- The antimicrobial peptide LL-37 induces synthesis and release of cysteinyl leukotrienes from human eosinophils – implications for asthma
ProteinLounge Pathway Builder used to draw a model for LL-37-mediated eosinophil recruitment and cellular signaling leading to cys-LT and ECP release(Fig 6).
- Cellular adaptive response of distal renal tubular cells to high-oxalate environment highlights surface alpha-enolase as the enhancer of calcium oxalate monohydrate crystal adhesion
Pathway Builder used to create background image for Gene expression data (Fig 3).
- The Role of the Tumour Suppressor p53 in the Elimination of Hepatitis B Virus-infected Hepatocytes - Implications for Viral Clearance
PathwayBuilder used to draw p53 pathway (Fig 1.2), DNA Damage Response Signaling Pathway (Fig 1.3), apoptosis signaling pathway (Fig 1.5), elimination of hepatitis B infected hepacytes (Fig 4.1), illustrate the concept The AP-1 element in the 5’ UTR of the CD95L gene is responsible for CD95L expression in HBV-infected hepatocytes" (Fig 4.2), HBV infection triggering the phosphorylation of p53 through the DNA damage response (Fig 4.3), HDV infection (Fig 4.4), and Caspase independent apoptosis induction (Fig 4.5).
- METHODS FOR IDENTIFICATION OF NOVEL PROTEIN DRUG TARGETS AND BIOMARKERS UTILIZING FUNCTIONAL NETWORKS
Patent. Mentions Protein Lounge as a potential tool to determine Protein-Protein Interaction to supplement high-throughput experimentation(Table 5).
- Network Expansion and Pathway Enrichment Analysis towards Biologically Significant Findings from Microarrays
Searched curated T2D-associated genes using Oracle SQL Developer with comprehensive integrated pathway data in HPD version 2.1 (which includes pathway data from Protein Lounge)
- Molecular And Cellular Networks in Critical Illness Associated Muscle Weakness: Skeletal Muscle Proteostasis in the Intensive Care Unit
Banduseela, V. C. 2012. Molecular And Cellular Networks in Critical Illness Associated
Muscle Weakness: Skeletal Muscle Proteostasis in the Intensive Care Unit. Acta Universitatis
Upsaliensis. Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Medicine 841. 63 pp. Uppsala. ISBN 978-91-554-8542-9. IGF-1/AKT/mTor pathway, autophagy lysosome pathway, the branches of the UPR pathway and proteostasis network and protein fates pathway drawn using pathway builder(Figs 2, 3, 5 & 6).
- Methods of predicting response of a neoplasm to an EGFR inhibitor and detecting interactions between EGFR and an EGFR regulatory protein
Plans to use the Protein Lounge Protein Intraction Database to identify potential EGFR interactive proteins.
- Pathophysiology of GPCR Homo- and Heterodimerization:
Special Emphasis on Somatostatin Receptors
Somvanshi RK and U Kumar. Pharmaceuticals 5: 417-446. Used PathwayBuilder from ProteinLounge to depict regulation of receptor signaling through G-proteins(Fig 1A-D).
- Interaction among apoptosis-associated sequence variants and joint effects on aggressive prostate cancer
ProteinLounge database used to determine 73 apoptosis related genes. ProteinLounge tools used to visualize gene-gene and protein-protein interactions.
- Characterization of the role of Hydroxyprostaglandin dehydrogenase 15-(NAD)in human regulatory T cells
Modified ProteinLounge IL-2 pathway (Fig 2).
- Srp20 regulates TrkB pre‐mRNA splicing to generate TrkB‐Shc transcripts with implications for Alzheimer''s disease
Pathway Build Tool with minor modifications used: TrkB alternative transcripts and protein isoforms(Fig 1) and Various TrKB compounds (Fig 9).
- Pro- and anti-angiogenic agents
ProteinLounge graphics used to explain the formation of a capillary network around a tumour body(Fig 2).
- INTEGRATIVE SYSTEM BIOLOGY STUDIES ON HIGH THROUGHPUT
GENOMICS AND PROTEOMICS DATASET
Madhankumar Sonachalam. Thesis. Protein Lounge Pathway Database mentioned as a source for Human Pathway Database
- PRODUCER CELLS FOR REPLICATION COMPETENT RETROVIRAL VECTORS
Patent. Plans to use the ProteinLounge siRNA database to find suitable siRNA sequences and targets.
- MMMDB: Mouse Multiple Tissue Metabolome Database
Mentioned as Pathway Database.
- Functional genomics studies of Rhipicephalus (Boophilus) annulatus ticks in response to infection with the cattle protozoan parasite, Babesia bigemina
Protein Lounge database was used to analyze protein ontology.
- Role of estrogen and estrogen receptors in cancer pathology
Pathway Builder Tool used to create ligand-dependent pathways of estrogen (Fig 1).
- Database Resources for Proteomics-Based Analysis of Cancer
Zhang GL, DS DeLuca, and V Brusic. Protein Microarray for Disease Analysis: Methods and Protocols, Methods in Molecular Biology, 723: 349-364. Human Pathway Database is mentioned as containing data from Protein Lounge.
- Effects of Novel Angiogenesis Inhibitors for the Treatment of Cancer on the Cardiovascular System.
VEGF Pathway Figure. Protein Lounge Pathway Templates.
- Zymosan suppresses leukotriene C4 synthase activity in differentiating monocytes: antagonism by aspirin and protein kinase inhibitors.
Used Pathway Builder to design a graphic representing proposed mechanisms for control of LTC4S activity during differentiation of monocytic cells(Figure not labeled).