BrainBase: a curated knowledgebase for brain diseases

Liu, Lin; Zhang, Yang; Niu, Guangyi; Li, Qianpeng; Zhao, Li; Zhu, Tongtong; Feng, Changrui; Liu, Xiaonan; Zhang, Yuansheng; Xu, Tianyi; Chen, Ruru; Teng, Xufei; Zhang, Rongqin; Zou, Dong; Ma, Lina; Zhang, Zhang

doi:10.1093/nar/gkab987

Cited by 13 publications

(9 citation statements)

References 65 publications

(67 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Gene Ontology enrichment analysis of these overlapping 620 proteins using WebGestalt [33] revealed biological processes related to nervous system such as development of synapse and axon (Figure 2D). We further mapped the identified proteins to the list of proteins in BrainBase which contains curated entries associated with brain‐related diseases [34]. Among them, 3120 central nervous system disease‐related genes were compared to the identified proteins in our study, which resulted in 662 overlapping proteins corresponding to 44 different diseases.…”

Section: Resultsmentioning

confidence: 99%

Four‐dimensional proteomics analysis of human cerebrospinal fluid with trapped ion mobility spectrometry using PASEF

et al. 2023

View full text Add to dashboard Cite

A quadrupole time-of-flight mass spectrometer coupled with a trapped ion mobility spectrometry (timsTOF) operated in parallel accumulation-serial fragmentation (PASEF) mode has recently emerged as a platform capable of providing fourdimensional (4D) features comprising of elution time, collision cross section (CCS), mass-to-charge ratio, and intensity of peptides. The PASEF mode provides ∼100% ion sampling efficiency both in data-dependent acquisition (DDA) and data-independent acquisition (DIA) modes without sacrificing sensitivity. In addition, targeted measurements using PASEF integrated parallel reaction monitoring (PRM) mode have also been described. However, only limited number of studies have used timsTOF for analysis of clinical samples. Although Orbitrap mass spectrometers have been used for biomarker discovery from cerebrospinal fluid (CSF) in a variety of neurological diseases, these Orbitrap-derived datasets cannot readily be applied for driving experiments on tim-sTOF mass spectrometers. We generated a catalog of peptides and proteins in human CSF in DDA mode on a timsTOF mass spectrometer and used these data to build a spectral library. This strategy allowed us to use elution times and ion mobility values from the spectral library to design PRM experiments for quantifying previously discovered biomarkers from CSF samples in Alzheimer's disease. When the same samples were analyzed using a DIA approach combined with a spectral library search, a higher number of proteins were identified than in a library-free approach. Overall, we have established a spectral library of CSF as a resource and demonstrated its utility for PRM and DIA studies, which should facilitate studies of neurological disorders.

show abstract

Section: Resultsmentioning

confidence: 99%

Four‐dimensional proteomics analysis of human cerebrospinal fluid with trapped ion mobility spectrometry using PASEF

et al. 2023

View full text Add to dashboard Cite

show abstract

“…BrainBase ( https://ngdc.cncb.ac.cn/brainbase , detailed in ( 35 ) in this issue) is a curated knowledgebase for brain diseases with the aim to provide a whole picture of brain diseases and associated genes. Compared to the previous version that contains 4248 associations and 3996 genes in August 2020, the current version houses 7175 disease-gene associations, spanning a total of 123 brain diseases and linking with 5662 genes.…”

Section: Recent Updatesmentioning

confidence: 99%

Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2022

Partners¹

2021

Nucleic Acids Research

Self Cite

423

162

View full text Add to dashboard Cite

The National Genomics Data Center (NGDC), part of the China National Center for Bioinformation (CNCB), provides a family of database resources to support global research in both academia and industry. With the explosively accumulated multi-omics data at ever-faster rates, CNCB-NGDC is constantly scaling up and updating its core database resources through big data archive, curation, integration and analysis. In the past year, efforts have been made to synthesize the growing data and knowledge, particularly in single-cell omics and precision medicine research, and a series of resources have been newly developed, updated and enhanced. Moreover, CNCB-NGDC has continued to daily update SARS-CoV-2 genome sequences, variants, haplotypes and literature. Particularly, OpenLB, an open library of bioscience, has been established by providing easy and open access to a substantial number of abstract texts from PubMed, bioRxiv and medRxiv. In addition, Database Commons is significantly updated by cataloguing a full list of global databases, and BLAST tools are newly deployed to provide online sequence search services. All these resources along with their services are publicly accessible at https://ngdc.cncb.ac.cn.

show abstract

“…The enrichment of Genome-Wide Association Studies (GWAS) Catalog 2019 were performed by enrichr [22]. We also performed over-enrichment analysis of sex-biased genes in a curated brain diseased and drugtarget genes from BrainBase database [23] using Fisher's exact test. To compare enriched terms across brain regions, top five significantly enriched categories of each brain regions were selected and plotted for visualizations for the enrichment.…”

Section: Gene Enrichment Analysis and Disease Related Gene Analysismentioning

confidence: 99%

“…It is well documented that males and females have differential response to many drugs. We used drug-target interactions covering 2118 drugs or chemicals and 623 genes from BrainBase database [23] to calculate the enrichment for drugs in sex-biased genes. Many drug targets were enriched for sex-biased genes (P value <0.0001) in both males and females, particularly in FC, PL and TC brain regions.…”

Section: Sex-biased Drug Responsementioning

confidence: 99%

Integrated analysis of robust sex-biased gene signatures in human brain.

Wapeesittipan

Joshi

2023

Preprint

View full text Add to dashboard Cite

Background: Sexual dimorphism is highly prominent in mammals with many physiological and behavioral differences between male and female form of the species. Accordingly, the fundamental social and cultural stratification factors for humans is sex. The sex differences are thought to emerge from a combination of genetic and environmental factors. It distinguishes individuals most prominently on the reproductive traits, but also affects many of the other related traits and manifest in different disease susceptibilities and treatment responses across sexes. Sex differences in brain have raised a lot of controversy due to small and sometimes contradictory sex-specific effects. Many studies have been published to identify sex-biased genes in one or several brain regions but the assessment of the robustness of these studies is missing. We therefore collected huge amount of publicly available transcriptomic data to first estimate whether consistent sex differences exist and further explore their likely origin and functional significance. Results and Conclusion: In order to systematically characterise sex specific differences across human brain regions, we collected transcription profiles for more than 16,000 samples from about fifty datasets across eleven brain regions. By systematic integration of the data from multiple studies, we identified robust transcription level differences in human brain across to identify male-biased and female-biased genes in each brain region. Firstly, both male and female-biased genes were highly conserved across primates and showed a high overlap with sex-biased genes in other species. Female-biased genes were enriched for neuron-associated processes while male-biased genes were enriched for membranes and nuclear structures. Male-biased genes were enriched on the Y chromosome while female-biased genes were enriched on the X chromosome, which included X chromosome inactivation escapees explaining the origins of some sex differences. Male-biased genes were enriched for mitotic processes while female-biased genes were enriched for synaptic membrane and lumen. Finally, sex-biased genes were enriched for drug-targets and more female-biased genes were affected by adverse drug reactions than male-biased genes. In summary, by building a comprehensive resource of sex differences across human brain regions at gene expression level, we explored their likely origin and functional significance. We have also developed a web resource to make the entire analysis available for the scientific community for further exploration, available at https://joshiapps.cbu.uib.no/SRB app/.

show abstract

BrainBase: a curated knowledgebase for brain diseases

Cited by 13 publications

References 65 publications

Four‐dimensional proteomics analysis of human cerebrospinal fluid with trapped ion mobility spectrometry using PASEF

Four‐dimensional proteomics analysis of human cerebrospinal fluid with trapped ion mobility spectrometry using PASEF

Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2022

Integrated analysis of robust sex-biased gene signatures in human brain.

Contact Info

Product

Resources

About