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PDDB Frequently Asked Questions(29888)

The questions in the PDDB FAQ are organized into categories which match the links in the left navigation bar.
 
Getting Started
How do I search for a gene?
What are gene pages?
How do I create a PDDB account?
Do you have a list of data sources that you are using within the site and where is the list located?
What public data is available for bulk download and how do I access it?
 
Gene Expression
 
Tissue Expression
What is Tissue Expression?
How is the gene expression data normalized?

Expression Profiles
What is Expression Profiles?

 
Genetics
 
PDMart
What is PD Mart?
What can I do with PD Mart?
What datasets are available?

Genomics
 
GBrowse
What is GBrowse?
Where can I find help on GBrowse?
How do I get to a gene/region in GBrowse?

BLAT Search
What is BLAT Search?
How do I see hits in genomic context?

General
 
Gene Dossier
What is the Gene Dossier?
How do I get more information?
How are the PD-related publications for genes generated?

Connect the Dots
What is Connect the Dots?
How do I use Connect the Dots?

Poster Pages
What are Poster Pages?
How do I create a poster?
How do I share a Poster with Collaborators?

My PDDB
What is My PDDB?
Why create a PDDB account?

Networks & Pathways
 
Cytoscape
What is Cytoscape?
How are interactions between an input protein and "neighbors" determined?

KEGG Pathways
What are KEGG Pathways?

 

 
 
expander Getting Started    Top  
How do I search for a gene?

Enter the identifier in the Search box found in the upper right corner. The Search accepts genes. Some example search terms are: TP53, RB, and EGFR. The results page has a summary of each gene that matched the search term and provides links to pages with more information.

What are gene pages?

Gene pages pull together as much data about one gene as possible.  In light of the fact that disease-research can be focused on a gene, independent of the model organism in which it is studied, and that data from human is sometimes sparse, we have combined data from human, mouse and rat. In order to do so, we have combined data from a number of homology sources, including Homologene, RGD, and MGI.  As new information or tools become available, we add them to the gene page.

How do I create a PDDB account?

Creating an account is simple and fast; just fill out the short form on the login page (this page is accessible via the 'Log In' link in the upper right corner of most PDDB pages). If you require access to private data, please include an email address when registering, and check the 'Request access to private data' box; we will then contact you by email to arrange the details.

Do you have a list of data sources that you are using within the site and where is the list located?

The list of data sources is available by clicking on the number next to Version at the bottom of most PDDB pages.

What public data is available for bulk download and how do I access it?

To see the public data available, click on the Downloads link in the navigation bar.

expander Gene Expression    Top  
expander Tissue Expression    Top  
What is Tissue Expression?

Tissue Expression contains human tissue and cell-type specific gene expression data from the Novartis GNF SymAtlas database.
Su AI, Wiltshire T, Batalov S, Lapp H, Ching KA, Block D, Zhang J, Soden R, Hayakawa M, Kreiman G, Cooke MP, Walker JR, Hogenesch JB (2004) A gene atlas of the mouse and human protein-encoding transcriptomes. Proc Natl Acad Sci U S A. 2004 Apr 20;101(16):6062-7

How is the gene expression data normalized?

The normalization of gene expression data is rank transformation based on signal intensities within the array.  This normalization is performed before the data is added to PDDB.

expander Expression Profiles    Top  
What is Expression Profiles?

Expression Profiles shows differential gene expression across different experimental conditions described in Hwang, D. et al. (2009) A Systems Approach to Prion Disease. Molecular Systems Biology. Pubmed ID: 19308092.

expander Genetics    Top  
expander PDMart    Top  
What is PD Mart?

PD Mart is a tool for retrieving marker and genotype data, and it outputs that data in a variety of formats. It is based on the ideas and libraries of the Biomart.

What can I do with PD Mart?
  • You can retrieve marker information using lists of marker IDs, gene IDs, or chromosomal position; this marker information includes positions, aliases, associated assays, and functional data.
  • PD Mart contains data for both NCBI35 and NCBI36, and can map between the builds.
  • Genotype data can be filtered and output in PED format. For examples, please refer to the PD Mart Help page.
What datasets are available?
  • Markers: dbSNP130 and dbSNP131.
expander Genomics    Top  
expander GBrowse    Top  
What is GBrowse?

The Generic Genome Browser (GBrowse) is a combination of database and interactive web pages for manipulating and displaying annotations on genomes.
Stein LD, Mungall C, Shu S, Caudy M, Mangone M, Day A, Nickerson E, Stajich JE, Harris TW, Arva A, Lewis S. The generic genome browser: a building block for a model organism system database. Genome Res. 2002 Oct;12(10):1599-610.

Where can I find help on GBrowse?

A GBrowse tutorial can be found here

How do I get to a gene/region in GBrowse?

There are a number of ways to view a gene/region in GBrowse. From a non-GBrowse page, enter the search term in the search box in the upper right corner of the page, and on the results page follow the GBrowse link to the relevant organism. From a GBrowse page select the data source of interest from the 'Data Source' and enter the gene or region to be displayed in the 'Landmark or Region' box.

expander BLAT Search    Top  
What is BLAT Search?

BLAT is an effective tool for performing fast and accurate nucleotide alignments between genomic DNA and mRNA taken from the same species.
Kent WJ, BLAT--the BLAST-like alignment tool. Genome Res. 2002 Apr;12(4):656-64.

How do I see hits in genomic context?

The BLAT tool is fully integrated into the PDDB version of Gbrowse. On the results page if you hover over a hit on the idiogram there is an option to visualize your hit in Gbrowse, by clicking on this you should easily be able to see your hit in genomic context.

expander General    Top  
expander Gene Dossier    Top  
What is the Gene Dossier?

The Gene Dossier presents a concise table view of a gene or a list of genes emphasizing PD-specific data.

How do I get more information?

The gene names, check mark icons, and magnifying glass icons are links that lead to more information.

How are the PD-related publications for genes generated?

We link publications to genes using information in several databases, including Entrez Gene and UniProt. We filter these publications to generate a subset relevant to Prion Disease.

expander Connect the Dots    Top  
What is Connect the Dots?

Connect the Dots is a translator for biological identifiers: it can translate among gene symbols, Entrez Gene IDs, Affymetrix probesets, and many more.  All the possible translations are shown on the Create Query screen.

How do I use Connect the Dots?

The three main steps are:  you enter the identifiers you would like to translate, select the type of identifier from the drop-down menu, and select the identifier outputs you want. See the Connect the Dots help page for more details on using Connect the Dots.

expander Poster Pages    Top  
What are Poster Pages?

Posters can be used to group specific topics or datasets, host supplementary material for publications, serve as a data distribution point for particular experiments, or share data among a group of collaborators.

How do I create a poster?

To create a poster page you need to log in. If you have not already done so, you will need to create a new user account. Once logged in click the Poster Pages link in the left navigation bar and follow the 'create a new poster' link. You will then have the option to update the poster title from 'Untitled' to a name of your choice and to add a section by adding a section title and clicking the 'add section' button.

How do I share a Poster with Collaborators?

Posters can be shared with other registered PDDB users by granting read permission on posters and poster sections. You will need to know the PDDB username of the person with which to share the poster. Click on a poster and follow the 'Edit this poster' link at the top of a poster page.  Click on the 'Change poster privileges' link under the poster title. Grant read privileges on the poster by adding the username to 'Readers' section of the form and clicking the 'Add new reader' button. This allows the user to view the poster but not edit it. To allow a user to edit the poster, add them to the 'Writers' section of the form and click the 'Add new writer' button. To allow groups of people to read or edit the poster, change the drop-down menu to be 'group' instead of 'user' and add the groupname to the appropriate section of the form.

expander My PDDB    Top  
What is My PDDB?

My PDDB contains lists of genes, genetic markers (SNPs), and candidate regions (or loci). You can use these lists as starting points for many PDDB programs. Some lists are pre-defined by PDDB staff and are visible to all users. Other lists are created by users and are only visible to the user who created them.

Why create a PDDB account?

PDDB has many features which can only be used when the user has created an account and is logged in. Logging into PDDB allows the user to create and save private lists, such as genes in a genomic region of interest, for use in subsequent logins. Lists of genes and markers can be used as input for several of the tools on PDDB using the 'send list to tool' facility. Private data can also only be viewed and downloaded when logged in.

expander Networks & Pathways    Top  
expander Cytoscape    Top  
What is Cytoscape?

Cytoscape is an open source program for visualizing molecular interaction networks and integrating these interactions with gene expression profiles and other data. The Cytoscape project is an ongoing collaboration among several institutions and companies. Further information about Cytoscape is available at www.cytoscape.org.

How are interactions between an input protein and "neighbors" determined?

PDDB downloads data from several public sources. The interactions in these sources are combined, stored in the PDDB database, and displayed using Cytoscape for PDDB users.

expander KEGG Pathways    Top  
What are KEGG Pathways?

KEGG pathways are maps representing molecular interaction and reaction networks.  The pathways are generated by the KEGG: Kyoto Encyclopedia of Genes and Genomes database.