Multi-level Knowledge base for Major Depressive Disorder (MK4MDD) is an innovative informatics tool to integrate different levels of data in published MDD experimental studies and show the dynamic interplay of components in pathophysiological cascade of MDD.
MK4MDD has three notable features: 1) it is the first multi-level knowledge base for MDD. It contains comprehensive disease related components which were categorized into 7 levels in pathophysiological cascade of MDD (genetic/epigenetic locus, protein and other molecule, cell and molecular pathway, neural system, cognition and behavior, symptoms and signs, and environment). Users could acquire systematic knowledge for MDD from the database; 2) MK4MDD emphasizes on the interplay of different levels of data by collecting literature-reported relationships, so that all data in MK4MDD form a cross-linked data network.; 3) MK4MDD is not only a knowledge resource, but also an analysis platform. The powerful search and visualization tools facilitate researchers to generate new hypothesis.
MK4MDD aims to bridge the big gap between DNA sequences and macroscopic human mind. Meanwhile, it demonstrates a novel research framework for interdisciplinary research, which could be applied to other complex psychiatry disorders.
Citation: If you use MK4MDD in your research, please cite the publication: Guo, L., W. Zhang, S. Chang, L. Zhang, J. Ott and J. Wang (2012). "MK4MDD: A Multi-Level Knowledge Base and Analysis Platform for Major Depressive Disorder." PLoS ONE 7(10): e46335. PubMed
|Genetic/Epigenetic Locus||MDD related genetic loci, such as SNPs, genes and genomic regions. and epigenetic modification sites in chromatin.
Most of the genetic loci are from genetic studies (association studies, linkage studies etc.); some genes are from functional studies, such as animal model studies.
Data Statistics: SNP 544 | Gene 1239 | Region 46 | Epigenetic site 478
|Protein and Other Molecule|| MDD related proteins and small molecules (such as transmitters). These studies mainly focus on biological functions of these components.
Data Statistics: Protein 1019 | Molecule 82
|Cell and Molecular Pathway||MDD related cell type such as pyramidal neuron, lymphocytes and
intracellular or intercellular molecular pathways that have been recorded in GO,
Biocarta, or KEGG.
Data Statistics: Pathway 103 | Cell 25
|Neural System||MDD related changes in electroneurographic signals and comprehensive systems,
which usually contain multiple molecules, molecular pathways and cells (such as transmitter system),
and structural and functional brain changes.
In most studies, participants are MDD patients and normal controls.
Data Statistics: Neurobiological system 39 | Brain morphology and function 338
|Cognition and Behavior||Cognitive impairments and cognitive characteristics of MDD patients
(attention, memory, learning, language, emotional regulation and so on),
as well as depression/anxiety-like behaviors from animal models.
Data Statistics: Cognition and behavior 45
|Symptoms and Signs||Clinical signs and diagnostic symptoms for MDD in DSM-IV (except cognitive impairments).
Data Statistics: Symptoms 32 | Signs 24
|Environment||Environmental events that are putative risk factors for MDD.
Data Statistics: Environment 27