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bigWig dot plot

bigWig track now supports rendering in dot plot mode. At the configuration panel (by clicking "CONFIG" on right), choose a value to turn a bigWig track to render it as dot plot.

Under the hood it retrieves X times more amount of data points from the .bw file at the view range, and render them as dots, compared to the usual bar plot with 1x number of data points.

A good use case is to examine copy number variation from DNA sequencing coverage or relative allele fraction data.

Credit: Scott Newman
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2DMAF is back

We have brought back the 2DMAF plot feature, for comparing mutant allele fraction of a pair of related samples (e.g. tumor diagnosis and relapse).

To access, visit https://pecan.stjude.org/pp, click Apps > 2DMAF plot.

For info, see the original post: https://plus.google.com/u/0/+XinZhou_s/posts/TLYfqRU1c45

Embedded

We have restored this feature and you should be able to continue embed ProteinPaint in a variety of setting, including web sites or HTML documents.

Sorry for any inconvenience caused. Comment back if you have any issues with the tool.

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Accessing remotely hosted resources from ProteinPaint

We have resolved a technical limit that used to prevent ProteinPaint from accessing remotely hosted files, e.g. http://ftp.ebi.ac.uk

As an example, here shows how to link an ENCODE RNA-seq track (hg19) to ProteinPaint:

https://pecan.stjude.org/pp?block=on&genome=hg19&bigwigurl=GM12878,http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlLongRnaSeqGm12878CytosolPapMinusRawSigRep1.bigWig

Let us know if your resources cannot be accessed by ProteinPaint. You can send me private message if you need to keep your URLs secrete.


Credit: Derek Davenport

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COSMIC v80 (hg19 and hg38)

ProteinPaint now hosts the latest COSMIC dataset for both hg19 and hg38 genome. The data includes SNV/indel and fusion genes.

hg19 COSMIC data can be accessed at https://pecan.stjude.org/.
And please visit https://pecan.stjude.org/pp to access hg38 data.

Thanks to +Michael Edmonson for help in data curation.

Data source: http://cancer.sanger.ac.uk/cosmic

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Summary view of all gene isoforms

Happy new year to all of you! We invite you to find out a new feature about ProteinPaint, which is the multi-isoform summary view.

The screenshot shows how such view looks like for the JAK2 gene. It is assembled by the exons from all the isoforms. As you can tell from the isoform names on left, top 7 are from RefSeq, and bottom 3 are GENCODE.

https://pecan.stjude.org/proteinpaint/jak2

To get this view, click on the JAK2 NM_xxxx on top left, then click the option "Aggregation of xx isoforms" to convert to the summary view. Note that this option will be missing if there is only one isoform available for your gene.

In the view, thick boxes are coding exons, while gray boxes are UTRs or noncoding exons. The last two GENCODE isoforms are noncoding transcripts.

For this example, the protein domain data is loaded for just one RefSeq isoform (the one with color bands).

A panel on the right shows the configuration panel for the gene track (by clicking the Config" button on right). You can toggle the checkboxes to *add/remove isoforms.

To reorder isoforms in the view, simply drag on the isoform names to go up or down.

Let us know of any problems. Have fun browsing!


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Figure legend

We have resumed producing the legend part in the SVG output of gene view. The legend will cover protein domain, mutation class, and mutation origin.

The protein domain legend will not show if not in gene view (e.g. in genome browser view).

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hg38 ClinVar is available

ProteinPaint now hosts the latest ClinVar dataset for both hg19 and hg38 human reference genomes.

To access the hg38 version, please visit https://pecan.stjude.org/pp and select "hg38" before searching for a gene.

(searching on pecan.stjude.org will give you hg19-based results)

Data source: +NCBI
Data processing: +Michael Edmonson

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COSMIC v79 (hg38)

ProteinPaint now hosts the latest COSMIC dataset for hg38 genome. The data includes SNV/indel and fusion genes.

To access, please visit https://pecan.stjude.org/pp and follow the same procedure as specified in the post of "hg38 ClinVar".

Great thanks to +Michael Edmonson for help in curating these datasets!

Data source: http://cancer.sanger.ac.uk/cosmic

COSMIC v79 (hg19)

ProteinPaint now hosts the version 79 of the COSMIC database, including coding gene point mutations and fusion genes, for the human hg19 genome.

Credit: +Michael Edmonson
Data source: http://cancer.sanger.ac.uk/
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