized a small but a closely connected set of these susceptibility genes enriched for podocyte differentiation, several of which were characterized as genes encoding critical transcriptional factors (TFs) involved in DN development and podocyte function. …”

Functional Validation and Network-Based Prioritization of Key Transcriptional Factors of Diabetic Kidney Disease by Ikhlak Ahmed (6428939)

“…Further, we recognized a small but a closely connected set of these susceptibility genes enriched for podocyte differentiation, several of which were characterized as genes encoding critical transcriptional factors (TFs) involved in DN development and podocyte function. …”

Differentiation of human pluripotent stem cells into two distinct NKX6.1 populations of pancreatic progenitors by Idil I. Aigha (14913774)

“…<h3>Background</h3><p dir="ltr">The expression of a specific combination of transcription factors (TFs) in the multipotent progenitor cells (MPCs) is critical for determining pancreatic cell fate. …”

Network-based identification of key master regulators associated with an immune-silent cancer phenotype by Raghvendra Mall (581171)

“…We follow a network-based protocol to identify transcription regulators (TRs) associated with poor immunologic antitumor activity. …”

Gene Expression Landscape of Chronic Myeloid Leukemia K562 Cells Overexpressing the Tumor Suppressor Gene PTPRG by Giulia Lombardi (3944720)

“…With the first method (Method 1), we implemented GSEA, followed by the identification of transcription factors. With the second method (Method 2), we first selected the transcription factors from the set of differentially expressed genes and implemented GSEA on this set. …”

Enhanced differentiation of human pluripotent stem cells into pancreatic progenitors co-expressing PDX1 and NKX6.1 by Bushra Memon (4792767)

“…<h3>Background</h3><p dir="ltr">Pancreatic progenitors (PPs) co-expressing the two transcription factors (TFs) PDX1 and NKX6.1 are recognized as the indispensable precursors of functional pancreatic β cells. …”

Transcriptomic Analyses Revealed Systemic Alterations in Gene Expression in Circulation and Tumor Microenvironment of Colorectal Cancer Patients by Hibah Shaath (5599658)

“…Herein, we performed transcriptome analyses on peripheral blood mononuclear cells (PBMCs), CRC tumor tissue and adjacent normal tissue from 10 CRC patients and PBMCs from 15 healthy controls. Up regulated transcripts from CRC PBMCs were associated with functions related to immune cell trafficking and cellular movement, while downregulated transcripts were enriched in cellular processes related to cell death. …”

An integrated multi-omic approach demonstrates distinct molecular signatures between human obesity with and without metabolic complications: a case–control study by Fayaz Ahmad Mir (11828354)

“…We measured in whole blood samples 754 human microRNAs (miRNAs), 704 metabolites using unbiased mass spectrometry metabolomics, and 25,682 transcripts, which include both protein coding genes (PCGs) as well as non-coding transcripts. …”

Molecular Classification of Breast Cancer Utilizing Long Non-Coding RNA (lncRNA) Transcriptomes Identifies Novel Diagnostic lncRNA Panel for Triple-Negative Breast Cancer by Hibah Shaath (5599658)

“…Focusing on TNBC, findings from the discovery cohort were validated in an additional two cohorts, identifying 13 common lncRNA transcripts enriched in TNBC. Binary regression analysis identified a four lncRNA transcript signature (ENST00000425820.1, ENST00000448208.5, ENST00000521666.1, and ENST00000650510.1) with the highest diagnostic power for TNBC. …”

Comprehensive Transcriptome and Pathway Analyses Revealed Central Role for Fascin in Promoting Triple-Negative Breast Cancer Progression by Rayanah Barnawi (8737584)

“…We identified 129 upregulated and 114 downregulated mRNA transcripts, while 14 miRNAs were differentially expressed in FSCN1^KD. …”

Integrated Transcriptome and Pathway Analyses Revealed Multiple Activated Pathways in Breast Cancer by Radhakrishnan Vishnubalaji (3563306)

“…Additionally, BC tissue exhibited marked enrichment in genes promoting cellular proliferation, migration, survival, and DNA replication and repair. …”

Divergent wiring of repressive and active chromatin interactions between mouse embryonic and trophoblast lineages by Stefan Schoenfelder (115930)

“…Interactions that are prominent in TSCs are enriched for enhancer–gene contacts involving key TSC transcription factors, as well as TET1, which helps to maintain the expression of TSC-relevant genes. …”

Upregulation of β-catenin due to loss of miR-139 contributes to motor neuron death in amyotrophic lateral sclerosis by Sophie Hawkins (18421377)

“…We identify the downregulation of miR-139, an MN-enriched microRNA, in FUS and sporadic ALS MN. We discover that miR-139 downregulation leads to the activation of canonical WNT signaling and demonstrate that the WNT transcriptional mediator β-catenin is a major driver of MN degeneration in ALS. …”

DNA methylation signatures in Blood DNA of Hutchinson–Gilford Progeria syndrome by Yosra Bejaoui (8552574)

“…Differentially methylated probes were enriched for phosphatidylinositol biosynthetic process, phospholipid biosynthetic process, sarcoplasm, sarcoplasmic reticulum, phosphatase regulator activity, glycerolipid biosynthetic process, glycerophospholipid biosynthetic process, and phosphatidylinositol metabolic process. …”

Systems biology analysis reveals NFAT5 as a novel biomarker and master regulator of inflammatory breast cancer by Andrea Remo (447375)

“…</p><h3>Results</h3><p dir="ltr">Using in-silico modeling of network-based strategy, we identified three top enriched MRs (NFAT5, CTNNB1 or β-catenin, and MGA) strongly linked to the IBC phenotype. …”

Long non-coding RNA MALAT1 promotes steatosis in HepG2 cells by modulating target gene expression in presence of Exendin-4 by Olfa Khalifa (10914452)

“…MALAT1 (metastasis associated with lung adenocarcinoma transcript 1) is a well-conserved lncRNA that has been linked to a variety of illnesses, including cancer. …”

Regulation of the aryl hydrocarbon receptor in cancer and cancer stem cells of gynecological malignancies: An update on signaling pathways by Lubna Therachiyil (4246156)

“…Exposure to environmental pollutants such as polycyclic aromatic hydrocarbons is associated with an increased the risk of CSC enrichment in gynecological cancers. One of the important pathways that mediates the metabolism and bioactivation of these environmental chemicals is the transcription factor, aryl hydrocarbon receptor (AhR). …”

Development and application of an integrated allele-specific pipeline for methylomic and epigenomic analysis (MEA) by Julien Richard Albert (655437)

“…<h3>Background</h3><p dir="ltr">Allele-specific transcriptional regulation, including of imprinted genes, is essential for normal mammalian development. …”

PRAME promotes epithelial-to-mesenchymal transition in triple negative breast cancer by Ghaneya Al-Khadairi (14153274)

“…Gene ontology analyses revealed enrichment of genes that are dysregulated in ovarian and esophageal cancer and are involved in transcription and apoptosis. …”