How to deal with multi-named genes - Revision history

Laivey: /* BLAST */

2011-02-24T15:59:50Z

‎BLAST

Laivey: /* Summary */

2011-02-24T15:58:57Z

‎Summary

Laivey: /* Finding Your Gene of Interest */

2011-02-24T14:41:08Z

‎Finding Your Gene of Interest

Laivey at 13:35, 24 February 2011

2011-02-24T13:35:48Z

Laivey: /* Navigating NCBI' */

2011-02-24T02:44:12Z

‎Navigating NCBI'

Laivey at 02:43, 24 February 2011

2011-02-24T02:43:41Z

Laivey: /* Summary */

2011-02-24T02:42:36Z

‎Summary

Laivey: /* Summary */

2011-02-24T02:41:55Z

‎Summary

Laivey at 02:35, 24 February 2011

2011-02-24T02:35:47Z

Laivey: /* Finding Your Gene of Interest */

2011-02-24T02:34:26Z

‎Finding Your Gene of Interest

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-Then go to [http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastn&BLAST_PROGRAMS=megaBlast&PAGE_TYPE=BlastSearch&SHOW_DEFAULTS=on&LINK_LOC=blasthome/ BLAST] and paste the FASTA sequence into the BLAST box. Click BLAST and you compare the nucleotide sequence of ''ATP5O'' against all organisms in the BLAST database. The name of the protein the nucleotide sequence hit encodes is clearly shown, making it easy to detect whether or not you have discovered more ''ATP5O/OSCP'' genes that encode OSCP protein.
+Then go to [http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastn&BLAST_PROGRAMS=megaBlast&PAGE_TYPE=BlastSearch&SHOW_DEFAULTS=on&LINK_LOC=blasthome/ BLAST] and paste the FASTA sequence into the BLAST box. Click BLAST and you compare the nucleotide sequence of ''ATP5O'' against all organisms in the BLAST database. The name of the protein the nucleotide sequence hit encodes is clearly shown, making it easy to detect whether or not you have discovered the ''ATP5O/OSCP'' gene in a species that encodes OSCP protein.
 =='''Summary'''==
 Genes may have one or more names across species, or even within the same species. As in the case with ''OSCP'' in the ''Drosophila'' page, all of the alternative names for the gene are not always listed, therefore additional investigation can be quite fruitful when it comes to research. Utilize as many database as you can, such a NCBI, Pubmed, GeneCards and BLAST  to discover if there is variance in the name of your gene of interest. Knowing all the names a gene has been assigned, will help maximize the amount of information you find about the gene of interest.

← Older revision		Revision as of 15:58, 24 February 2011
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	=='''Summary'''==		=='''Summary'''==

−	Genes may have one or more names across species, or even within the same species. As in the case with ''OSCP'' in the ''Drosophila'' page, all of the alternative names for the gene are not ~~alway~~ listed, therefore additional investigation can be quite fruitful when it comes to research. Utilize as many database as you can, such a NCBI, Pubmed, GeneCards and BLAST to discover if there is variance in the name of your gene of interest. Knowing all the names a gene has been assigned, will help maximize the amount of information you find about the gene of interest.	+	Genes may have one or more names across species, or even within the same species. As in the case with ''OSCP'' in the ''Drosophila'' page, all of the alternative names for the gene are not always listed, therefore additional investigation can be quite fruitful when it comes to research. Utilize as many database as you can, such a NCBI, Pubmed, GeneCards and BLAST to discover if there is variance in the name of your gene of interest. Knowing all the names a gene has been assigned, will help maximize the amount of information you find about the gene of interest.

@@ Line 4: / Line 4: @@
 =='''Finding Your Gene of Interest'''==
-Say you just are sitting in Biology class and your teacher mentions ATP synthase has a subunit within its complex that is resistant to oligomyocin called Oligomyocin Sensitivity Conferring Protein. She mentions the gene that encodes the OSCP protein also have the gene name ''OSCP''. This sparks your interest, and you want to investigate this gene more. After class you immediately run home, and go to [http://www.ncbi.nlm.nih.gov/gene/ NCBI Gene] and search for "OSCP."
+Say you just are sitting in Biology class and your teacher mentions ATP synthase has a subunit within its complex that is resistant to oligomyocin called Oligomyocin Sensitivity Conferring Protein. She mentions the gene that encodes the OSCP protein also has the gene name ''OSCP''. This sparks your interest, and you want to investigate this gene more. After class you immediately run home, and go to [http://www.ncbi.nlm.nih.gov/gene/ NCBI Gene] and search for "OSCP."
 [[File:GENE.jpg]]
 =='''Navigating NCBI'''==

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-One always must be leery of the possibility that a gene may have multiple names. When investigating a gene, information can be overlooked by assuming a gene only has one name within its own and across species. This tutorial demonstrates how to determine if a gene has been assigned multiple names.
+When investigating a gene, one always must be leery of the possibility that the gene of interest may be referred to by multiple names within the research world.  Important Information can be overlooked by assuming a gene only has one name within and across species. This tutorial demonstrates ways to determine if a gene has been assigned multiple names.
 =='''Finding Your Gene of Interest'''==
-Say you just are sitting in Biology class and your teacher mentions ATP synthase has a subunit within its complex that is resistant to oligomyocin called Oligomyocin Sensitivity Conferring Protein, gene name ''OSCP''. This sparks your interest, and you want to investigate this gene more. After class you immediately run home, and go to [http://www.ncbi.nlm.nih.gov/gene/ NCBI Gene] and search for "OSCP."
+Say you just are sitting in Biology class and your teacher mentions ATP synthase has a subunit within its complex that is resistant to oligomyocin called Oligomyocin Sensitivity Conferring Protein. She mentions the gene that encodes the OSCP protein also have the gene name ''OSCP''. This sparks your interest, and you want to investigate this gene more. After class you immediately run home, and go to [http://www.ncbi.nlm.nih.gov/gene/ NCBI Gene] and search for "OSCP."
 [[File:GENE.jpg]]
@@ Line 14: / Line 14: @@
-Perfect! You get a hit for ''OSCP'' in ''Drosophila melanogaster''. You review the page and realize you want to research ''OSCP'' in other organisms, including humans. You then NCBI Gene search "OSCP homo sapiens." You get hits, but none specifically say OSCP. The first hit is for a gene called ''ATP50''.
+Perfect! You get a hit for ''OSCP'' in ''Drosophila melanogaster''. You review the page and with great excitement, you realize you want to research ''OSCP'' in other organisms, including humans. You then NCBI Gene search "OSCP homo sapiens." You get hits, but none specifically say OSCP. The first hit is for a gene called ''ATP50''.
 [[File:ATP50.jpg]]

← Older revision		Revision as of 02:44, 24 February 2011
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−	==''Navigating NCBI'''==	+	=='''Navigating NCBI'''==

	[[File:OSCP.jpg]]		[[File:OSCP.jpg]]

← Older revision		Revision as of 02:43, 24 February 2011
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−	One always must be leery of the possibility that a gene may have multiple names. When investigating a gene, information can be overlooked by assuming a gene only has one name across species. This tutorial demonstrates how to determine if a gene ~~is referred to by~~ multiple names ~~across species~~.	+	One always must be leery of the possibility that a gene may have multiple names. When investigating a gene, information can be overlooked by assuming a gene only has one name within its own and across species. This tutorial demonstrates how to determine if a gene has been assigned multiple names.

← Older revision		Revision as of 02:42, 24 February 2011
Line 51:		Line 51:
	=='''Summary'''==		=='''Summary'''==

−	Genes may have one or more names across species, or even within the same species. As in the case with OSCP on the ''Drosophila'' page, all of the alternative names for the gene are not alway listed, therefore additional investigation can be quite fruitful when it comes to research. Utilize as many database as you can, such a NCBI, Pubmed, GeneCards and BLAST to discover if there is variance in the name of your gene of interest. Knowing all the names a gene has been assigned, will help maximize the amount of information you find about the gene of interest.	+	Genes may have one or more names across species, or even within the same species. As in the case with ''OSCP'' in the ''Drosophila'' page, all of the alternative names for the gene are not alway listed, therefore additional investigation can be quite fruitful when it comes to research. Utilize as many database as you can, such a NCBI, Pubmed, GeneCards and BLAST to discover if there is variance in the name of your gene of interest. Knowing all the names a gene has been assigned, will help maximize the amount of information you find about the gene of interest.

← Older revision		Revision as of 02:41, 24 February 2011
Line 51:		Line 51:
	=='''Summary'''==		=='''Summary'''==

−	~~Gene~~ may have one or more names across species. As in the case with OSCP on the Drosophila page, the alternative ~~name~~ for the gene are not alway listed. Utilize as many database such a NCBI, Pubmed, ~~GeneCard~~ and ~~Blast~~ to discover if there is variance in the names.	+	Genes may have one or more names across species, or even within the same species. As in the case with OSCP on the ''Drosophila'' page, all of the alternative names for the gene are not alway listed, therefore additional investigation can be quite fruitful when it comes to research. Utilize as many database as you can, such a NCBI, Pubmed, GeneCards and BLAST to discover if there is variance in the name of your gene of interest. Knowing all the names a gene has been assigned, will help maximize the amount of information you find about the gene of interest.