Integration and visualization of genome-wide data

Integration and visualization of genome-wide data

Data integration and visualization

http://genomeview.org/

http://www.broadinstitute.org/igv/

Stand-alone genome browsers

http://genome.ucsc.edu/

http://www.ensembl.org/

http://www.ncbi.nlm.nih.gov/mapview/

Web-based genome browsers

Web-based Genome Browsers

• Software designed to enable a user to access and display genome sequence data

• Visual integration and correlation of different types of information

• Organize large amounts of genome sequence data

Web-based Genome Browsers

• UCSC, Ensembl and NCBI are based on the same reference genome

• The three genome browser mainly change at interface level and annotations available.

• Some genomes are available in one genome browser but not the other.

UCSC genome browser http://genome.ucsc.edu/

88 species annotated in UCSC genome browser •MAMMALS •VERTEBRATES •DEUTEROSTOMES •NEMATODES •OTHER (Sea Hare, Yeast)

NO plants

UCSC genome browser

• Allows aligning to genome sequence via BLAT

• Table Browser

• Creation of PDF

• Provides access to all the data produced by the project, and to the software used to analyze and present it

• Site produces and maintains annotation tracks

http://genome.ucsc.edu/

Annotation tracks

• Genomic data: known genes, predicted genes, ESTs, mRNAs, CpG islands, assembly gaps and coverage, chromosomal bands, homologies, Chip-Seq data, DNAse-Seq data, Expression data, …

• Annotation tracks are both computed at UCSC from publicly available sequence data and provided by collaborators

• Users can also add their own custom tracks to the browser

UCSC genome browser search

UCSC genome browser search

UCSC genome browser layout http://genome.ucsc.edu/

Current chromosomal location, navigation and search bar.


Graphical visualization of the chromosome and current view location


Coordinates on reference genome


Annotation tracks


Annotation tracks

Genes

SNPs

H3K27Ac Epig. marker

ChIP-Seq data (TF binding sites)

Conservation of sequence in mammals (PhyloP)

Multiple alignments

Repeated sequences


GENES


GENES

H3K27Ac


GENES

H3K27Ac SNPs

Tracks available

Below the main view of UCSC genome browser many more tracks are available. Tracks are grouped in: •Mapping and sequencing tracks •Phenotype and Disease Associations •Genes and Gene Prediction Tracks •Literature •mRNA and EST Tracks •Expression •Regulation •Comparative Genomics •Neandertal Assembly and Analysis •Denisova Assembly and Analysis •Variation and Repeats

Tracks group

Different visualization options: -Hide -Dense -Full -Squish -Pack

Example search: BRCA1


Transcripts isoforms



Activate Catalogue Of Somatic Mutations In Cancer (COSMIC) track





Get DNA for By clicking on a feature (for example a gene) with the right button it’s possible to get access to the feature menu. By clicking on Get DNA for gene name it’s possible to download the gene sequence

Get DNA for

Get DNA for

Get DNA for

Get DNA for

Display of custom tracks


Paste here your own track data!!

Tracks formats

• BED: flexible format to define data lines that are displayed in an annotation track.

• GTF: gene transfer format, generally used to display gene annotation data

• WIG: allows to display countinuos valued data • BAM: standard alignment format for NGS

sequence aligners • VCF: variants call format, used to display

sequence variants • Many more…

BED file format

Name Description

chrom* The name of the chromosome (e.g. chr3, chrY, chr2_random) or scaffold (e.g. scaffold10671).

chromStart* The starting position of the feature in the chromosome or scaffold. The first base in a chromosome is numbered 0.

chromEnd* The ending position of the feature in the chromosome or scaffold.

name Defines the name of the BED line.

score A score between 0 and 1000.

strand Defines the strand - either '+' or '-'.

thickStart The starting position at which the feature is drawn thickly .

thickEnd The ending position at which the feature is drawn thickly

itemRgb An RGB value of the form R,G,B (e.g. 255,0,0).

blockCount The number of blocks (exons) in the BED line.

blockSizes A comma-separated list of the block sizes. The number of items in this list should correspond to blockCount.

BlockStarts A comma-separated list of block starts.

track name=junctions description="TopHat junctions" test_chromosome 180 402 JUNC00000001 46 + 180 402 255,0,0 2 70,52 0,170 test_chromosome 349 550 JUNC00000002 38 + 349 550 255,0,0 2 51,50 0,151

33 * Required fields

Flexible format, easy to adapt from blast and blat outputs…

BED file example

chr7 127471196 127472363 Pos1 0 +

chr7 127472363 127473530 Pos2 100 +

chr7 127473530 127474697 Pos3 100 +

chr7 127474697 127475864 Pos4 1000 +

chr7 127475864 127477031 Neg1 1000 -

chr7 127477031 127478198 Neg2 0 -

chr7 127478198 127479365 Neg3 0 -

chr7 127479365 127480532 Pos5 0 +

chr7 127480532 127481699 Neg4 0 -




Display of custom tracks Cliccando con il tasto destro sulla traccia posso modificare come viene mostrata:

Display of custom tracks Se seleziono “full”

Display of custom tracks By clicking on the name of the track it’s possible to configure how the track is displayed



Posso ad esempio cambiare il nome della traccia e la descrizione ma anche colorare la traccia in maniera differente a seconda dello strand

track name='my data' description='this is an example track' colorByStrand="255,0,0 0,0,255"


chr7 127471196 127472363 Pos1 0 +

chr7 127472363 127473530 Pos2 100 +

chr7 127473530 127474697 Pos3 100 +

chr7 127474697 127475864 Pos4 1000 +

chr7 127475864 127477031 Neg1 1000 -

chr7 127477031 127478198 Neg2 0 -

chr7 127478198 127479365 Neg3 0 -

chr7 127479365 127480532 Pos5 0 +

chr7 127480532 127481699 Neg4 0 -


track name='my data' description='this is an example track' useScore=1

By using the useScore=1 option it’s possible to show the tracks in shades of gray depending on the score column value


chr7 127471196 127472363 Pos1 0 +

chr7 127472363 127473530 Pos2 100 +

chr7 127473530 127474697 Pos3 100 +

chr7 127474697 127475864 Pos4 1000 +

chr7 127475864 127477031 Neg1 1000 -

chr7 127477031 127478198 Neg2 0 -

chr7 127478198 127479365 Neg3 0 -

chr7 127479365 127480532 Pos5 0 +

chr7 127480532 127481699 Neg4 0 -

UCSC Genome Browser Tools




Extracting informations with the Table Browser

All the data displayed on UCSC genome browser is contained in a public MySQL server (relational database) which can be: • accessed directly with standard mysql command • or can be accessed using the Table browser

Useful to retrieve data associated with a track in text format, to calculate intersections between tracks, and to retrieve DNA sequence covered by a track.


Clade Genoma Versione del genoma



Track type


Track


Track



Descrizione dei dati contenuti nella tabella


Filtering


Filtering





Allows to intersect the selected track with another track.


Select output format


Select which features to save into the BED file


Ensembl http://www.ensembl.org

71 species in Ensembl database

Includes automatic annotations on eukariotes made by Ensembl

EnsemblGenomes http://www.ensemblgenomes.org/

Extension to standard Ensembl: •Ensembl Bacteria •Ensembl Fungi •Ensembl Metazoa •Ensembl Plants •Ensembl Protists

Accessing data in Ensembl

Search Ensembl data

Search Ensembl data

Search Ensembl data

Search Ensembl data

Report on transcripts encoded by gene ENSG00000012048

Search Ensembl data

Visualization of the region on a genome browser

Search Ensembl data

Variations in ENSG00000012048

Search Ensembl data

Ensembl genome browser layout

Chromosome view

Region view


Chromosome view

Region view

By clicking on a gene name more informations and links are shown


Tracks

Configuring displayed tracks

By clicking on “Configure this page” button it’s possible to configure the tracks shown


Click on a leaf on the tree to select a group


Configure the track by clicking on the tick box


Save and close


A new track has been added to the view

Phylogenetic trees

Phylogenetic trees

NCBI Map Viewer

NCBI is the source of data also for Ensembl and UCSC Genomes available: •28 Vertebrates •17 Invertebrates •19 Protozoa •118 Plants

http://www.ncbi.nlm.nih.gov/mapview/

NCBI Map Viewer layout Chromosome selection

Chromosome ideogram Unigene clusters Unigene clusters

Zoom

“Navigation” Ideogram

Configuring the view



Stand-alone Genome Browsers Integrative Genomics Viewer

-Stand-alone (Java) -Easily configurable -Useful when you want to work on your own data -No need to upload the data on public servers -Memory limited to java instance memory-hungry if many tracks are loaded.

http://www.broadinstitute.org/igv/

Integrative Genomics Viewer

Chromosome location

Conservation data

1000 genomes data

Alignments

Coverage

Gene annotations

dbSNP

More tracks can be loaded (expression, methylation, GC content, …)

Documents

Integration and visualization of genome-wide data