Select the data source for your analysis

PubMed The Cancer Genome Atlas Cancer Cell Line Encyclopedia Genie ICGC
Name Target Type Gender Ethnicity Age

Principal component analyses (PCA) transforms the data into a coordinate system and presents it as an orthogonal projection. This allows for key “components” of variation in the data to be viewed with ease. Each point represents the orientation of a sample in the transcriptional space and each colour represents the origin of excision of the sample.

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

The expression of selected gene(s) across both the samples and the groups are presented

Gene of interest

Gene set for the analysis

Run analysis

This analytical module allows to visualise changes in gene expression, 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)
Gene expression tracks
Over [z-score > 1.0]
Under [z-score < -1.0]

Sample of interest

View

Correlations for user-defined genes are calculated using the Pearson Product Moment Correlation Coefficient (PMCC) value. An interactive heatmap of results is presented for each comparative group in the study.

Genes of interest (min 3, max 50 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 integrate and visualise discrete genetic events, such as DNA copy-number alterations (CNAs) and mutations, or relative linear copy-number values with continuous mRNA abundance data for user-defined gene.

Gene of interest

Gene set for the analysis

Run analysis

This analytical module allows to integrate and visualise discrete genetic events, such as DNA copy-number alterations (CNAs) with continuous mRNA abundance data 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)
Gene expression tracks
Over [z-score > 1.0]
Under [z-score < -1.0]
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

Interactions among proteins of interest can be explored with the colour of each node (genes) defined according to expression within a selected group.

Genes of interest (max 5 genes)

Interaction score threshold

Gene set for the analysis

Experimental group

Run analysis