Lab Notes - Revision history

Anbaay at 14:35, 13 April 2017

2017-04-13T14:35:38Z

Anbaay at 14:06, 11 April 2017

2017-04-11T14:06:38Z

Anbaay at 17:43, 4 April 2017

2017-04-04T17:43:49Z

Anbaay at 14:59, 30 March 2017

2017-03-30T14:59:09Z

Anbaay at 14:52, 30 March 2017

2017-03-30T14:52:57Z

Anbaay at 02:45, 23 March 2017

2017-03-23T02:45:20Z

Anbaay at 14:01, 21 March 2017

2017-03-21T14:01:46Z

Anbaay at 14:00, 21 March 2017

2017-03-21T14:00:06Z

Anbaay at 14:30, 16 March 2017

2017-03-16T14:30:11Z

Anbaay at 14:16, 16 March 2017

2017-03-16T14:16:30Z

@@ Line 28: / Line 28: @@
 *<b>	Ccng1</b> Cyclin gene, involved in the cell cycle and unlikely to be of interest here
 *<b>	Hnrnpk</b> Found with FUS [http://bit.ly/2ppmbAL string]
-*<b>	Zbtb26</b>
+*<b>	Zbtb26</b> Not enough Info
 *<b>	Wdr6</b> WD repeats are minimally conserved regions of approximately 40 amino acids typically bracketed by gly-his and trp-asp (GH-WD), which may facilitate formation of heterotrimeric or multiprotein complexes. The encoded protein interacts with serine/threonine kinase 11, and is implicated in cell growth arrest.<br>
-*<b>	Zxdc</b>
+*<b>	Zxdc</b> Not enough information
-*<b>	Gm12790</b>
+*<b>	Gm12790</b> predicted gene- not enough info
 *<b>	Ubtf</b> - The encoded protein plays a critical role in ribosomal RNA transcription as a key component of the pre-initiation complex, mediating the recruitment of RNA polymerase I to rDNA promoter regions. The encoded protein may also play important roles in chromatin remodeling and pre-rRNA processing, and its activity is regulated by both phosphorylation and acetylation.<br>
 *<b>	Luc7l3</b> This protein localizes with a speckled pattern in the nucleus, and could be involved in the formation of splicesome via the RE and RS domains.
-*<b>	Gm11800</b>
+*<b>	Gm11800</b> Predicted gene- not enough info
-*<b>	Cox17</b> cytochrome oxidase (COX) is a key complex found in the mitchondrial respiration chain. Cox17 is an assembly protein that helps this complex form and is thought to recruit copper to the complex, which helps activate it. The protein is ubiquitously produced in cells and implicated in embryonic development. [https://books.google.com/books?id=ie5ZmOYHpVEC&pg=PA134&lpg=PA134&dq=COX17+knockout&source=bl&ots=zc4jFzh6tI&sig=066Ad3idU_vpqBSpm8xZ9W-XXEA&hl=en&sa=X&ved=0ahUKEwjc6cDuyuvSAhWEC8AKHYTfDrsQ6AEISTAJ#v=onepage&q=COX17%20knockout&f=false Book]; pg 134)
+*<b>	Cox17</b> cytochrome oxidase (COX) is a key complex found in the mitchondrial respiration chain. Cox17 is an assembly protein that helps this complex form and is thought to recruit copper to the complex, which helps activate it. The protein is ubiquitously produced in cells and implicated in embryonic development. [https://books.google.com/books?id=ie5ZmOYHpVEC&pg=PA134&lpg=PA134&dq=COX17+knockout&source=bl&ots=zc4jFzh6tI&sig=066Ad3idU_vpqBSpm8xZ9W-XXEA&hl=en&sa=X&ved=0ahUKEwjc6cDuyuvSAhWEC8AKHYTfDrsQ6AEISTAJ#v=onepage&q=COX17%20knockout&f=false Book]; pg 134) According to NCBI and gene, this gene is no longer a candidate for COX deficiency
-*<b>	Gm14300</b>
+*<b>	Gm14300</b> predicted gene- not enough info
 *<b>	Fus</b>This gene encodes a multifunctional protein component of the heterogeneous nuclear ribonucleoprotein (hnRNP) complex. The hnRNP complex is involved in pre-mRNA splicing and the export of fully processed mRNA to the cytoplasm. This protein belongs to the FET family of RNA-binding proteins which have been implicated in cellular processes that include regulation of gene expression, maintenance of genomic integrity and mRNA/microRNA processing.(GENE) Defects in this gene are implicated in ALS(6) [https://www.ncbi.nlm.nih.gov/books/NBK1450/#als-overview.Causes ASL causes]<br>
-*<b>	Gm14296</b>
+*<b>	Gm14296</b> predicted gene- not enough info
-*<b>	Nop56</b>
+*<b>	Nop56</b> a Protein Coding gene. Diseases associated with NOP56 include Spinocerebellar Ataxia 36 and Spinocerebellar Ataxia Type36. Among its related pathways are Chaperonin-mediated protein folding and rRNA processing in the nucleus and cytosol. GO annotations related to this gene include poly(A) RNA binding and snoRNA binding.
 *<b>	Hnrnpr</b> THIS ONE INTERACTS WITH FUS [http://string-db.org/cgi/network.pl?taskId=pEGMR9YJAbim String]
-*<b>	Rsrp1</b>
+*<b>	Rsrp1</b> arginine and serine rich protein 1
 *<b>	Rhox5</b>

@@ Line 27: / Line 27: @@
 Up/Down Genes Identified:<br>
 *<b>	Ccng1</b> Cyclin gene, involved in the cell cycle and unlikely to be of interest here
-*<b>	Hnrnpk</b>
+*<b>	Hnrnpk</b> Found with FUS [http://bit.ly/2ppmbAL string]
 *<b>	Zbtb26</b>
 *<b>	Wdr6</b> WD repeats are minimally conserved regions of approximately 40 amino acids typically bracketed by gly-his and trp-asp (GH-WD), which may facilitate formation of heterotrimeric or multiprotein complexes. The encoded protein interacts with serine/threonine kinase 11, and is implicated in cell growth arrest.<br>

@@ Line 41: / Line 41: @@
 *<b>	Gm14296</b>
 *<b>	Nop56</b>
-*<b>	Hnrnpr</b>
+*<b>	Hnrnpr</b> THIS ONE INTERACTS WITH FUS [http://string-db.org/cgi/network.pl?taskId=pEGMR9YJAbim String]
 *<b>	Rsrp1</b>
 *<b>	Rhox5</b>

@@ Line 20: / Line 20: @@
 <br>
 <B> Methods for Fus Investigation</b>
-Started with paper [http://illiad.davidson.edu/pdf/283460.pdf, http://illiad.davidson.edu/pdf/283460.pdf FUS Overview] <br> -> They describe many mutations of the FUS protein and how they can affect neuronal cells. Needed to verify that at least some of the mutations were producing inept proteins (so the data can be applied to transcription levels of healthy protein) <br>->this was accomplished by analyzing all reported mutations in their supplementary data [http://www.nature.com/nrneurol/journal/v10/n6/abs/nrneurol.2014.78.html#supplementary-information table of mutation] and cross-referencing them with GenePeeks research tool [https://research.genepeeks.com/genes/ENSG00000089280/#/variants Fus Results] to find uncontested pathologic nonsense mutations.
+Started with paper [http://illiad.davidson.edu/pdf/283460.pdf, http://illiad.davidson.edu/pdf/283460.pdf FUS Overview] <br> -> They describe many mutations of the FUS protein and how they can affect neuronal cells. Needed to verify that at least some of the mutations were producing inept proteins (so the data can be applied to transcription levels of healthy protein) <br>->this was accomplished by analyzing all reported mutations in their supplementary data [http://www.nature.com/nrneurol/journal/v10/n6/abs/nrneurol.2014.78.html#supplementary-information table of mutation] and cross-referencing them with GenePeeks research tool [https://research.genepeeks.com/genes/ENSG00000089280/#/variants Fus Results] to find uncontested pathologic nonsense mutations. <br> [https://www.ncbi.nlm.nih.gov/clinvar/variation/37070/ Tremors in ClinVar] Our mouse model shows tremors and a nonsense mustation is implicated in these sorts of tremors (could be from down regulation?)

← Older revision		Revision as of 14:52, 30 March 2017
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	Excel: Gene names need to be truncated using command- left(A1, 18)<br>		Excel: Gene names need to be truncated using command- left(A1, 18)<br>
		+	<br>
		+	<br>
		+	<B> Methods for Fus Investigation</b>
		+	Started with paper [http://illiad.davidson.edu/pdf/283460.pdf, http://illiad.davidson.edu/pdf/283460.pdf FUS Overview] <br> -> They describe many mutations of the FUS protein and how they can affect neuronal cells. Needed to verify that at least some of the mutations were producing inept proteins (so the data can be applied to transcription levels of healthy protein) <br>->this was accomplished by analyzing all reported mutations in their supplementary data [http://www.nature.com/nrneurol/journal/v10/n6/abs/nrneurol.2014.78.html#supplementary-information table of mutation] and cross-referencing them with GenePeeks research tool [https://research.genepeeks.com/genes/ENSG00000089280/#/variants Fus Results] to find uncontested pathologic nonsense mutations.
		+

	Many of the investigated genes,<b>Wdr6,Ubtf,Luc7l3,</B>Fus, are implicated in broad transcriptional functions.		Many of the investigated genes,<b>Wdr6,Ubtf,Luc7l3,</B>Fus, are implicated in broad transcriptional functions.

@@ Line 18: / Line 18: @@
 Excel: Gene names need to be truncated using command-  left(A1, 18)<br>
 <b>Andy Genes:</b><br>
-Up/Down and in P_M:<br>
+Up/Down Genes Identified:<br>
 *<b>Gabpa</b> - This gene encodes one of three GA-binding protein transcription factor subunits which functions as a DNA-binding subunit. Because of its chromosomal localization and ability to form heterodimers with other polypeptides, this gene may play a role in the Down Syndrome phenotype.<br>
 *<b>Dyrk1a</b> - Dual-specificity tyrosine phosphorylation-regulated kinase (DYRK) family; localized in the Down syndrome critical region of chromosome 21, and is considered to be a strong candidate gene for learning defects associated with Down syndrome;  It catalyzes its autophosphorylation on serine/threonine and tyrosine residues. It may play a significant role in a signaling pathway regulating cell proliferation and may be involved in brain development.<br>
@@ Line 29: / Line 49: @@
 </center>
-Up/Down and ''not'' in P_M:<br>
+Same Direction (Up/up or down/down) and ''not'' in P_M:<br>
 *<b>	Ets2</b> - HSA 21 - This gene encodes a transcription factor which regulates genes involved in development and apoptosis. The encoded protein is also a protooncogene and shown to be involved in regulation of telomerase. <br>
 *<b>	Dscr3</b> - HSA21 - The DSCR3 (Down syndrome critical region gene 3) gene is found in this region and is predictated to contain eight exons. DSCR3 is expressed in most tissues examined. (this link also characterized the critical region). <br>