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Video demos and tutorials on using MPD

The series of short tutorials listed below was produced in April 2013.

A study problem set (2013) is also available.

For specific questions and suggestions we invite you to contact our help desk at any time.

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1. Intro and using MPD search
Some background (0:16)     Where our data comes from (0:43)     Strains in MPD (1:05)     Strain panels in MPD (1:22)     Some basic searches (1:36)     Google-driven MPD site search (2:15)     Getting help (2:40)    



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2. Finding and visualizing phenotype strain survey data
A typical phenotype measurements listing (0:45)     Visualizing a measurement (1:40)     Table of strain averages (2:10)     Seeing individual animal scores (2:23)     Measurement sets / series (2:30)     Browse all phenotypes (2:55)     More on measurements listings (3:12)     All interventions (drugs, diets, etc.) (4:15)     All methodologies (4:34)    



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3. Creating a collection using the shopping cart
What measurements are in my collection? (0:35)     Adding to your cart (0:48)     Using tools with your cart (1:55)     When to use shopping cart, and when not to (2:25)     Shopping cart caveats (2:35)    



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4. Phenotype viewing and analysis tools
Getting started (0:25)     Finding the Apply Tools button (0:38)     Selecting specific phenotype data to look at (0:54)     Deciding which data to use (1:28)     Going around again (2:10)     Getting to the tools for a single measurement (2:25)     Pheno toolbox (2:53)     Strain bars (3:05)     Individual animals (3:45)     Matrix of p values (4:04)     Strain distribution plots (4:50)    



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5. Phenotype viewing and analysis tools (2nd row)
We demo the 2nd row tools, and far right tools, in MPD's pheno toolbox.
Data table tool (0:16)     Color grid (0:38)     Find strains that best meet your criteria (0:45)     Side-by-side plot w/ p values (1:22)     Overlay plot (1:50)     Overlaid lines plot (1:59)     Sex differences (2:20)     Strain outliers (2:34)     Number of animals tested table (2:48)     Custom downloads (2:57)    



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6. Phenotype correlations and ratios tools (3rd row)
We demo the 3rd row tools in MPD's pheno toolbox.
Scatterplots (1:00)     Correlations matrix (1:30)     Search all MPD for phenotypes that are correlated (1:56)     Computing ratios or differences (2:40)     Taking a ratio and seeing what's correlated (3:15)    



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7. Phenotype vs. genotype tools (4th row)
We demo the 4th row tools in MPD's pheno toolbox.
Find genes where selected strains are polymorphic (0:30)     GWAS analysis on UCLA's EMMA server (1:45)     Phenotype dumps for EMMA server (2:40)     Find correlated gene expression probesets (2:55)    



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8. Ontologies in MPD
Navigating (0:50)     Seeing MPD measurements that are mapped (1:38)     Restart / search (1:55)     From category pages (2:20)     Context link (2:40)     Verbose descriptions (3:00)     In MPD search (3:15)     MP ontology "abnormal" phrasing (3:40)    



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9. Finding out about a strain – phenotype
In this session we randomly choose strain FVB/NJ to investigate.
Finding FVB (0:26)     FVB "hub" page (1:05)     FVB JaxMice data sheet (1:20)     Data averages for FVB (1:50)     Dump all FVB phenotypes (2:40)     FVB outlier analysis (2:58)     FVB in shopping cart collection (3:26)     Intervention studies involving FVB (3:37)    



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10. Finding out about a strain – genotype and gene expression
We continue investigating a specific strain (FVB/NJ in this case).
SNPs and genotype for FVB (0:30)     Find genes where FVB is polymorphic vs other strain (0:56)     Gene expression data where FVB is an outlier (2:30)    



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11. Limiting to one strain panel; Comparing two specific strains
This session covers the above two topics.
Limiting to one strain panel (0:20)     Compare 2 specific strains (1:30)     List measurements where 2 strains differ the most (2:40)    



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12. SNP and genotype variation queries
Available data sets (0:20)     Simple example query (0:38)     Avoid backing up (1:55)     Simple example query 2 (2:10)     Indels in the result (2:48)     SVs in the result (2:57)     Download your result in CSV (3:08)     Polymorphism matrix (3:10)     Hap block view (3:17)     Query on 11 different rs numbers (3:24)    



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13. A large-region SNP retrieval, and capturing a gene set
Large-region SNP retrieval example (0:25)     Capturing the genes that came up, as a gene set (1:40)     Gene set help page (2:25)     Capturing a gene set from the 'Find genes' tool (2:35)    



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14. Genes, markers, genomic regions, and gene expression functionality
In this session we randomly choose mouse gene Dab1 to investigate.
MPD search on a gene symbol (0:45)     Gene info page for Dab1 (0:50)     SNPs/variation for Dab1 (1:15)     Gene expression for Dab1 (1:36)     GX: paring down by data set (2:14)     GX: phenotypes mathematically correlated to Dab1 (3:20)     Finding info on an arbitrary genomic region (4:10)    



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