Dog CNV Database [Tutorial]

TUTORIAL

TABLE of CONTENTS

I. DESCRIPTIVE STATISTICS

I.1. Breeds name and symbol lists
I.2. CNV lists
I.3. Breed-specific and shared between breed CNV data
I.4-5. CNV query output examples

II. SEARCH CNV by CHROMOSOME and DISPLAY CNV GENE CONTENT

III. QUERY OPTIONS

IV. SEARCH CNVs by BREEDS

V. VISUALIZING DOG CNVs in the UCSC GENOME BROWSER

I. DESCRIPTIVE STATISTICS

I.1. Breeds name and symbol lists

I.2. CNV lists

I.2.1 : Full list of CNV

I.2.2 : Deletion : CNV that have been deleted (fewer than the normal number) with less than two copies

I.2.3 : Duplicated : more than the normal copy number

I.2.4 : Complex : CNV detected with deletion and duplication

I.3. Breed-specific and shared between breed CNV data

I.3.1 Shared CNV are found in ≥ 2 breeds

I.3.2 Specific CNVs found exclusively in a breed

I.4 : I.3.1 link displays all CNV shared by ≥2 breeds

Sort the ouput by breed, chromosome or breed number.

I.5 : Output example of CNVs shared exactly by two breeds

II. SEARCH CNV by CHROMOSOME and DISPLAY CNV GENE CONTENT

II.1. Search CNV by chromosome

II.1.1 Ouput example

II.2. Display CNV gene content

II.2.2 Ouput displays CNV coordinates, UCSC context, dog gene content and CanFam2 coordinates. ENSCAF is clickable to display additionnal features

II.3. Extended gene content data display OMIM link, UCSC track link, Human and Mouse orthologuous genes

III. QUERY OPTIONS

III.1 III.1 Search CNV that intersect canine genes : Text area to query by keyword

III.1.1 Output example for FBXO2 query

III.2 Search CNV by genomic coordinates

IV. SEARCH CNVs by BREEDS

IV.1. Query CNV in a selected breed : will display CNV shared by the selected breed and any other breeds if any

IV.2. Multiple queries : Selected a breed and a given chromosome

IV.3. Multiple queries : Select two breeds : will display CNVs shared by these two breeds and any others

IV.4. Output display of multiple queries -IV.3- : display CNVs shared by Dachshund and Cavalier King Charles and a link to extract CNV gene content

IV.5. Ouput example of gene content

V. VISUALIZING DOG CNVs in the UCSC GENOME BROWSER

V.1. Link to access canine CNV at UCSC Genome Browser

V.2. Select canine genome coordinates

V.3. A UCSC track displays all SNPs from the canine HD-array within the interval

V.4. CNVs are represented by red or blue bars : red for deletion, blue for duplicated CNV. Breed symbol is on the left.

V.5. UCSC custom tracks

-home page- http://www.eurolupa.org/

I. DESCRIPTIVE STATISTICS I.1. Breeds name and symbol lists I.2. CNV lists I.2.1 : Full list of CNV I.2.2 : Deletion : CNV that have been deleted (fewer than the normal number) with less than two copies I.2.3 : Duplicated : more than the normal copy number I.2.4 : Complex : CNV detected with deletion and duplication I.3. Breed-specific and shared between breed CNV data I.3.1 Shared CNV are found in ≥ 2 breeds I.3.2 Specific CNVs found exclusively in a breed I.4 : I.3.1 link displays all CNV shared by ≥2 breeds Sort the ouput by breed, chromosome or breed number. I.5 : Output example of CNVs shared exactly by two breeds


II. SEARCH CNV by CHROMOSOME and DISPLAY CNV GENE CONTENT
II.1. Search CNV by chromosome II.1.1 Ouput example II.2. Display CNV gene content II.2.2 Ouput displays CNV coordinates, UCSC context, dog gene content and CanFam2 coordinates. ENSCAF is clickable to display additionnal features II.3. Extended gene content data display OMIM link, UCSC track link, Human and Mouse orthologuous genes


III. QUERY OPTIONS
III.1 III.1 Search CNV that intersect canine genes : Text area to query by keyword III.1.1 Output example for FBXO2 query III.2 Search CNV by genomic coordinates


IV. SEARCH CNVs by BREEDS
IV.1. Query CNV in a selected breed : will display CNV shared by the selected breed and any other breeds if any IV.2. Multiple queries : Selected a breed and a given chromosome IV.3. Multiple queries : Select two breeds : will display CNVs shared by these two breeds and any others IV.4. Output display of multiple queries -IV.3- : display CNVs shared by Dachshund and Cavalier King Charles and a link to extract CNV gene content IV.5. Ouput example of gene content


V. VISUALIZING DOG CNVs in the UCSC GENOME BROWSER
V.1. Link to access canine CNV at UCSC Genome Browser V.2. Select canine genome coordinates V.3. A UCSC track displays all SNPs from the canine HD-array within the interval V.4. CNVs are represented by red or blue bars : red for deletion, blue for duplicated CNV. Breed symbol is on the left. V.5. UCSC custom tracks