Epithelial-Mesenchymal Transition gene database (dbEMT) Home
Pediatric cancer database

Data collection of dbEMT and how to use dbEMT:

1. Data collection of dbEMT database

    Four steps to collect Epithelial-Mesenchymal Transition genes

    Curation Epithelial-Mesenchymal Transition genes from literature

2. Information for Epithelial-Mesenchymal Transition genes

    General information and literature evidence

    Gene expression profile

    Gene regulation

    Mutation information

    Protein-protein interaction

3. Query and search database

    Text search of Epithelial-Mesenchymal Transition gene

    Quick access information in database

    Blast all protein and nucleotide sequences

4. Browse database

    By chromosome and gene symbols

    By KEGG pathway

5. Data download

Data collection of dbEMT database

The primary aim of the database is to support Epithelial-Mesenchymal Transition research by maintaining a high quality Epithelial-Mesenchymal Transition gene database that serves as a comprehensive, fully classified, richly and accurately annotated Epithelial-Mesenchymal Transition gene resource, with extensive cross-references and querying interfaces freely accessible to the scientific community.

Four steps to collect Epithelial-Mesenchymal Transition genes

Construction of this Epithelial-Mesenchymal Transition gene database for Human genes involved four main steps: query Epithelial-Mesenchymal Transition-related literatures; identification of the description related to Epithelial-Mesenchymal Transition; mapping the description of Epithelial-Mesenchymal Transition genes from literatures to Entrez gene database IDs; extensive annotations of cellular function, gene expression, mutation, methylation, transcription factor, post-translational modification, and protein-protein interaction.

In detail, curation about Epithelial-Mesenchymal Transition genes from the literature includes five steps before finally being included in the dbEMT database: exhaustive searching for relevant abstracts from the PubMed databases using the key words "Epithelial-Mesenchymal Transition gene;" extracting the description for the Epithelial-Mesenchymal Transition gene from text; grouping the descriptions extracted from PubMed abstracts records by their topics using Entrez related topic function; extraction of gene name from the grouped descriptions of the Epithelial-Mesenchymal Transition genes; lastly, mapping the gene name to Entrez geneID.

Exhaustive search:
To gain precise abstracts related to Epithelial-Mesenchymal Transition, we queried PubMed using the expression: ("Epithelial-mesenchymal transition"[Title/Abstract] OR "Epithelial mesenchymal transition"[Title/Abstract] OR "EMT"[Title/Abstract]) AND (("genome-wide association study" [Title/Abstract] OR "genome wide association study" [Title/Abstract]) OR ("gene"[Title/Abstract] AND ("association"[Title/Abstract] OR "microarray" [Title/Abstract] OR "expression" [Title/Abstract] OR "linkage" [Title/Abstract] OR "proteomics" [Title/Abstract] OR "genetic" [Title/Abstract] OR "metabolomics" [Title/Abstract] OR "copy number variation" [Title/Abstract] OR "idiopathic" [Title/Abstract] OR "hereditable" [Title/Abstract] OR "family" [Title/Abstract] OR "mouse model" [Title/Abstract] OR "animal model" [Title/Abstract] OR "microRNA" [Title/Abstract] OR "mutation" [Title/Abstract] OR "SNP" [Title/Abstract] OR "drug" [Title/Abstract] OR "transporter" [Title/Abstract]))) with a return of 1507 PubMed abstracts on 19th, Dec 2013.

Extracting description:
To evaluate the information about Epithelial-Mesenchymal Transition gene, the sentences containing keywords cancer, pediatric, childhood, or tumor were extracted from all the PubMed abstracts.

Group abstracts:
All the downloaded abstracts are grouped based on topic according to related articles provided by the Entrez. This allows us, quickly and easily, to assess if and how certain gene names are highly related with Epithelial-Mesenchymal Transition genes. Also, it allows us to access if and how some reference relate to other highly confirmed references about Epithelial-Mesenchymal Transition gene descriptions.

In this step, we manually check the abstracts, assess the context given, and add relevant comments and features to the entry. Often from reading the abstract, we can judge whether the described gene belongs to Epithelial-Mesenchymal Transition genes. In these cases, care is taken to look at other references about the same gene. The description line for each Epithelial-Mesenchymal Transition gene is added to the new entry.

Mappping the gene symbols:
A major step in the process of curating an article is mapping the gene name in text to an Entrez gene ID, which will serve as the initial information to crosslink the gene in other public databases. Much care is taken with the synonyms of the gene symbol, and some synonyms deleted or transferred Entrez gene ID.

Information for Epithelial-Mesenchymal Transition genes  [ top ]

Information is represented on six different types of pages, including general information view, literature highlight view, gene expression view, gene regulation view, gene mutation view, and gene interaction view.

The general information page is like the following:

In this page, users can find the data source and our curated descriptions for Epithelial-Mesenchymal Transition genes from literature. It is easy to switch to other annotations by clicking the hyperlink at the top of the page.

User can find the details of the literatures with keywords highlighted in the literature highlight page as below. The keyword "pediatric" and "childhood" is marked in red; keywords such as "cancer" and "pathway" are marked in brown; and the keywords such as "mutation" and "expression" are marked in black as shown in below.

The gene expression page is as below:

In the page, users can find gene expression profiles from 184 human tumor samples and 84 normal tissue samples from BioGPS. It is easy to view all the sample information by clicking the hyperlink in the profile images. Some genes have multiple probes; to provide an unbiased view for users, we presented all the gene expressions from all probes without any modification.

User can obtain all the sample inforamtion by clicking on the expression images.

The gene regulation page appears as follows:

The transcription factor regulation and post-transcriptional modification information were integrated from the TRANSFAC and dbPTM databases. In addition, the methylation in promoter regions was annotated based on data from the DiseaseMeth database.

The gene mutation page appears as follows:

All the mutations from Pediatric Cancer Genome Project (PCGP) were collected from its public website data portal All the other cancer related mutations were collected from the COSMIC database.

The gene interaction page appears as follows:

All the related protein-protein interactions were collected from the PathwayCommon database; we further divided the interactions into three main types, including "Physical Interaction," "Metabolic Interaction," and "Signaling Interaction."

Query and sequence search against database   [ top ]

All the Epithelial-Mesenchymal Transition genes and their annotations in our database are searchable. The text search (Query) and sequence-based blast (Blast) are provided.

Text search of various annotation in our database

Users can search against the dbEMT by typing its name, accession IDs and its characteristics, including genomic location, interaction partner, mutation, biological pathway, and genetic disease. In total, we provided four different search forms for users, including "Gene General Information Search", "Literature Search", "Mutation Search", and "Other Annotation Search" allow users to access general information, literature-based information, mutation, and other annotation information respectively.

The search is performed by typing keywords into any field separately or into several fields simultaneously in the query forms. Generally, text search information in the each searching form mainly includes three steps. Take the basic information query as an example below

  • select a specific annotation or field from from the dropdown menu in basic gene information and mutation query forms.

  • Input your interesting keyword.

  • In addition, the basic gene information and mutation query forms support the logical 'And,' 'Or,' and 'Not' operators to combine multiple keywords.

    The search result shows the list of matched Epithelial-Mesenchymal Transition genes linked to the detailed gene information page below.

    Quick search a list of genes in database:

    To quickly access the information in the database, a quick search form is provided at the top of each page.

    Blast all sequences of genes in our database

    In the BLAST menu, users can search the dbEMT database based on their input sequences. The high similarity Epithelial-Mesenchymal Transition genes with input sequences will be listed in the BLAST result page. In the input page, users can choose various sequence alignment options such as E-value and identity. The matched sequence signatures are visualized on the query sequence.

    To do a sequence-based search for all the Epithelial-Mesenchymal Transition genes, please access the BLAST pagepage.

    The output of BLAST is as below

    Click on the hyperlink in the Blast result page, users can access the Epithelial-Mesenchymal Transition genes in our database.

  • Browse database  [ top ]

    The dbEMT database supports browsing Epithelial-Mesenchymal Transition genes using cancer types and curated organ and tissue types. In the cancer type page, users can explore the 288 Epithelial-Mesenchymal Transition types. In addition, to help users get a bird's eye view for specific topic of Epithelial-Mesenchymal Transition genes, the classified organ and tissue types were provided.

    In addtion, dbEMT also supports annotation-based browsing including chromosome.

    Using different chromosomes

    From the Browser page, users can browse the genes in dbEMT by their chromosome location. Moreover, users can obtain the Epithelial-Mesenchymal Transition gene lists from genomics regions, KEGG pathway and gene symbol information.

    By KEGG pathway

    From KEGG pathway list, users can easily browser all the related KEGG pathways.

    Data analysis and download   [ top ]

    Users can freely download all the Epithelial-Mesenchymal Transition genes in dbEMT for academic researchers, but not for profit purposes. Please access Download page.

    If users have any suggestion to add new comment to records in current dbEMT or to revise wrong information in current dbEMT,please send us email directly.