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Video demos and tutorials on using MPD

The series of short tutorials listed below was produced in April 2013. Please keep in mind that the current MPD application has evolved somewhat since then especially in terms of page layouts and locations of some things such as the pheno tool icons.

A study problem set (2013) is also available.

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

Videos may take a moment or two to load, depending on your connection speed.
 


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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