Vkuehn Week 5 - Revision history

Vkuehn: Finished week 5!

2013-09-27T04:30:29Z

Finished week 5!

Vkuehn: Added Screenshots!!

2013-09-27T04:04:46Z

Added Screenshots!!

Vkuehn at 04:03, 27 September 2013

2013-09-27T04:03:03Z

Vkuehn: added rest of uniprot

2013-09-27T03:59:09Z

added rest of uniprot

Vkuehn: some more of the uniprot

2013-09-27T03:55:35Z

some more of the uniprot

Vkuehn: added screenshot

2013-09-27T03:44:46Z

added screenshot

Vkuehn: Got started

2013-09-27T03:42:45Z

Got started

New page

===''UniProt Exercise''===
* Opened and read Bioinformatics For Dummies
* The location where Proteins end up and how they get there are unique

* The folding and domains are very important and help determine the 3D structure
* Searched for the protein P00533 it is an epidermal growth factor receptor

← Older revision		Revision as of 04:30, 27 September 2013
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	[[File:Second EBI database.png.png]]		[[File:Second EBI database.png.png]]
	[[http://www.ebi.ac.uk/pdbe-srv/view/entry/1ivo/summary.html]]		[[http://www.ebi.ac.uk/pdbe-srv/view/entry/1ivo/summary.html]]
		+	===Summary of Epidermal Growth Factor Receptor===
		+	EGFR is a growth factor protein which is a receptor tyrosine binding ligand that activates signals to help convert extracellular cues into corresponding cellular responses. It is found in the cell membrane of homo sapiens and other membranes in the cell [[http://www.uniprot.org/uniprot/P00533]] . It belongs to the protein kinase sub family. The mRNA sequence that corresponds to the protein is 5,532 base pairs in length and its 3D structure has a complex of 2 biomacromolecules. [[http://www.ebi.ac.uk/pdbe-srv/view/entry/1ivo/summary.html]]
		+
		+	===Questions===
		+	# The purpose of this exercise was to familiarize ourselves with Uniprot and to get used to gathering information about one protein from other databases. It made it clear what some of the benefits are of certain databases over others.
		+	# I learned that certain databases can be more clear and helpful in terms of visuals, which helps me personally understand how proteins are shaped of their size and structure. I also learned that using these databases is not as intimidating as it seems and that is is pretty easy to navigate back and forth between them.
		+	# Some things I think I could work on is learning which information is most useful and what to focus on in these databases. There is so much information but I was not sure what was the most important amongst all of it.

@@ Line 14: / Line 14: @@
 [[http://www.ebi.ac.uk/ena/data/view/X00588]]
 * Here is an example of a 3D database result for the epidermal protein:
-[[image:second_EBI_database.png]]
+[[File:Second EBI database.png.png]]
 [[http://www.ebi.ac.uk/pdbe-srv/view/entry/1ivo/summary.html]]

@@ Line 11: / Line 11: @@
 * The comments section is very useful for gathering information about the protein such as: function, catalytic activity, tissue specificity
 * The cross-reference section is very useful for gathering other information in new databases. For example, EMBL-EBI gives a visual overview of the base pairs and other details:
+[[image:First_EBI_database.png]]
 [[http://www.ebi.ac.uk/ena/data/view/X00588]]
 * Here is an example of a 3D database result for the epidermal protein:
+[[image:second_EBI_database.png]]
 [[http://www.ebi.ac.uk/pdbe-srv/view/entry/1ivo/summary.html]]

← Older revision		Revision as of 03:59, 27 September 2013
Line 11:		Line 11:
	* The comments section is very useful for gathering information about the protein such as: function, catalytic activity, tissue specificity		* The comments section is very useful for gathering information about the protein such as: function, catalytic activity, tissue specificity
	* The cross-reference section is very useful for gathering other information in new databases. For example, EMBL-EBI gives a visual overview of the base pairs and other details:		* The cross-reference section is very useful for gathering other information in new databases. For example, EMBL-EBI gives a visual overview of the base pairs and other details:
		+
		+	[[http://www.ebi.ac.uk/ena/data/view/X00588]]
		+	* Here is an example of a 3D database result for the epidermal protein:
		+
		+	[[http://www.ebi.ac.uk/pdbe-srv/view/entry/1ivo/summary.html]]

← Older revision		Revision as of 03:55, 27 September 2013
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	* Here are the results:		* Here are the results:
	[[image:Screen_Shot_2013-09-26_at_8.53.20_PM.png]]		[[image:Screen_Shot_2013-09-26_at_8.53.20_PM.png]]
		+
		+	* As new information comes out, older accession numbers don't go away, they just get stored as secondary accession numbers, but the most up to date information is only displayed
		+	* The comments section is very useful for gathering information about the protein such as: function, catalytic activity, tissue specificity
		+	* The cross-reference section is very useful for gathering other information in new databases. For example, EMBL-EBI gives a visual overview of the base pairs and other details:

← Older revision		Revision as of 03:44, 27 September 2013
Line 5:		Line 5:
	* The folding and domains are very important and help determine the 3D structure		* The folding and domains are very important and help determine the 3D structure
	* Searched for the protein P00533 it is an epidermal growth factor receptor		* Searched for the protein P00533 it is an epidermal growth factor receptor
		+	* Here are the results:
		+	[[image:Screen_Shot_2013-09-26_at_8.53.20_PM.png]]