Knguye66 Week 9 - Revision history

Knguye66: /* Data and Files */ add file

2019-11-07T01:17:31Z

‎Data and Files: add file

Kdahlquist: /* Data and Files */ link to file

2019-11-07T00:58:48Z

‎Data and Files: link to file

Knguye66: /* Data and Files */ add file

2019-11-06T23:28:10Z

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Knguye66: /* Data and Files */ add file

2019-11-06T23:26:35Z

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Knguye66: /* Methods/Results */ add information

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Knguye66: /* Methods/Results */ add methods

2019-11-05T23:29:34Z

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Knguye66: add answers to q

2019-11-05T23:16:13Z

add answers to q

Knguye66: /* Acknowledgements */ add wiki sig again

2019-10-29T04:07:58Z

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Knguye66: /* Data and Files */ fix file

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 ==== Data and Files ====
-* [[Media:Wt_significantprofiles_kn.pptx | "Interface options" & Significant Profiles (.pptx)]]
+* [[Media:File:BIOL367 F19 KN slide.pptx | One-way ANOVA (wt), STEM Results, Profiles, & GRNsight (.pptx)]]
 * [[Media:Wt_profile-45_GOlist_kn.xlsx | Profile#45 GOlist, Genelist, Yeastract rank tf, & Gene regulatory network (Excel)]]
 * [[Media:Regulation_Matrix_profile45.xlsx | Regulation Matrix (adjacency matrix)]]

@@ Line 71: / Line 71: @@
 * [[Media:Wt_profile-45_GOlist_kn.xlsx | Profile#45 GOlist, Genelist, Yeastract rank tf, & Gene regulatory network (Excel)]]
 * [[Media:Regulation_Matrix_profile45.xlsx | Regulation Matrix (adjacency matrix)]]
 ==== Conclusion ====

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 ==== Data and Files ====
 * [[Media:Wt_significantprofiles_kn.pptx | "Interface options" & Significant Profiles (.pptx)]]
-* [[Media:Wt_profile-45_GOlist_kn.xlsx | Profile#45 GOlist (Excel)]]
+* [[Media:Wt_profile-45_GOlist_kn.xlsx | Profile#45 GOlist, Genelist, Yeastract rank tf, & Gene regulatory network (Excel)]]
 * [[Media:Regulation_Matrix_profile45.xlsx | Regulation Matrix (adjacency matrix)]]

@@ Line 72: / Line 72: @@
 * [[Media:Wt_significantprofiles_kn.pptx | "Interface options" & Significant Profiles (.pptx)]]
 * [[Media:Wt_profile-45_GOlist_kn.xlsx | Profile#45 GOlist (Excel)]]
 ==== Conclusion ====

← Older revision		Revision as of 23:33, 5 November 2019
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	To build the mathematical model, the list of transcription factors that were chosen were the first 20 on the Excel sheet from the YEASTRACT database table. The top 20 were chosen (including CIN5, GLN3, and HAP4) because they were ranked from the most significant to least. This would then give significant results to analyze later.		To build the mathematical model, the list of transcription factors that were chosen were the first 20 on the Excel sheet from the YEASTRACT database table. The top 20 were chosen (including CIN5, GLN3, and HAP4) because they were ranked from the most significant to least. This would then give significant results to analyze later.
		+
		+	Visualizing Your Gene Regulatory Networks with GRNsight:

	==== Data and Files ====		==== Data and Files ====

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 #*** The chemical reactions and pathways occurring in the nucleus and resulting in the breakdown of a ribosomal RNA (rRNA) molecule, including RNA fragments released as part of processing the primary transcript into multiple mature rRNA species, initiated by the enzymatic addition of a sequence of adenylyl residues (polyadenylation) at the 3' end the target rRNA. (Source: PMID:17652137, GOC:krc, PMID:15173578, PMID:18591258, PMID:15935758, GOC:dgf, PMID:15572680)
-Using YEASTRACT to Infer which Transcription Factors Regulate a Cluster of Genes
+Using YEASTRACT to Infer which Transcription Factors Regulate a Cluster of Genes:
 - Profile #45 -
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 #*** % in YEASTRACT: 7.79%
 #*** p-value: 0.361027186229152
 ==== Data and Files ====

← Older revision		Revision as of 23:16, 5 November 2019
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	#*** The chemical reactions and pathways occurring in the nucleus and resulting in the breakdown of a ribosomal RNA (rRNA) molecule, including RNA fragments released as part of processing the primary transcript into multiple mature rRNA species, initiated by the enzymatic addition of a sequence of adenylyl residues (polyadenylation) at the 3' end the target rRNA. (Source: PMID:17652137, GOC:krc, PMID:15173578, PMID:18591258, PMID:15935758, GOC:dgf, PMID:15572680)		#*** The chemical reactions and pathways occurring in the nucleus and resulting in the breakdown of a ribosomal RNA (rRNA) molecule, including RNA fragments released as part of processing the primary transcript into multiple mature rRNA species, initiated by the enzymatic addition of a sequence of adenylyl residues (polyadenylation) at the 3' end the target rRNA. (Source: PMID:17652137, GOC:krc, PMID:15173578, PMID:18591258, PMID:15935758, GOC:dgf, PMID:15572680)

		+	Using YEASTRACT to Infer which Transcription Factors Regulate a Cluster of Genes
		+
		+	- Profile #45 -
		+
		+	# How many transcription factors are green or "significant"?
		+	#* 19 transcription factors are green.
		+	# Are CIN5, GLN3, and/or HAP4 are not on the green list? If so, what is their "% in user set", "% in YEASTRACT", and "p value".
		+	#* CIN5, GLN3, and HAP4 are on the table, but not on the green list (instead, on the pink).
		+	#** '''CIN5:'''
		+	#*** % user set: 16.82%
		+	#*** % in YEASTRACT: 4.17%
		+	#*** p-value: 0.999999999999975
		+	#** '''GLN3:'''
		+	#*** % user set: 37.34%
		+	#*** % in YEASTRACT: 8.38%
		+	#*** p-value: 0.031507090452519
		+	#** '''HAP4:'''
		+	#*** % user set: 15.71%
		+	#*** % in YEASTRACT: 7.79%
		+	#*** p-value: 0.361027186229152
	==== Data and Files ====		==== Data and Files ====

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 This section is in acknowledgement to partner Christina Dominguez ([[User:Cdomin12]]), as well as, Marcus Avila ([[User:Mavila9]]) and Jonar Cowan ([[User:Jcowan4]]). I would also like to acknowledge Dr. Dahlquist ([[User:KDahlquist]]) for introducing and teaching the topic and direction of this assignment.
-"Except for what is noted above, this individual journal entry was completed by me and not copied from another source." [[User:Knguye66|Knguye66]] ([[User talk:Knguye66|talk]]) 21:05, 28 October 2019 (PDT)
+"Except for what is noted above, this individual journal entry was completed by me and not copied from another source." [[User:Knguye66|Knguye66]] [[User:Knguye66|Knguye66]] ([[User talk:Knguye66|talk]]) 21:07, 28 October 2019 (PDT)
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← Older revision		Revision as of 04:06, 29 October 2019
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	* Gene Association. (n.d.) Retrieved from https://lmu.app.box.com/s/zlr1s8fjogfssa1wl59d5shyybtm1d49		* Gene Association. (n.d.) Retrieved from https://lmu.app.box.com/s/zlr1s8fjogfssa1wl59d5shyybtm1d49
	* The Short Time-series Expression Miner (STEM) version 1.3.12. (n.d.). Retrieved from http://www.cs.cmu.edu/~jernst/stem/		* The Short Time-series Expression Miner (STEM) version 1.3.12. (n.d.). Retrieved from http://www.cs.cmu.edu/~jernst/stem/
		+	* Geneontology (Unifying Biology) (n.d.). Retrieved from http://geneontology.org/