Difference between revisions of "Mpetredi Week 5"
From LMU BioDB 2013
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| + | ==[[user:mpetredi|'''Mitchell Petredis''']]== | ||
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| + | [[Week 5]] | ||
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==UniProt Exercise Journal== | ==UniProt Exercise Journal== | ||
#Navigated to http://www.uniprot.org instead of http://web.expasy.org/docs/swiss-prot_guideline.html as per week 5 instruction | #Navigated to http://www.uniprot.org instead of http://web.expasy.org/docs/swiss-prot_guideline.html as per week 5 instruction | ||
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#Clicked the 2.7.10.1 hyperlink. | #Clicked the 2.7.10.1 hyperlink. | ||
#*Redirected to http://enzyme.expasy.org/EC/2.7.10.1. This link describes the receptor "protein-tyrosine kinase." | #*Redirected to http://enzyme.expasy.org/EC/2.7.10.1. This link describes the receptor "protein-tyrosine kinase." | ||
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| − | |||
#Located Quick Search Box (Under Query) | #Located Quick Search Box (Under Query) | ||
#Noticed the quick links around the top of the page, under the Quick Search box. Each link directs you to a specific section of the entry | #Noticed the quick links around the top of the page, under the Quick Search box. Each link directs you to a specific section of the entry | ||
| − | #*[[http://www.uniprot.org/uniprot/P00533#section_name Names]] | + | #*[[http://www.uniprot.org/uniprot/P00533#section_name Names]]: States all the ways P00533 can be identified |
| − | #*[[http://www.uniprot.org/uniprot/P00533#section_attribute Attributes]] | + | #*[[http://www.uniprot.org/uniprot/P00533#section_attribute Attributes]]: States the sequence length, sequence status, sequence processing, and protein existence of a subject. |
| − | #* | + | #*[[http://www.uniprot.org/uniprot/P00533#section_comments General annotation]]: AKA Comments. Provides additional, brief information about the function, catalytic activity, enzyme regulation, subunit structure, sub cellular location, tissue specificity, post-translational modification, involvement in decease, and sequence similarities. Check this section first to get a basic idea of a subject before proceeding to the more fully detailed information. |
| − | #* | + | #*[[http://www.uniprot.org/uniprot/P00533#section_terms Ontologies]]: Applies keywords relevant to the subject's properties. |
| − | #* | + | #*[[http://www.uniprot.org/uniprot/P00533#section_interactions Interactions]]: Vaguely describes the other subjects P00533 interacts with. |
| − | #* | + | #*[[http://www.uniprot.org/uniprot/P00533#section_alternative Alt products]]: States the isomers of the subject created by alternative splicing. |
| − | #* | + | #*[[http://www.uniprot.org/uniprot/P00533#section_features Sequence annotation]] |
| − | #* | + | #*[[http://www.uniprot.org/uniprot/P00533#section_seq Sequences]] |
| − | #* | + | #*[[http://www.uniprot.org/uniprot/P00533#section_ref References]]: Contains all materials used when compiling the report on P00533. |
| − | #* | + | #*[[http://www.uniprot.org/uniprot/P00533#section_web Web links]] |
| − | #* | + | #*[[http://www.uniprot.org/uniprot/P00533#section_x-ref Cross-refs]]: This section provides other links pertaining to the same subject. Each link performs a different function from the others. |
| − | + | #**[[http://www.ebi.ac.uk/ena/data/view/X00588 EMBL]]: Mostly contains raw data and results presented in an outline format. | |
| + | #**[[http://www.ebi.ac.uk/interpro/entry/IPR000494 InterPro]]: Information is presented in paragraph form with many descriptors. | ||
| + | #**[[http://www.ebi.ac.uk/pdbe-srv/view/entry/2EB3 PDB]]: Displays virtual models of the subject (P00533 in this case) and mentions what certain colors on the model indicates. | ||
| + | #**[[http://pfam.sanger.ac.uk/family/PF00757 Pfam]]: Also displays a virtual model of the subject, but with less detail than PDB. It does provide other links to similar subjects and databases related to the searched subject | ||
| + | #**[[http://www.ncbi.nlm.nih.gov/protein/NP_005219.2 RefSeq]]: Directed to NCBI that contains similar or the information as uniprot, but not structured as easily as uniprot. | ||
| + | #**[[http://www.ncbi.nlm.nih.gov/gene/1956 GeneID]]: Also directed to NCBI, but the presented information has less content and looks cleaner. Contains many links to other pages on and off NCBI. | ||
| + | #*[[http://www.uniprot.org/uniprot/P00533#section_general Entry info]] | ||
| + | #*[[http://www.uniprot.org/uniprot/P00533#section_documents Documents]] | ||
| + | #*[[http://www.uniprot.org/uniprot/P00533#section_customize Customize]]: Use this to change the default ordering of sections. | ||
| + | # Near the top right corner, information about the subject can be formatted for text, xml, ref/xml, gff, or fasta via designated orange buttons. | ||
==P00533, or Epidermal Growth Factor Receptor: A Brief Summary== | ==P00533, or Epidermal Growth Factor Receptor: A Brief Summary== | ||
| − | ( | + | I learned that P00533 is one of the many IDs for the epidermal growth factor receptor (EGFR), a human protein that can result in the formation of lung cancer. EGFR is completely sequenced with a length of 1210 AA that exists at the protein level. A very detailed report can be found at http://www.uniprot.org/uniprot/P00533, where anyone can find everything currently known about EGFR along with other links about EGFR from other freely available databases. |
==Individual Assignment Response to Questions== | ==Individual Assignment Response to Questions== | ||
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#I learned how to locate relevant information pertaining to this course. | #I learned how to locate relevant information pertaining to this course. | ||
#I currently don't know how I will utilize the information for a certain sequence or protein in my project for this course. | #I currently don't know how I will utilize the information for a certain sequence or protein in my project for this course. | ||
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| + | [[Category: Individual Homework]] | ||
| + | [[Category: Journal Entry]] | ||
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| + | [[User:Mpetredi|Mpetredi]] ([[User talk:Mpetredi|talk]]) 14:28, 26 September 2013 (PDT)Mitchell Petredis | ||
Latest revision as of 21:33, 26 September 2013
Contents |
[edit] Mitchell Petredis
[edit] UniProt Exercise Journal
- Navigated to http://www.uniprot.org instead of http://web.expasy.org/docs/swiss-prot_guideline.html as per week 5 instruction
- Typed P00533 in search box on uniprot website.
- Sent to http://www.uniprot.org/uniprot/P00533. Link describes Epidermal growth factor receptor (EGFR).
- Clicked the 2.7.10.1 hyperlink.
- Redirected to http://enzyme.expasy.org/EC/2.7.10.1. This link describes the receptor "protein-tyrosine kinase."
- Located Quick Search Box (Under Query)
- Noticed the quick links around the top of the page, under the Quick Search box. Each link directs you to a specific section of the entry
- [Names]: States all the ways P00533 can be identified
- [Attributes]: States the sequence length, sequence status, sequence processing, and protein existence of a subject.
- [General annotation]: AKA Comments. Provides additional, brief information about the function, catalytic activity, enzyme regulation, subunit structure, sub cellular location, tissue specificity, post-translational modification, involvement in decease, and sequence similarities. Check this section first to get a basic idea of a subject before proceeding to the more fully detailed information.
- [Ontologies]: Applies keywords relevant to the subject's properties.
- [Interactions]: Vaguely describes the other subjects P00533 interacts with.
- [Alt products]: States the isomers of the subject created by alternative splicing.
- [Sequence annotation]
- [Sequences]
- [References]: Contains all materials used when compiling the report on P00533.
- [Web links]
- [Cross-refs]: This section provides other links pertaining to the same subject. Each link performs a different function from the others.
- [EMBL]: Mostly contains raw data and results presented in an outline format.
- [InterPro]: Information is presented in paragraph form with many descriptors.
- [PDB]: Displays virtual models of the subject (P00533 in this case) and mentions what certain colors on the model indicates.
- [Pfam]: Also displays a virtual model of the subject, but with less detail than PDB. It does provide other links to similar subjects and databases related to the searched subject
- [RefSeq]: Directed to NCBI that contains similar or the information as uniprot, but not structured as easily as uniprot.
- [GeneID]: Also directed to NCBI, but the presented information has less content and looks cleaner. Contains many links to other pages on and off NCBI.
- [Entry info]
- [Documents]
- [Customize]: Use this to change the default ordering of sections.
- Near the top right corner, information about the subject can be formatted for text, xml, ref/xml, gff, or fasta via designated orange buttons.
[edit] P00533, or Epidermal Growth Factor Receptor: A Brief Summary
I learned that P00533 is one of the many IDs for the epidermal growth factor receptor (EGFR), a human protein that can result in the formation of lung cancer. EGFR is completely sequenced with a length of 1210 AA that exists at the protein level. A very detailed report can be found at http://www.uniprot.org/uniprot/P00533, where anyone can find everything currently known about EGFR along with other links about EGFR from other freely available databases.
[edit] Individual Assignment Response to Questions
- The purpose of this exercise was to become more familiar with the layout of information presented by UniProt for a particular sequence or protein.
- I learned how to locate relevant information pertaining to this course.
- I currently don't know how I will utilize the information for a certain sequence or protein in my project for this course.Mpetredi (talk) 14:28, 26 September 2013 (PDT)Mitchell Petredis
