Data integration of CMGene and how to use CMGene:
1. Data integration of CMGene database Four steps to collect cancer metastasis genes Curation cancer metastasis genes from literature 2. Information for cancer metastasis genes General information and literature evidence Gene expression profile Gene regulation Mutation information Protein-protein interaction 3. Query and search database Text search of cancer metastasis gene Quick access information in database Blast all protein and nucleotide sequences 4. Browse database By chromosome and cancer type By marked KEGG pathway 5. Data download
Data integration of CMGene database
The primary aim of the database is to support cancer metastasis research by maintaining a high quality cancer metastasis gene database that serves as a comprehensive, fully classified, richly and accurately annotated cancer metastasis gene resource, with extensive cross-references and querying interfaces freely accessible to the scientific community.
Four steps to collect cancer metastasis genes
Construction of this cancer metastasis gene database for Human genes involved four main steps: query cancer metastasis-related literatures; identification of the description related to cancer metastasis; mapping the description of cancer metastasis 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 cancer metastasis genes from the literature includes five steps before finally being included in the CMGene database: exhaustive searching for relevant abstracts from the PubMed databases using the key words "cancer metastasis gene;" extracting the description for the cancer metastasis 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 cancer metastasis genes; lastly, mapping the gene name to Entrez geneID.
Exhaustive search: To gain precise abstracts related to cancer metastasis, we queried PubMed using the expression: ("cancer metastasis"[Title/Abstract] OR ("metastatic"[Title/Abstract] AND ("cancer"[Title/Abstract] OR "tumor"[Title/Abstract] OR "carcinoma" [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 "hereditable"[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]))) AND "humans" [MeSH Terms]. This query return a total of 8054 PubMed abstracts on 20th, Jan 2015. In addition, we also use the regular expression to search GeneRif database using "Metastasis" and "Metastatic" on 24 Mar, 2015. As a result, 5989 PubMed abstracts were collected. Combined with PubMed searching results, we have 9158 PubMed abstract for manual curation.
Curation of cancer metastasis genes from literatures
Extracting description: To evaluate the information about cancer metastasis 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 cancer metastasis genes. Also, it allows us to access if and how some reference relate to other highly confirmed references about cancer metastasis gene descriptions. Curation: 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 cancer metastasis genes. In these cases, care is taken to look at other references about the same gene. The description line for each cancer metastasis 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 cancer metastasis 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, gene homolog 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 cancer metastasis 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 "metastasis" 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 cancer related mutations were collected from the COSMIC database. The gene homolog page appears as follows: All the homologs from NCBI HomoloGene were collected from its public website data portal 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 cancer metastasis 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 CMGene 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. Step 1: select a specific annotation or field from from the dropdown menu in basic gene information and mutation query forms. Step 2: input the interesting keywords. Step 3: 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 cancer metastasis 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 CMGene database based on their input sequences. The high similarity cancer metastasis 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 cancer metastasis 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 cancer metastasis genes in our database.
Browse database [ top ]
The CMGene database supports browsing cancer metastasis genes using curated cancer types. In the cancer type page, users can explore the top 17 cancer types associated with over 100 genes. In addtion, CMGene also supports annotation-based browsing including chromosome.
Using different chromosomes From the Browser page, users can browse the genes in CMGene by their chromosome location. Moreover, users can obtain the cancer metastasis gene lists from different cancer type and highlighted KEGG pathways.
Data analysis and download [ top ]
Users can freely download all the cancer metastasis genes in CMGene 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 CMGene or to revise wrong information in current CMGene,please send us email directly.

Data integration of CMGene and how to use CMGene:

1. Data integration of CMGene database

Four steps to collect cancer metastasis genes

Curation cancer metastasis genes from literature

2. Information for cancer metastasis genes

General information and literature evidence

Gene expression profile

Gene regulation

Mutation information

Protein-protein interaction

3. Query and search database

Text search of cancer metastasis gene

Quick access information in database

Blast all protein and nucleotide sequences

4. Browse database

By chromosome and cancer type

By marked KEGG pathway

5. Data download

Data integration of CMGene database

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

Four steps to collect cancer metastasis genes

Construction of this cancer metastasis gene database for Human genes involved four main steps: query cancer metastasis-related literatures; identification of the description related to cancer metastasis; mapping the description of cancer metastasis 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 cancer metastasis genes from the literature includes five steps before finally being included in the CMGene database: exhaustive searching for relevant abstracts from the PubMed databases using the key words "cancer metastasis gene;" extracting the description for the cancer metastasis 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 cancer metastasis genes; lastly, mapping the gene name to Entrez geneID.

Exhaustive search:
To gain precise abstracts related to cancer metastasis, we queried PubMed using the expression: ("cancer metastasis"[Title/Abstract] OR ("metastatic"[Title/Abstract] AND ("cancer"[Title/Abstract] OR "tumor"[Title/Abstract] OR "carcinoma" [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 "hereditable"[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]))) AND "humans" [MeSH Terms]. This query return a total of 8054 PubMed abstracts on 20th, Jan 2015. In addition, we also use the regular expression to search GeneRif database using "Metastasis*" and "Metastatic*" on 24 Mar, 2015. As a result, 5989 PubMed abstracts were collected. Combined with PubMed searching results, we have 9158 PubMed abstract for manual curation.

Curation of cancer metastasis genes from literatures

Extracting description:
To evaluate the information about cancer metastasis 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 cancer metastasis genes. Also, it allows us to access if and how some reference relate to other highly confirmed references about cancer metastasis gene descriptions.

Curation:
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 cancer metastasis genes. In these cases, care is taken to look at other references about the same gene. The description line for each cancer metastasis 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 cancer metastasis 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, gene homolog 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 cancer metastasis 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 "metastasis" 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 cancer related mutations were collected from the COSMIC database.

The gene homolog page appears as follows:

All the homologs from NCBI HomoloGene were collected from its public website data portal 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 cancer metastasis 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 CMGene 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.

Step 1: select a specific annotation or field from from the dropdown menu in basic gene information and mutation query forms.

Step 2: input the interesting keywords.

Step 3: 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 cancer metastasis 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 CMGene database based on their input sequences. The high similarity cancer metastasis 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 cancer metastasis 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 cancer metastasis genes in our database.

Browse database [ top ]

The CMGene database supports browsing cancer metastasis genes using curated cancer types. In the cancer type page, users can explore the top 17 cancer types associated with over 100 genes.

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

Using different chromosomes

From the Browser page, users can browse the genes in CMGene by their chromosome location. Moreover, users can obtain the cancer metastasis gene lists from different cancer type and highlighted KEGG pathways.

Data analysis and download [ top ]

Users can freely download all the cancer metastasis genes in CMGene 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 CMGene or to revise wrong information in current CMGene,please send us email directly.