PED Bioinformatics Portal

Select the data source for your analysis

PubMed The Cancer Genome Atlas Cancer Cell Line Encyclopedia Genie ICGC Data returned

Clinical

Disease
Type
Gender
Ethnicity
Race
Age

Start analysis

name	target	type	gender	ethnicity	race	age

cna
fusion
mutations

Genes-specific
Whole-genome

The copy number of selected genes across samples are presented as heatmap with genes and samples are represented by rows and columns, respectively.

Genes of interest (min 2, max 20 genes)

or paste your gene list here (separated by any wide space character [tab, space, new line])

Gene set for the analysis

Run analysis

This analytical module allows to visualise DNA copy-number alterations (CNAs) for the whole-genome.

The results are visualised in a CIRCOS plot, where each track represents individual genetic events. Users can click on a chromosome to see a detailed view of the chromosome on the UCSC genome browser. Similarly, users can click on any part of a track, which will expand the respective chromosomal region in the UCSC genome browser. Note: UCSC custom annotation tracks are viewable on the machine from which PED query is made and kept at least 48 hours after the last access time. PED users should be aware that current annotation tracks may contain data from your previous PED queries in the recent history. To view only the annotation data from your current session, go to My Data → Custom Tracks section of UCSC genome browser and delete previous PED annotation tracks.

Track legends (outward→inward)
Copy number (CN) alteration tracks
	Amplification [relative CN value > 1.0]
	Gain [1> relative CN value > 0.5]
	Loss [-0.5 < relative CN value < -1.0]
	Deletion [relative CN value < -1.0]

Sample of interest

View

This analytical module allows to screen user-defined gene for its fusions with other genes identified across all samples.

Gene of interest

Gene set for the analysis

Run analysis

Oncoprint
Functional annotation
Batch search
Mutations frequency

Here we present the oncoprint, a way for visualising the top mutated genes as well as the type of mutation in cancer samples

Genes of interest (min 2, max 50 genes)

or paste your gene list here (separated by any wide space character [tab, space, new line])

Run analysis

General

Sample
Gene
Effect
Chromosome
Reference
Alternative

Functional annotation

chr	start	end	reference	effect	gene	sample	alt

This module aims at mapping a list of mutations to the TCGA samples

Paste your list of mutations here (separated by any wide space character [tab, space])

The format for each mutation is Chr Start Reference Alt

Run analysis

This analytical module allows to screen user-defined gene for mutations identified across all samples.

Gene of interest

Gene set for the analysis

Run analysis