Shivum Desai Journal Week 14: Difference between revisions
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=Individual Journal Week | =Individual Journal Week 14= | ||
==Purpose== | ==Purpose== | ||
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:*http://www.pantherdb.org/help/PANTHERhelp.jsp | :*http://www.pantherdb.org/help/PANTHERhelp.jsp | ||
:*http://www.pantherdb.org/genes/gene.do?acc=HUMAN|HGNC=14134|UniProtKB=Q9NRR2 | :*http://www.pantherdb.org/genes/gene.do?acc=HUMAN|HGNC=14134|UniProtKB=Q9NRR2 | ||
=Contiuation of Week 14-Journal Club Paper Terms, Outline, and Powerpoint= | |||
All of this information was posted onto Anu's week 14 individual journal page. | |||
Link: [[AninditaVarshneya BIOL368 Week 14]] | |||
==Useful Links== | ==Useful Links== | ||
Latest revision as of 13:42, 5 December 2016
Individual Journal Week 14
Purpose
- The purpose of this experiment is to answer questions related to a scientific research database of our choosing.
Methods
- A database was selected from a group of databases.
- A list of questions were answered about the database.
- Acknowledgments and references were listed on the wiki page.
Conclusion
The database Panther V.10 was analyzed for many of its different aspects and classifications. This database was found to be specifically about proteins and their classifications, structure, and pathways. It contains information relating to many difference species of animals and is updated about once a year with a new version, thus an addition of more specifies and proteins. It is an open access database and is operated by Thomas lab at the University of Southern California and operates under a grant from the National Institute of General Medical Sciences.
Database: Panther V.10
Assignment Questions
1.Panther Classification System.
2. The purpose of this database is to provide protein classification based on function, classification, and then provide tools for analysis.
3.Panther contains the families and subfamilies of evolutionary classified proteins. It also contains the molecular function of a protein and its interactions at the biochemical level. lastly, it contains the function of each group of proteins as well as the pathways in which the proteins operate.
4. 104 different species and their proteins are in this database. Including: zebrafish, lizard, tomato, mosquito, cow, and humans.
5. This database can answer questions such as "What is the pathway of a the 'BLANK' protein?" Also, questions regarding the origin (Orthology) and specific of a protein can be answered. It also can provide the sequence information from which a specific protein is coded. There is also information regarding the phylogeny of a protein and its divergence from other species and its similarity to others.
6. This database is a specialty protein database. It is also a primary database and is curated in house electronically by algorithm and by human.
7. It is supported by a research grant from the National Institute of General Medical Sciences and is maintained by the Thomas lab at the University of Southern California.
8. Their funding source is a research grant from the National Institute of General Medical Sciences.
9. This database is open access.
10. The database is updated about once every year with the upload of a new version of the program which contains new proteins, their orthology, pathways, etc.
11. There is one link to the Gene Ontology Database.
12. Yes, the information can be downloaded directly from their website, but none of the links work so the type of the file is unknown. However, one can download other analysis program is the form of TGZ (similar to zip files), such as the Panther Scoring Tool.
13. I think the database is well organized however if a person without a great knowledge of proteins and their functions tried to use this database, they would most definitely run into some problems. But, it does have a help and tutorial section to guide new users. A sample query into calcium binding proteins was easily run.
Contiuation of Week 14-Journal Club Paper Terms, Outline, and Powerpoint
All of this information was posted onto Anu's week 14 individual journal page.
Link: AninditaVarshneya BIOL368 Week 14
Useful Links
Acknowledgments
I would like to acknowledge Dr. Dahlquist for her help on this weeks work. I would also like to acknowledge the PANTHER v.10 database for it information, which I used to complete this experiment. While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.
References
- Paul D. Thomas, Michael J. Campbell, Anish Kejariwal, Huaiyu Mi, Brian Karlak, Robin Daverman, Karen Diemer, Anushya Muruganujan, Apurva Narechania. 2003. PANTHER: a library of protein families and subfamilies indexed by function. Genome Res., 13: 2129-2141 .
- Huaiyu Mi, Qing Dong, Anushya Muruganujan, Pascale Gaudet, Suzanna Lewis and Paul D. Thomas 2010. PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium. Nucl. Acids Res.. 38: D204-D210.
- Paul D. Thomas, Anish Kejariwal, Nan Guo, Huaiyu Mi, Michael J. Campbell, Anushya Muruganujan, and Betty Lazareva-Ulitsky. 2006. Applications for protein sequence-function evolution data: mRNA/protein expression analysis and coding SNP scoring tools. Nucl. Acids Res.34: W645-W650.
- Paul D. Thomas, Anish Kejariwal, Nan Guo, Huaiyu Mi, Michael J. Campbell, Anushya Muruganujan, and Betty Lazareva-Ulitsky. 2006. Applications for protein sequence-function evolution data: mRNA/protein expression analysis and coding SNP scoring tools. Nucl. Acids Res.34: W645-W650.
