Linking to cumulative gene information through database, spreadsheet, or data analysis software

The detailed Gene information can be downloaded for the user-chosen datasets using the Gene Info tool. But the collective data in this resource for any gene can be also accessed directly by Excel spreadsheets or software by linking to the following URL :

By Genbank accession: http://www.biorag.org/perl/biorag.pl?id=xyz

By Unigene: http://www.biorag.org/perl/biorag.pl?uid= XYZ

By Locus Link: http://www.biorag.org/perl/biorag.pl?lid=xyz

where xyz= Genbank accession, Unigene id ( hs. Xyz or mm. XYZ), Locus Link Id.

To link Genbank Accessions from the Gene Inspector tool of GeneSpring
Follow the instructions given at the GeneSpring FAQ site at the URL http://www.sigenetics.com/cgi/HelpFaqGen.cgi?how_buttons

Simply retrieve the file by going to GeneSpring/data and locating the genome folder (i.e.data/Demo Chips/Human/) that you are working on. Find the file at the top level of this folder that ends in the extension “.genomedef” (not .genomedef.backup). Open this file in Notepad or a similar text editor.
For web link to this resource, add the following line
GeneHypertextLinks : BIORAG:http://www.biorag.org/perl/biorag.pl?id=<genbank>
It will look like this.

About data collection, storage, relationship, and updates.

In order to provide an up-to-date version of the genes, the data in this resource is updated twice a week from NCBI dbEST, Unigene, and LocusLink. The Update date is provided under the Update link. The associated data with the genes (Unigene, Locus Link, and Genbank accessions) that is: Pathways, Diseases, and Protein interactions is updated based on the latest changes (eg. changed Unigene, etc.) provided by the update. The relational database that stores the functional relationships resides on a 900 MHz processor Sun Fire 280R Unix Server that uses a 700 gigabyte RAID system for data storage. MySQL is used as the relational database management system. The website is driven by the Apache server.

All the data is collected from external resources and hence the annotation quality and accuracy is as provided by the parent annotation resources. This Resource collects data from various open public resources and integrates them together in a relational schema which can be further accessed through a common platform. For some of these external data resources, there are terms governing the use of their site and data. Wherever applicable you should review their terms of agreement before using the data.

The relationship between the biological entities has been set up using the following Entity-Relationship diagram. The database is developed using this ER schema.

1. No annotation found for a gene?

We have tried to capture all genes based on combined information from Unigene and Locus Link. A gene is represented locally in our database only if it is present in any one or both the resources from NCBI. If the query accessions you provide are not included in any one of the NCBI resources then the information for that particular accession will not be available.

2. You find the NCBI version of a record different than the one on the site on a given day?

The data is updated twice a week from NCBI, so between the intervals, if there are changes they will not be reflected on this resource. Also the updates are done using the FTP site of the NCBI and the contents are picked up from the NCBI data directories. We depend and rely on the accuracy and most up-to-date information from them.

3. You know that a given data is present for your gene of interest at a third-party website but the same data does not come up in this resource although the data is included from that site into our database? á

All the information about a gene from other databases like interactions and pathways is collected using the identifiers like Locus Link, Unigene, Genbank accessions, or the Hugo gene nomenclature. Any of these have to be present in an external resource for the related information to get integrated with any given gene. It is possible we will miss out on information on a few genes if proper identifiers are not found but an effort has been made that we capture all the information. á

Literature Citations and how to Cite or acknowledge this resource

Publications and presentations that have used this site:

 

J Biol Chem. 2003 Oct 23. Chauhan S, Davis K, Roberts J, Martin G, Demetriou MC, Sroka TC, Cress AE, Miesfeld RL. Androgen control of cell proliferation and cytoskeletal reorganization in human fibrosarcoma cells: Role of RhoB signaling.

Biochem Biophys Res Commun. 2003 Oct 17 ;310(2):421-32. Chauhan S, Pandey R, Way JF, Sroka TC, Demetriou MC, Kunz S, Cress AE, Mount DW, Miesfeld RL. Androgen regulation of the human FERM domain encoding gene EHM2 in a cell model of steroid-induced differentiation.

J Steroid Biochem Mol Biol. 2003 Mar 84(4):441-52. Chauhan S, Leach CH, Kunz S, Bloom JW, Miesfeld RL. Glucocorticoid regulation of human eosinophil gene expression.

Gene Expression of DU-145 Cells Stimulated with Human Laminin 5 or Laminin 10. Beck SK, Hoying J, Pandey R, Calaluce R, Barrera J, Mount DW, Nagle RB. (43rd ASCB annual meeting 03 Poster presentation)

Publications and Presentation on this resource:

Bioinformatics (2004) In Press Pathway Miner: Extracting Gene Association Networks from Molecular Pathways for Predicting the Biological Significance of Gene Expression Microarray Data. Pandey R, Guru RK, and Mount. DW.

BioRag (BioResource for Array Genes): An Online Resource for Analyzing and Interpret Microarray data.
Pandey R, Guru RK, and Mount DW (ISMB 03 Poster presentation).

Steroid Regulated Gene Expression Database. Pandey R, Appikatla V, Chauhan S, Mount DW and Miesfeld RL (2002). (Genomics & Proteomics in Endocrinology 02 Poster Presentation)

Citing Bioresource: If you have used this website for your research purpose, please cite or acknowledge this resource in your publications/presentations as “Bioresource for array genes at www.biorag.org.”