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BRAin INteractive Sequencing Analysis Tool (BRAIN-SAT); facilitating interactive transcriptome analyses (http://brainsat.eu/)

Dubbelaar, M. L.; Brummer, M. L.; Meijer, M.; Eggen, B. J. L.; Boddeke, E. W. G. M.

2019-08-30 neuroscience
10.1101/750000 bioRxiv
Show abstract

Over the last decade, a large number of glia transcriptome studies has been published. New technologies and platforms have been developed to allow access and interrogation of the published data. The increase in large transcriptomic data sets allows for innovative in silico analyses to address biological questions. Here we present BRAIN-SAT, the follow-up of our previous database GOAD, with several new features available on an interactive platform that enables access to recent, high quality bulk and single cell RNA-Seq data. The combination of several functions including gene searches, differential and quantitative expression analysis and a single cell expression analysis feature enables the exploration of published data sets at different levels. These different functionalities can be used for researchers and research companies in the neuroscience field to evaluate and visualize gene expression levels in a set of relevant publications. Here, we present a new platform with easy access to published gene expression studies for data exploration and gene of interest searches.

Matching journals

The top 8 journals account for 50% of the predicted probability mass.

1
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Top 0.2%
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8
PLOS ONE
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Top 29%
4.9%
50% of probability mass above
9
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○ 41 papers in training set
Top 0.2%
3.2%
10
NAR Genomics and Bioinformatics
◐ 242 papers in training set
Top 2%
2.8%
11
BMC Bioinformatics
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2.7%
12
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13
BMC Biology
○ 265 papers in training set
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1.9%
14
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Top 3%
1.7%
15
eneuro
● 439 papers in training set
Top 4%
1.7%
16
Frontiers in Neuroscience
○ 256 papers in training set
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1.5%
17
Biomedicines
○ 67 papers in training set
Top 2%
1.1%
18
Journal of Visualized Experiments
● 34 papers in training set
Top 0.4%
1.1%
19
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Top 0.4%
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20
Current Protocols
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21
Nucleic Acids Research
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22
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Biology of Sex Differences
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PLOS Computational Biology
● 1863 papers in training set
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STAR Protocols
○ 18 papers in training set
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Heliyon
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Top 8%
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28
iScience
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29
PROTEOMICS
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Frontiers in Genetics
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"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.