LEXAS - Lifescience experiment search and suggestion -

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Overview

LEXAS is a text-mining-based web application that helps life science researchers to efficiently design biological experiments.
With LEXAS, you can quickly find biological experiments and receive suggestions for the next experiments from machine learning models.


How to use

1. Enter a gene name and select an experimental method

2. The matching experiments are shown

How to read the result table

Suggestion

How to use

1. Enter the gene name that you have analyzed experimentally and select an information source

2. The genes to be analyzed in the next experiment are shown.

How to read the result table

List of information sources

In LEXAS, we refer to an information source annotated manually by trained researchers or medical doctors as a knowledgebase, and an objective information source such as expression levels as a database.

Information SourceInformation typeDescriptionTerm in the result table
Gene OntologyKnowledgebaseBiological process, molecular function, and cellular component GO: XXXXX
Mouse genome informaticsDatabasePhenotypes of knockout miceMP: XXXXX
Human phenotype ontologyDatabasePhenotypic abnormalities in humanHP: XXXXX
Online Mendelian Inheritance in ManKnowledgebaseGenetic diseasesOMIM: XXXXX
OrphanetKnowledgebaseGenetic diseasesORPHA: XXXXX
Human protein atlas (1)DatabaseSubcellular localization(A name of cellular component)
Human protein atlas (2)DatabaseExpression levels among human tissues(A name of tissue)-(H/L)-(Level)*
BioGRIDDatabaseProtein-protein interactionBG: XXXXX
DepMapDatabaseCancer cell growth under CRISPR/Cas9 mediated suppression of genesDepMap
ENCODEDatabaseTranscription factorTF: XXXXX
Word2VecKnowledgebaseThe similarity of the usage of gene terms in the MEDLINE abstractWord2Vec

* (example) Testis-H5: Expression level of a gene in testis is much higher than those in other tissues.
* (example) Testis-H1: Expression level of a gene in testis is a little higher than those in other tissues.

Contributors

Graduate School of Pharmaceutical Sciences, The University of Tokyo

Kei K Ito
Daiju Kitagawa

Graduate School of Information Science and Technology, The University of Tokyo

Yoshimasa Tsuruoka

Contact/Feedback

lexas.f.utokyo [at] gmail.com

Version

VersionDateContent
1.01
current: December 3, 202120120 genes in 1 organism (human) Examples of usage are posted on the website.
1.0
October 25, 202120120 genes in 1 organism (human)

Acknowledgement

LEXAS relies on many information sources:

PubMed centralHGNCGOMGIHPOOMIMOrphanetHPABioGRIDDepMapENCODESTRING

We gratefully acknowledge these resources.

Software

LEXAS is built using Python version 3.6.9

Citation

LEXAS: a web application for life science experiment search and suggestion
Kei K Ito, Yoshimasa Tsuruoka, Daiju Kitagawa
bioRxiv 2021.12.05.471323;
doi: https://doi.org/10.1101/2021.12.05.471323

Licensing

Search

Creative Commons License

All data and download files in LEXAS "Search" are licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.

When using the LEXAS "Search" data, please indicate proper credit and do not add any modifications to the data.

Suggestion

Creative Commons License

All data and download files in LEXAS "Suggestion" are licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.

When using the LEXAS "Suggestion" data, please indicate proper credit and inform the users of any modifications that you added to the data.

Source code

The source code may be used for non-commercial purposes. If you want to use the source code for a commercial purpose, please contact the following email addresses.
Miho Sakao : sakao [at_mark] todaitlo.jp