Talk:Jenna Reed - Revision history

Jereed at 18:59, 11 March 2018

2018-03-11T18:59:45Z

Jereed at 18:57, 11 March 2018

2018-03-11T18:57:40Z

Jereed at 18:50, 11 March 2018

2018-03-11T18:50:52Z

Jereed at 18:46, 11 March 2018

2018-03-11T18:46:05Z

Jereed at 02:47, 14 February 2018

2018-02-14T02:47:32Z

Jereed: /* 2/8/18 */ new section

2018-02-14T02:46:45Z

‎2/8/18: new section

Jereed: /* 2/13/18 */ new section

2018-02-14T02:46:32Z

‎2/13/18: new section

Jereed at 02:44, 14 February 2018

2018-02-14T02:44:31Z

Jereed at 02:44, 14 February 2018

2018-02-14T02:44:07Z

Jereed: Created page with "2/8/18 Bio343 HTSeq Results Male Mutant 25 and 24 = paired reads, Male mouse 2078, C201R 15 and 14 = paired reads, Male mouse 2073, C201R 3 and 2 = paired reads, Male mouse..."

2018-02-13T14:43:06Z

Created page with "2/8/18 Bio343 HTSeq Results Male Mutant 25 and 24 = paired reads, Male mouse 2078, C201R 15 and 14 = paired reads, Male mouse 2073, C201R 3 and 2 = paired reads, Male mouse..."

New page

2/8/18

Bio343 HTSeq Results

Male Mutant
25 and 24 = paired reads, Male mouse 2078, C201R
15 and 14 = paired reads, Male mouse 2073, C201R
3 and 2 = paired reads, Male mouse 2079, C201R

Male WT
21 and 20 = paired reads, Male mouse 2076, WT
19 and 18 = paired reads, Male mouse 2075, WT
17 and 16 = paired reads, Male mouse 2074, WT

Female Mutant
13 and 12 = paired reads, Female mouse 2072, C201R
11 and 10 = paired reads, Female mouse 2071, C201R
9 and 8 = paired reads, Female mouse 2070, C201R

Female WT
23 and 22 = paired reads, Female mouse 2077, WT
7 and 6 = paired reads, Female mouse 2081, WT
5 and 4 = paired reads, Female mouse 2080, WT

Gene Cards
Gene Weaver
GO rilla
FNTM
String
NCBI

2/8/18
" Loaded data from "Histories Shared with Me"

NefL >>> deltaCMT 1F 2E
NefH >>> deltaALS
Sphk2 >>> kinase
Male v Female
MaleWT v MaleCMT
FemaleWT v FemaleCMT
Gm4210
NefM (neurofilament medium)
Close with NefL, and Gm2410
Calca >>> calcium regulator

About this data
" Took the spinal cord of the mice and sent it off for RNASeq
" 2-fold change
o -0.7 = 1.62 fold change
o -0.8 = 1.74 fold change
o -7.56 = 128fold change, p=10^-14
o What's our fold-change cutoff?
" JAX had a strict cutoff and got only 20 genes
" Lack of signal because of CMT could cause repression of transcription (because usually ligand binding induces transcription)
" RNASeq data will always have differential expression from natural variation
o Is it enough differential expression that it could be caused by the disease?

@@ Line 1: / Line 1: @@
-== 2/8/18 ==
+== CMT: 2/8/18 ==
 /8/18
@@ Line 36: / Line 36: @@
-== 2/13/18 ==
+== CMT: 2/13/18 ==
 /13/18
@@ Line 60: / Line 60: @@
-== 2/15/18: GeneWeaver Lecture ==
+== CMT: 2/15/18: GeneWeaver Lecture ==
@@ Line 157: / Line 157: @@
-== 2/22/18 ==
+== CMT: 2/22/18 ==
@@ Line 220: / Line 220: @@
-== 2/27/18: Notes for Results & Conclusion ==
+== CMT: 2/27/18: Notes for Results & Conclusion ==
 Nefl: neurofilament light polypeptide

← Older revision		Revision as of 18:57, 11 March 2018
Line 218:		Line 218:
	Atp1a1		Atp1a1
	Regulation of muscle contraction		Regulation of muscle contraction
		+
		+
		+	== 2/27/18: Notes for Results & Conclusion ==
		+
		+	Nefl: neurofilament light polypeptide
		+	GeneCards:
		+	Has not been connected to ALS, but has been associated with CMT
		+	Related pathways: RET Signaling & Post-NMDA receptor activation events
		+	RET Signaling: (Takahashi, 2001)
		+	Works with glial cell line-derived neurotrophic factor (GDNF)
		+	Promotes neuron survival
		+	Related neurotrophic factors could be used as therapies for neurodegenerative diseases
		+	Post-NMDA Receptor Activation Events
		+	Involved in calcium ion influx
		+	Establishes long-term synaptic changes
		+	Appear to be more related to central nervous system rather than peripheral
		+	NMDA agonists are treatment Alzheimer's in US and Europe
		+	OMIM
		+	Implicated in CMT2E (pretty similar phenotype to 2D) and CMT1F, so may play a role here
		+	(Lin et al., 2009)
		+	Previously connected motor neuron degradation with the binding of a destabilizing protein (190RhoGEF) to Nefl mRNA
		+	Result was downregulation of Nefl mRNA in neurons
		+	Nefm co-expression increased in response
		+
		+	Nefm: neurofilament medium polypeptide
		+	GeneCards:
		+	Associated with ALS
		+	GO annotations: related to structural molecule activity and structural constituents of the cytoskeleton
		+
		+	Nefh: neurofilament heavy polypeptide
		+	GeneCards:
		+	Associated with ALS and CMT previously
		+	GO annotations: Related to protein kinase binding and microtubule binding
		+	OMIM
		+	Collard et al. (1995) hypothesized that axonal degeneration is caused by blocking the transport of molecules needed for axonal maintenance by road-blocking the transport network (may be part of ALS pathogenesis)
		+	Rebelo et al. (2016)
		+	Implicated in CMT2CC
		+	Frameshift mutations in NEFH resulted in aggregation of protein, which could block the transport for axonal maintenance molecules
		+	Elder et al. (1998)
		+	Created Nefh knockout mice to study connection between neurofilament levels and axon size
		+	Resulted in slight reduction of neurofilament levels, yet a drastic reduction in axon diameter
		+	Supports the idea that the issue is about disrupting transport on the intracellular network rather than a degeneration of the network itself
		+	Shows that the Nefh gene plays a strong role in axonal development (and reduced axon size is part of the CMT2D phenotype, which is why it may be important to study)
		+	Need more info on how Nefh may affect axon size
		+	Rebelo et al. (2016): looked at NEFH mutations and saw aggregation of abnormal proteins. Found similar mutation in NEFL, which they note is known to be related to CMT. Perhaps the mutant GARS proteins bind to NEFH proteins and cause them to aggregate because they can't be used (similar to the NEFL explanation)
		+
		+
		+	All 3 of these genes are under-expressed in our research mice. Under-expression means that the integrity of the axoskeleton around the neurons is not good, so intracellular transport to and from these neurons may be affected
		+
		+	As seen with Nefl, interference with the mRNA causes downregulation of the mRNA, which could explain why the gene is showing under-expression in our mice
		+
		+	In the Lin et al. (2009) study, Nefm expression increased to compensate for the downregulation of Nefl, but perhaps in CMT2D, it interferes with all three types of neurofilament mRNA
		+	Could the mutant GARS proteins have gained the function to bind with the neurofilament mRNA (like the destabilizing protein mentioned in Lin et al., 2009)?
		+	Research may also support this explanation for Nefh
		+
		+	Discussion
		+	Nefl: Potential toxic gain-of-function where the mutant GARS proteins interfere with neurofilament mRNA by binding to it, resulting in downregulation of the neurofilament genes
		+	Nefh: blocks transport on intracellular network (may be similar mechanism to Nefl issue)
		+	Need more info on how Nefh may affect axon size
		+	Each of the focus genes above have orthologs in mice, meaning researchers could study these genes in relation to Gars fairly easily
		+	May have a section connecting to ALS, as I think the potential mechanisms I'm discussing have a role in ALS.
		+	Reiterate need to research better treatment options

← Older revision		Revision as of 18:50, 11 March 2018
Line 155:		Line 155:
	Annotations should automatically be generated when you create your set		Annotations should automatically be generated when you create your set
	Once you've created your gene sets, you can share it with groups and begin analysis		Once you've created your gene sets, you can share it with groups and begin analysis
		+
		+
		+	== 2/22/18 ==
		+
		+
		+	Final Paper: 5-10 pages, including figures
		+	Zotero style = Cell
		+	Figures embedded in text
		+	Have figure legends (not in a text box)
		+	Suggested writing order
		+	Title > 7
		+	Authors (you first, partner second) > 6
		+	Abstract (200-word limit) > 5
		+	Intro > 4
		+	Methods > 1
		+	Results > 2 (figures first, then writing)
		+	Discussion > 3
		+	References > 8 (Zotero)
		+
		+	GO-rilla:
		+	MUTvWT (ranked by p-value)
		+	Nefm (medium polypeptide)
		+	Nefh (heavy polypeptide)
		+	Nefl (light polypeptide)
		+	Calca (calcitonin/calcitonin-related polypeptide, alpha
		+	Slc31a1 (solute carrier family 31, member 1)
		+	Tnnt1 (troponin t1, skeletal, slow)
		+	Atp1a1 (atpase, na+/k+ transporting, alpha 1 polypeptide)
		+	Myh7 (myosin, heavy polypeptide 7, cardiac muscle, beta)
		+
		+	p = 10-7-10-9
		+
		+	When sorted by fold change: MUTvWT
		+	intermediate filament-based process
		+	Prph - peripherin
		+
		+
		+	Genes of Interest:
		+	Nefm
		+	Nefh
		+	Nefl
		+
		+	If I need them (in order of use):
		+	Calca
		+	Atp1a1
		+	Prph
		+	Tnnt1
		+	Slc31a1 & Myh7
		+
		+
		+	Nefl, Nefm, & Nefh:
		+	Intermediate filament-based process
		+	Intermediate filament cytoskeleton organization
		+	Neurofilament cytoskeleton organization
		+	Intermediate filament organization
		+	Intermediate filament bundle assembly
		+	Neurofilament bundle assembly
		+	Axon development
		+	Calca
		+	Regulation of muscle contraction (not shown on figure)
		+	Regulation of anatomical structure size (not shown on figure)
		+	Atp1a1
		+	Regulation of muscle contraction

← Older revision		Revision as of 18:46, 11 March 2018
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	Tsix >>> p-adj is less than 0.05 for both MUT_MALEvFEMALE and WT_MALEvFEMALE		Tsix >>> p-adj is less than 0.05 for both MUT_MALEvFEMALE and WT_MALEvFEMALE
		+
		+
		+	== 2/15/18: GeneWeaver Lecture ==
		+
		+
		+	Why GeneWeaver?
		+	Integrative functional genomics
		+	Goal is to integrate the genetic investigation of humans and animal models
		+	Data repository has a number of different types of data
		+	Microarrays
		+	Published data
		+	Annotations
		+	GWAS
		+	QTL
		+	Tools
		+	Can do set-set matches
		+	Can match your set of gene with your other set of genes or with another set of genes in the database
		+	ODE IDs are a reference to find the consilience among associations of biomolecular entities and related concenpts
		+	http://beta.geneweaver.org/ >>> new version
		+	Types of functional genomics data
		+	Mapping Data
		+	QTL Positional candidates (mouse, rat)
		+	GWAS Candidate (from original studies)
		+	Expression Data
		+	DRG (Drug Related Genes) >>> from literature
		+	ABA (Allen Brain Atlas) >>> mice
		+	CTD (Comparative Toxicogenomics Database) >>> from 9 different species
		+	Functional Annotations
		+	GO (Gene Ontology Annotations) > human, house
		+	MP (Mammalian Phenotype Ontology)
		+	HP (Human phenotype ontology)
		+	OMIM (Online Mendelian Inheritance in Man)
		+	MeSH (Medical Subject Headings)
		+	Pathway Data
		+	KEGG (Kyoto Encyclopedia of Genes and Genomes)
		+	MSigDB (Molecular Signatures Databases)
		+	PC (Pathway Commons)
		+
		+	How do we use GeneWeaver?
		+	Tier III = data curated from literature (gold standard)
		+	Tier I and II = public resource data (II is pre-processed somehow)
		+	Search
		+	On results, "+" give you more basic info (description, authors, etc.) or gene set
		+	Clicking on gene set name will allow you to view the gene set
		+	Gene list on bottom of gene set entry
		+	Gene Symbol >>> can be changed to show identifier numbers for datasets
		+	Homology shows which species there is a homologous gene in
		+	Linkouts can take you to entry in each database
		+	Under a search, you can select genesets, then hit "Add Selected to Project" (at top of search results) and you can add it to an existing project or create a new project
		+	Top Toolbar: Analyze GeneSet
		+	Can select all genesets in a project, or can expand project (+) and select specific sets
		+
		+	Analyzing a GeneSet
		+	HiSim Graph
		+	Usually default parameters are fine
		+	On resulting graph
		+	Can zoom in or out
		+	Right = 4 genesets
		+	Hover mouse over it to get a little data info
		+	Moving right to left, you'll encounter nodes (intersection between our genesets)
		+	Hovering over the node will show you what genes interact between the two genesets
		+	Furthest left nodes show the most connected genes (genes that are in the most genesets)
		+	Left clicking on a node will make it disappear so that we only show what we do care about (left clicking on it again will make it reappear)
		+	Right clicking (or shift+left click) on the node will make a more detailed node summary page appear
		+	Visualization
		+	Classic = more descriptive without clicking on things
		+	Modern = easier to see connections
		+	Contains my projects and projects that have been shared with me
		+	GeneSet Graph
		+	Shows us which genes are connected to which datasets
		+	Left to right = less connected gene sets to most connected gene sets
		+	Color lines match color of gene set boxes
		+	Difference between this and HiSim Graph
		+	HiSim = emphasizes the sets and the relationship between the sets
		+	GeneSet = highlights the genes
		+	Different ways of visualizing the same thing
		+	Tool Options >>> MinDegree
		+	Allows you to limit it so that the graph only shows genes that have X number of connections
		+	e.g. if you change the MinDegree to 4 and hit "Re-Run Tool," the graph will only show genes that are in at least 4 of the data sets
		+	Jaccard Similarity Status
		+	Top Toolbar
		+	Manage Genesets > Manage Projects
		+	Can view/edit all your projects
		+	Little arrow with dots on points = share project
		+	Can share project with a group that you're part of
		+	Top Toolbar >>> Manage GeneSets >>> Upload GeneSet
		+	Give set a descriptive name
		+	Figure Label = shorter version of GeneSet Name (something that will fit on an analysis label)
		+	Score Type: no way to upload a gene set with two different score types
		+	Can upload gene set twice, each one with a different score type, then threshold the gene sets
		+	Choose access restriction and you can share which groups you want
		+	Select species (Mus musculus)
		+	Gene Identifier: can't use a mix of gene identifiers, but some databases have conversion tools
		+	Gene List: File Upload only takes plain text
		+	If you copy and paste from excel, it should automatically format properly
		+	Annotations should automatically be generated when you create your set
		+	Once you've created your gene sets, you can share it with groups and begin analysis

← Older revision		Revision as of 02:46, 14 February 2018
Line 58:		Line 58:
	RNASeq data will always have differential expression from natural variation		RNASeq data will always have differential expression from natural variation
	Is it enough differential expression that it could be caused by the disease?		Is it enough differential expression that it could be caused by the disease?
		+
		+	== 2/13/18 ==
		+
		+	2/13/18
		+
		+	mut/WT log2 500/1000 = 0.5 Anything less than 1 is negative
		+
		+	DESeq2 >>> run htseq-count data with features After doing a DESeq2 run, two files will appear in the history First one is tabular. Download that, open in Text Wrangler, then copy and paste that in excel Second one is a pdf. Download and open that to see data visualizations
		+
		+	54 & 55 >>> DESeq2 for "Female_MUTvWT" 56 & 57 >>> DESeq2 for "Male_MUTvWT" 58 & 59 >>> DESeq2 for "MUT_MALEvFEMALE" 60 & 61 >>> DESeq2 for "WT_MALEvFEMALE" 62 & 63 >>> DESeq2 for "MUT_v_WT"
		+
		+	Research method for today: look at what genes are significant in each dataset and see where there is overlap between datasets
		+
		+	In excel sheet: DESeq2 data for all 5 comparisons P-value < 0.05 highlighted in yellow P-adjusted <0.05 highlighted in green List of just the p-adjusted <0.05 genes for all 5 comparisons together
		+
		+	General observations:
		+
		+	of genes with p-adj < 0.05
		+	Female_MUTvWT: 72
		+
		+	Sphk2 >>> p-adj is less than 0.05 for both MUT_MALEvFEMALE and WT_MALEvFEMALE Sphingosine Kinase 2 Paralog with Sphk1, which codes for the other enzyme that has the same function Encodes for an enzyme that catalyzes the phosphorylation of sphingosine into sphingosine 1-phosphate sphingosine 1-phosphate = important in cell migration, proliferation, apoptosis Implicated in some cancers (breast cancer proliferation, chemoresistance) Related pathways: Calcium signaling pathway (could be connection to CMT2D), Metabolism
		+
		+	Tsix >>> p-adj is less than 0.05 for both MUT_MALEvFEMALE and WT_MALEvFEMALE

@@ Line 1: / Line 1: @@
 /8/18
 Bio343 HTSeq Results
-Male Mutant
+Male Mutant 25 and 24 = paired reads, Male mouse 2078, C201R 15 and 14 = paired reads, Male mouse 2073, C201R 3 and 2 = paired reads, Male mouse 2079, C201R
-Male WT
+Male WT 21 and 20 = paired reads, Male mouse 2076, WT 19 and 18 = paired reads, Male mouse 2075, WT 17 and 16 = paired reads, Male mouse 2074, WT
-Female Mutant
+Female Mutant 13 and 12 = paired reads, Female mouse 2072, C201R 11 and 10 = paired reads, Female mouse 2071, C201R 9 and 8 = paired reads, Female mouse 2070, C201R
-Female WT
+Female WT 23 and 22 = paired reads, Female mouse 2077, WT 7 and 6 = paired reads, Female mouse 2081, WT 5 and 4 = paired reads, Female mouse 2080, WT
 == 2/13/18 ==
@@ Line 81: / Line 58: @@
 Tsix >>> p-adj is less than 0.05 for both MUT_MALEvFEMALE and WT_MALEvFEMALE

← Older revision		Revision as of 02:46, 14 February 2018
Line 81:		Line 81:

	Tsix >>> p-adj is less than 0.05 for both MUT_MALEvFEMALE and WT_MALEvFEMALE		Tsix >>> p-adj is less than 0.05 for both MUT_MALEvFEMALE and WT_MALEvFEMALE
		+
		+	== 2/8/18 ==
		+
		+	2/8/18
		+
		+	Bio343 HTSeq Results
		+
		+	Male Mutant 25 and 24 = paired reads, Male mouse 2078, C201R 15 and 14 = paired reads, Male mouse 2073, C201R 3 and 2 = paired reads, Male mouse 2079, C201R
		+
		+	Male WT 21 and 20 = paired reads, Male mouse 2076, WT 19 and 18 = paired reads, Male mouse 2075, WT 17 and 16 = paired reads, Male mouse 2074, WT
		+
		+	Female Mutant 13 and 12 = paired reads, Female mouse 2072, C201R 11 and 10 = paired reads, Female mouse 2071, C201R 9 and 8 = paired reads, Female mouse 2070, C201R
		+
		+	Female WT 23 and 22 = paired reads, Female mouse 2077, WT 7 and 6 = paired reads, Female mouse 2081, WT 5 and 4 = paired reads, Female mouse 2080, WT
		+
		+
		+	Gene Cards Gene Weaver GO rilla FNTM String NCBI
		+
		+
		+	2/8/18 Loaded data from "Histories Shared with Me"
		+
		+
		+	NefL >>> deltaCMT 1F 2E NefH >>> deltaALS Sphk2 >>> kinase
		+
		+	Male v Female
		+	MaleWT v MaleCMT
		+	FemaleWT v FemaleCMT
		+	Gm4210 NefM (neurofilament medium) Close with NefL, and Gm2410 Calca >>> calcium regulator
		+
		+	About this data: Took the spinal cord of the mice and sent it off for RNASeq 2-fold change
		+
		+	-0.7 = 1.62 fold change
		+	-0.8 = 1.74 fold change
		+	-7.56 = 128fold change, p=10^-14
		+	What's our fold-change cutoff? JAX had a strict cutoff and got only 20 genes Lack of signal because of CMT could cause repression of transcription (because usually ligand binding induces transcription) RNASeq data will always have differential expression from natural variation Is it enough differential expression that it could be caused by the disease?

@@ Line 48: / Line 48: @@
 Calca >>> calcium regulator
-About this data
+About this data: Took the spinal cord of the mice and sent it off for RNASeq
 -fold change
       -0.7 = 1.62 fold change
@@ Line 55: / Line 54: @@
       -7.56 =  128fold change, p=10^-14
 What's our fold-change cutoff?
-     JAX had a strict cutoff and got only 20 genes
+JAX had a strict cutoff and got only 20 genes
 Lack of signal because of CMT could cause repression of transcription (because usually ligand binding induces transcription)
 RNASeq data will always have differential expression from natural variation
 Is it enough differential expression that it could be caused by the disease?

@@ Line 34: / Line 34: @@
 /8/18
-"	Loaded data from "Histories Shared with Me"
+Loaded data from "Histories Shared with Me"
@@ Line 40: / Line 40: @@
 NefH >>> deltaALS
 Sphk2 >>> kinase
-	Male v Female
+     Male v Female
-	MaleWT v MaleCMT
+     MaleWT v MaleCMT
-	FemaleWT v FemaleCMT
+     FemaleWT v FemaleCMT
 Gm4210
 NefM (neurofilament medium)
@@ Line 49: / Line 49: @@
 About this data
-"	Took the spinal cord of the mice and sent it off for RNASeq
+     Took the spinal cord of the mice and sent it off for RNASeq
-"	2-fold change
+-fold change
-o	-0.7 = 1.62 fold change
+     -0.7 = 1.62 fold change
-o	-0.8 = 1.74 fold change
+     -0.8 = 1.74 fold change
-o	-7.56 =  128fold change, p=10^-14
+     -7.56 =  128fold change, p=10^-14
-o	What's our fold-change cutoff?
+What's our fold-change cutoff?
-"	JAX had a strict cutoff and got only 20 genes
+     JAX had a strict cutoff and got only 20 genes
-"	Lack of signal because of CMT could cause repression of transcription (because usually ligand binding induces transcription)
+Lack of signal because of CMT could cause repression of transcription (because usually ligand binding induces transcription)
-"	RNASeq data will always have differential expression from natural variation
+RNASeq data will always have differential expression from natural variation
-o	Is it enough differential expression that it could be caused by the disease?
+Is it enough differential expression that it could be caused by the disease?