Meningioma protein-protein interaction network.
BACKGROUND
Meningioma is one of the most common central nervous system tumors that derived from meningothelial (arachnoid cap) cells. This paper identified the network-based Protein-Protein Interactions (PPI) for meningioma relative to healthy control.


METHODS
Gene expression data including 384 gene or protein names extracted from a number of beforehand investigations.


RESULTS
Out of these 384 proteins, 176 were found to be exclusively expressed in meningiomas and 208 proteins were down-regulated. The networks of related differentially expressed genes were explored using cytoscape and the PPI analysis methods such as MCODE and ClueGO. Results analysis introduced a number of hub proteins and 27 clusters (protein complex) with distinctive seed genes. Identified ClueGO Pathways based on subnetworks mined by MCODE composed of positive regulation in RBC homeostasis, dysregulation of transport from ER to Golgi, disruption regulation of cell cycle and antigen processing and presentation of exogenous peptide antigen and neutralization of exogenous dsRNA. Combination of over expression of TCEA1, UBE2E1, XRCC5, IFIT1, IFIT-3, MCM2, and MCM7 and under expression of CDC25A, SEC31A, and CDK6 can serve as diagnostic biomarker panel for meningiomas.


CONCLUSIONS
These introduced network-based biomarkers for the meningioma patterns may be helpful in diagnosis, prognosis and treatment processes however biomarker validation is necessary.
Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran.rezaei.tavirani@ibb.ut.ac.ir.
Hakimeh
H
Zali
Proteomics Research Center, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
Mostafa
M
Rezaei Tavirani
D048868:Adaptor Proteins, Signal Transducing; D014408:Biomarkers, Tumor / Q000235:genetics*; D002352:Carrier Proteins / Q000235:genetics; D051361:Cyclin-Dependent Kinase 6 / Q000235:genetics; D004265:DNA Helicases / Q000235:genetics; D057225:Data Mining; D015536:Down-Regulation; D015870:Gene Expression; D063990:Gene Ontology; D006801:Humans; D047908:Intracellular Signaling Peptides and Proteins / Q000235:genetics; D000072200:Ku Autoantigen; D008577:Meningeal Neoplasms / Q000235:genetics* / Q000378:metabolism; D008579:Meningioma / Q000235:genetics* / Q000378:metabolism; D064111:Minichromosome Maintenance Complex Component 2 / Q000235:genetics; D064168:Minichromosome Maintenance Complex Component 7 / Q000235:genetics; D060066:Protein Interaction Maps; D016601:RNA-Binding Proteins; D035602:Transcriptional Elongation Factors / Q000235:genetics; D044763:Ubiquitin-Conjugating Enzymes / Q000235:genetics; D015854:Up-Regulation; D033921:Vesicular Transport Proteins / Q000235:genetics; D020687:cdc25 Phosphatases / Q000235:genetics
D048868:Adaptor Proteins, Signal Transducing; D014408:Biomarkers, Tumor; D002352:Carrier Proteins; C484290:IFIT1 protein, human; C116468:IFIT3 protein, human; D047908:Intracellular Signaling Peptides and Proteins; D016601:RNA-Binding Proteins; C507455:SEC31A protein, human; D035602:Transcriptional Elongation Factors; D033921:Vesicular Transport Proteins; C018648:transcription factor S-II; C489963:UBE2E1 protein, human; D044763:Ubiquitin-Conjugating Enzymes; C495911:CDK6 protein, human; D051361:Cyclin-Dependent Kinase 6; C517004:CDC25A protein, human; D020687:cdc25 Phosphatases; D004265:DNA Helicases; C084859:MCM2 protein, human; C101624:MCM7 protein, human; D064111:Minichromosome Maintenance Complex Component 2; D064168:Minichromosome Maintenance Complex Component 7; C106893:XRCC5 protein, human; D000072200:Ku Autoantigen