Tag Archives: databases

The Database of Biomarkers: Depression – fMRI Biomarkers

The Database of Biomarkers: Depression – fMRI Biomarkers •    Potential Biomarkers: Activation patterns: “greater and more sustained signals in three regions: BA24 (dorsal anterior cingulate), BA31 (posterior cingulate), and BA6 (prefrontal cortex)” Potential Applications: Diagnostic biomarkers in late-life anxious depression … Continue reading

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The Database of Biomarkers: Depression – EEG Biomarkers

The Database of Biomarkers: Depression – EEG Biomarkers •    Potential Biomarkers: “Midline and right frontal (MRF) cortical area,  early decreases in theta-band cordance” Potential Applications: Predictive biomarker of remission in major depressive disorder (MDD) References: Cook IA, Hunter AM, Abrams … Continue reading

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The Database of Biomarkers: Depression – Proteomic and Pathway Biomarkers

The Database of Biomarkers: Depression – Proteomic and Pathway Biomarkers •    Potential Biomarkers: The tryptophan-kynurenine pathway Detections: Increased indoleamine 2,3-dioxygenase activity Potential Applications: Diagnostic biomarkers References: Christmas DM, Potokar J, Davies SJ. A biological pathway linking inflammation and depression: activation … Continue reading

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The Database of Biomarkers: Depression – Epigenetic Biomarkers

The Database of Biomarkers: Depression – Epigenetic Biomarkers •    Potential Biomarkers: “DNA methylation profiles of CpG I at the promoters of the brain-derived neurotrophic factor (BDNF)” Potential Applications: Diagnostic biomarker References: Fuchikami M, Morinobu S, Segawa M, Okamoto Y, Yamawaki … Continue reading

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The Database of Biomarkers: Depression – MicroRNA Biomarkers

The Database of Biomarkers: Depression – MicroRNA Biomarkers •    Potential Biomarkers: miR-30e, the polymorphism ss178077483 Potential Applications: Diagnostic biomarker for major depressive disorder (MDD) risks References: Xu Y, Liu H, Li F, Sun N, Ren Y, Liu Z, Cao X, … Continue reading

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The Database of Biomarkers: MicroRNA Biomarkers

The Database of Biomarkers: MicroRNA Biomarkers •    Associated diseases/conditions: Obesity and type 2 diabetes Potential Biomarkers: Serum miR-138, miR-15b, miR-376a (obesity); combination of miR-503 and miR-138 (diabetes) Potential Applications: Predictive biomarkers References: Pescador N, Pérez-Barba M, Ibarra JM, Corbatón A, … Continue reading

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The Database of Biomarkers: MicroRNA Biomarkers – Psychiatric Disorders

The Database of Biomarkers: MicroRNA Biomarkers – Psychiatric Disorders •    Associated diseases/conditions: Mild Cognitive Impairment (MCI), age-related brain changes Potential Biomarkers: Brain-enriched plasma the “miR-132 family” (miR-128/miR-491-5p, miR-132/miR-491-5p and mir-874/miR-491-5p) and the “miR-134 family” (miR-134/miR-370, miR-323-3p/miR-370 and miR-382/miR-370) Potential Applications: … Continue reading

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The Database of Biomarkers: MicroRNA Biomarkers – Cardiovascular Diseases

The Database of Biomarkers: MicroRNA Biomarkers – Cardiovascular Diseases •    Associated diseases/conditions: Atherosclerosis and stroke Potential Biomarkers: Serum miR-21 and miR-221 Potential Applications: Predictive biomarkers References: Tsai PC, Liao YC, Wang YS, Lin HF, Lin RT, Juo SH. Serum microRNA-21 … Continue reading

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The Database of Biomarkers: MicroRNA Biomarkers – Cancers

Associated diseases/conditions: Breast cancer in the Mexican population   Potential Biomarkers: Serum circulating miR-145, miR-155 and miR-382   Potential Applications: Diagnostic biomarkers   References: Mar-Aguilar F, Mendoza-Ramírez JA, Malagón-Santiago I, Espino-Silva PK, Santuario-Facio SK, Ruiz-Flores P, Rodríguez-Padilla C, Reséndez-Pérez D. … Continue reading

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The Database of Biomarkers: Proteomic and Pathway Biomarkers

Associated diseases/conditions: Depression   Potential Biomarkers: “Tumor Necrosis Factor (TNF) and its targets in the inflammatory cytokine pathway”   Detections: Protein expressions   Potential Applications: “Predictive biomarkers for treatment response (to the selective serotonin reuptake inhibitor (SSRI) antidepressant escitalopram)”   … Continue reading

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Bioinformatics Databases and Tools for the Discovery of Proteomic and Pathway Biomarkers

BioLayout (http://www.biolayout.org/) Feature: “For the visualization and analysis of network graphs” Cytoscape (http://www.cytoscape.org/) Feature: “Network visualization” E-Cell (http://www.e-cell.org/) Feature: Computational models GelBank (http://gelbank.anl.gov/) Feature: “comparison of 2DE patterns in the context of proteome sequence queries” Gene Ontology (http://www.geneontology.org/) Feature: “Standardizing … Continue reading

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Bioinformatics Resources for MicroRNA (miRNA) Studies and Biomarker Discovery

CircuitsDB (http://biocluster.di.unito.it/circuits/) Feature: “MicroRNA / Transcription Factor Regulatory Circuits in Human and Mouse” deepBase (http://deepbase.sysu.edu.cn/) Feature: “For annotating and discovering small and long ncRNAs” Gene Expression Omnibus database (http://www.ncbi.nlm.nih.gov/geo/) Feature: “The miRNA expression profile” HOCTARdb (http://hoctar.tigem.it/) Feature: “microRNA target prediction” … Continue reading

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Neuroscience Data and Neuroinformatics

Neuroscience Data and Neuroinformatics   Neuroscience Data   At least 50% genes of the mammalian genome are expressed by the nervous system (Sutcliffe et al., 1991). To understand brain-related diseases, it is necessary to map and study the expression patterns … Continue reading

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Neuroinformatics Databases about the Brain: Different Species

Neuroinformatics Databases about the Brain: Different Species   Species Source Name Purposes/Features/Methods Contents Applications URL References Mouse 3D digital atlas database of the mouse brain Lower spatial resolution images were utilized to enhance time efficiency for morphological phenotyping The in … Continue reading

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Neuroinformatics Databases about the Brain-Related Diseases

Neuroinformatics Databases about the Brain-Related Diseases Disease Source Name Purposes/Features/Methods Contents Applications URL References Autism National Database for Autism Research (NDAR) A secure database for data sharing, data harmonization, and collaboration in autism spectrum disorder researchers Data from more than … Continue reading

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Neuroinformatics Databases for the Structure-Function Studies of the Brain

Neuroinformatics Databases for the Structure-Function Studies of the Brain     Category Source Name The Needs/Challenges Purposes/Features/Methods Contents Applications URL References Neuroinformatics Databases about the Brain Structures The Internet Brain Volume Database (IBVD) Available data from neuroanatomic volumetric measurements; Various … Continue reading

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Neuroinformatics: An Introduction

Neuroinformatics: An Introduction The challenges in neuroinformatics   Challenges in making neuroinformatics databases and tools (Morse, 2008) The variety in spatial scales Various data types Traditional bioinformatics concentrates on Genomic and proteomic data Sequences (DNA, RNA, and protein molecules) Development … Continue reading

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