Bgee is a

database In computing, a database is an organized collection of data or a type of data store based on the use of a database management system (DBMS), the software that interacts with end users, applications, and the database itself to capture and a ...

maintained by the

SIB Swiss Institute of Bioinformatics The SIB Swiss Institute of Bioinformatics is an Academia, academic Nonprofit organization, not-for-profit Foundation (charity), foundation which federates bioinformatics activities throughout Switzerland. The institute was established on 30 ...

and the

University of Lausanne The University of Lausanne (UNIL; ) in Lausanne, Switzerland, was founded in 1537 as a school of Protestant theology, before being made a university in 1890. The university is the second-oldest in Switzerland, and one of the oldest universities ...

for retrieval and comparison of

gene expression Gene expression is the process (including its Regulation of gene expression, regulation) by which information from a gene is used in the synthesis of a functional gene product that enables it to produce end products, proteins or non-coding RNA, ...

patterns from

RNA-Seq RNA-Seq (named as an abbreviation of RNA sequencing) is a technique that uses next-generation sequencing to reveal the presence and quantity of RNA molecules in a biological sample, providing a snapshot of gene expression in the sample, also k ...

, scRNA-Seq,

Microarray A microarray is a multiplex (assay), multiplex lab-on-a-chip. Its purpose is to simultaneously detect the expression of thousands of biological interactions. It is a two-dimensional array on a Substrate (materials science), solid substrate—usu ...

In situ hybridization ''In situ'' hybridization (ISH) is a type of Hybridisation (molecular biology), hybridization that uses a labeled complementary DNA, RNA or modified nucleic acid strand (i.e., a Hybridization probe, probe) to localize a specific DNA or RNA seq ...

and EST studies, across multiple

animal Animals are multicellular, eukaryotic organisms in the Biology, biological Kingdom (biology), kingdom Animalia (). With few exceptions, animals heterotroph, consume organic material, Cellular respiration#Aerobic respiration, breathe oxygen, ...

species A species () is often defined as the largest group of organisms in which any two individuals of the appropriate sexes or mating types can produce fertile offspring, typically by sexual reproduction. It is the basic unit of Taxonomy (biology), ...

. Bgee provides an intuitive answer to the question ''where is a gene expressed?'' and supports research in

cancer Cancer is a group of diseases involving Cell growth#Disorders, abnormal cell growth with the potential to Invasion (cancer), invade or Metastasis, spread to other parts of the body. These contrast with benign tumors, which do not spread. Po ...

and

agriculture Agriculture encompasses crop and livestock production, aquaculture, and forestry for food and non-food products. Agriculture was a key factor in the rise of sedentary human civilization, whereby farming of domesticated species created ...

, as well as

evolutionary biology Evolutionary biology is the subfield of biology that studies the evolutionary processes such as natural selection, common descent, and speciation that produced the diversity of life on Earth. In the 1930s, the discipline of evolutionary biolo ...

. Bgee is based exclusively on curated, healthy

wild-type The wild type (WT) is the phenotype of the typical form of a species as it occurs in nature. Originally, the wild type was conceptualized as a product of the standard "normal" allele at a locus, in contrast to that produced by a non-standard, " ...

, expression data (i.e., no gene knock-out, no treatment, no

disease A disease is a particular abnormal condition that adversely affects the structure or function (biology), function of all or part of an organism and is not immediately due to any external injury. Diseases are often known to be medical condi ...

), to provide a comparable reference of healthy wild-type gene expression. Bgee produces calls of presence/absence of expression, and of differential over-/under-expression, integrated along with information of gene orthology, and of homology between

organs In a multicellular organism, an organ is a collection of tissues joined in a structural unit to serve a common function. In the hierarchy of life, an organ lies between tissue and an organ system. Tissues are formed from same type cells to a ...

. This allows comparisons of expression patterns between

. Bgee allows searches by

gene In biology, the word gene has two meanings. The Mendelian gene is a basic unit of heredity. The molecular gene is a sequence of nucleotides in DNA that is transcribed to produce a functional RNA. There are two types of molecular genes: protei ...

organ Organ and organs may refer to: Biology * Organ (biology), a group of tissues organized to serve a common function * Organ system, a collection of organs that function together to carry out specific functions within the body. Musical instruments ...

/ tissue /

cell type A cell type is a classification used to identify cells that share morphological or phenotypical features. A multicellular organism may contain cells of a number of widely differing and specialized cell types, such as muscle cells and skin cell ...

and developmental stage. Bgee is a part of Global Core Biodata Resources (GCBRs) representing "critical components for ensuring the

reproducibility Reproducibility, closely related to replicability and repeatability, is a major principle underpinning the scientific method. For the findings of a study to be reproducible means that results obtained by an experiment or an observational study or ...

and

integrity Integrity is the quality of being honest and having a consistent and uncompromising adherence to strong moral and ethical principles and values. In ethics, integrity is regarded as the honesty and Honesty, truthfulness or of one's actions. Integr ...

of life sciences research." Bgee is also an

ELIXIR An elixir is a sweet liquid used for medical purposes, to be taken orally and intended to cure one's illness. When used as a dosage form, pharmaceutical preparation, an elixir contains at least one active ingredient designed to be taken orall ...

Recommended Interoperability Resources that facilitate the

FAIR A fair (archaic: faire or fayre) is a gathering of people for a variety of entertainment or commercial activities. Fairs are typically temporary with scheduled times lasting from an afternoon to several weeks. Fairs showcase a wide range of go ...

-supporting activities in scientific research.

References

External links

* * * {{cite web , title = About Bgee , date = 4 January 2021 , url = https://www.sib.swiss/news/from-v1-to-v14-the-gene-expression-database-bgee-under-the-spotlight , publisher = SIB Swiss Institute of Bioinformatics Genetics databases Genomics Open science Ontology Evolutionary developmental biology Subfields of evolutionary biology Developmental biology Science and technology in Switzerland

References

Further reading

External links