Select the data source for your analysis

PubMed The Cancer Genome Atlas Cancer Cell Line Encyclopedia Genie ICGC
Patient Definition Age Smoking (years) Alcohol history Gender Stage TNM Staging Grade

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

The relationship between molecular subtype/gene(s) of interest and survival can be assessed.
Molecular subtype: Each sample is assigned to a risk group according to molecular subtype designation.
Defined gene(s): A univariate model is applied to the survival data and samples are assigned to risk groups based on the median dichotomisation of mRNA expression intensities of the selected gene(s).
Kaplan Meier plots are generated for each gene and a summary of survival covariates are presented in tabular format.

Genes of interest (max 20 genes)

Experimental Group

Gene set for the analysis

Run analysis

Cancer samples frequently contain a small proportion of infiltrating stromal and immune cells that might not only confound the tumour signal in molecular analyses but may also have a role in tumourigenesis and progression. We apply an algorithm1 that infers the tumour purity and the presence of infiltrating stromal/immune cells from gene expression data. All of these values are presented as a scatterplot, with a breakdown of scores for each sample available in tabular format from the target file.

Sample set 1

Sample name Description Tumour purity
TCGA.H6.8124.01A PDAC 98.24
TCGA.IB.AAUT.01A PDAC 11.24
TCGA.F2.6879.01A PDAC 83.5
TCGA.IB.AAUU.01A PDAC 77.98
TCGA.HV.A5A5.01A PDAC 51.16
TCGA.2L.AAQI.01A PDAC 97.81
TCGA.HV.A7OL.01A PDAC 62.15
TCGA.3A.A9IO.01A PDAC 99.99
TCGA.Q3.AA2A.01A PDAC 84.84
TCGA.HZ.7925.01A PDAC 37.65
TCGA.US.A77E.01A PDAC 86.03
TCGA.2J.AABE.01A PDAC 62.83
TCGA.FB.AAQ2.01A PDAC 99.49
TCGA.XD.AAUI.01A PDAC 72.14
TCGA.HZ.A77P.01A PDAC 58.45
TCGA.2J.AABR.01A PDAC 21.35
TCGA.3A.A9IL.01A PDAC 94.79
TCGA.3A.A9I9.01A PDAC 78.54
TCGA.HV.A5A6.01A PDAC 95.43
TCGA.3E.AAAZ.01A PDAC 95.47
TCGA.HZ.7923.01A PDAC 8.26
TCGA.US.A776.01A PDAC 99.7
TCGA.IB.7893.01A PDAC 52.35
TCGA.F2.A8YN.01A PDAC 85.7
TCGA.FB.AAQ6.01A PDAC 99.26
TCGA.HZ.A49I.01A PDAC 44.44
TCGA.2J.AABP.01A PDAC 33.85
TCGA.HZ.8636.01A PDAC 54.02
TCGA.HZ.8001.01A PDAC 22.62
TCGA.IB.7889.01A PDAC 40.52
TCGA.Z5.AAPL.01A PDAC 34.79
TCGA.FB.A545.01A PDAC 98.85
TCGA.HZ.A49H.01A PDAC 23.82
TCGA.HZ.8003.01A PDAC 24.01
TCGA.XD.AAUL.01A PDAC 61.15
TCGA.LB.A8F3.01A PDAC 97.12
TCGA.2J.AABO.01A PDAC 87.54
TCGA.IB.A6UG.01A PDAC 97.52
TCGA.FB.A7DR.01A PDAC 56.53
TCGA.LB.A7SX.01A PDAC 99.83
TCGA.2J.AABF.01A PDAC 34.56
TCGA.RB.A7B8.01A PDAC 37.74
TCGA.FB.AAPZ.01A PDAC 60.4
TCGA.IB.A5ST.01A PDAC 5.91
TCGA.IB.7885.01A PDAC 22.03
TCGA.FB.AAQ1.01A PDAC 84.13
TCGA.IB.A5SP.01A PDAC 98.17
TCGA.IB.7652.01A PDAC 45.43
TCGA.HZ.8317.01A PDAC 79.18
TCGA.YH.A8SY.01A PDAC 64.93
TCGA.IB.7897.01A PDAC 38.72
TCGA.2J.AABA.01A PDAC 76.59
TCGA.IB.AAUV.01A PDAC 7.5
TCGA.IB.7647.01A PDAC 45.66
TCGA.2L.AAQL.01A PDAC 72.02
TCGA.IB.7644.01A PDAC 81.7
TCGA.IB.AAUO.01A PDAC 86
TCGA.IB.7888.01A PDAC 4.94
TCGA.FB.A78T.01A PDAC 87.12
TCGA.2J.AABK.01A PDAC 99.92
TCGA.M8.A5N4.01A PDAC 48.53
TCGA.HZ.7918.01A PDAC 20.76
TCGA.F2.A7TX.01A PDAC 61.47
TCGA.HZ.8315.01A PDAC 42.38
TCGA.3A.A9IJ.01A PDAC 99.87
TCGA.IB.A7LX.01A PDAC 99.77
TCGA.PZ.A5RE.01A PDAC 53.3
TCGA.L1.A7W4.01A PDAC 98.41
TCGA.S4.A8RO.01A PDAC 92.41
TCGA.S4.A8RP.01A PDAC 69.91
TCGA.US.A77J.01A PDAC 15.58
TCGA.HZ.A77O.01A PDAC 91.99
TCGA.IB.AAUR.01A PDAC 5.98
TCGA.IB.AAUP.01A PDAC 9.63
TCGA.US.A774.01A PDAC 21.51
TCGA.3A.A9J0.01A PDAC 81.36
TCGA.US.A779.01A PDAC 98.83
TCGA.HZ.A4BK.01A PDAC 53.57
TCGA.2L.AAQJ.01A PDAC 78.31
TCGA.HZ.A9TJ.01A PDAC 99.68
TCGA.FB.AAPP.01A PDAC 97.13
TCGA.2J.AABV.01A PDAC 90.17
TCGA.2J.AABT.01A PDAC 40.52
TCGA.IB.8127.01A PDAC 56.67
TCGA.FB.AAPQ.01A PDAC 93.09
TCGA.IB.AAUM.01A PDAC 81.52
TCGA.HZ.A8P0.01A PDAC 84.21
TCGA.XD.AAUG.01A PDAC 48.42
TCGA.HZ.A49G.01A PDAC 10.19
TCGA.F2.A44G.01A PDAC 76.16
TCGA.IB.A7M4.01A PDAC 89.93
TCGA.HZ.8519.01A PDAC 58.82
TCGA.HZ.A8P1.01A PDAC 99.73
TCGA.HZ.8638.01A PDAC 86.76
TCGA.IB.7649.01A PDAC 22.1
TCGA.F2.6880.01A PDAC 99.95
TCGA.H8.A6C1.01A PDAC 72.79
TCGA.F2.7273.01A PDAC 19.09
TCGA.IB.7887.01A PDAC 72.85
TCGA.HZ.A77Q.01A PDAC 0
TCGA.H6.A45N.01A PDAC 28.76
TCGA.2J.AAB8.01A PDAC 73.15
TCGA.FB.AAQ3.01A PDAC 75.52
TCGA.YY.A8LH.01A PDAC 99.91
TCGA.HZ.7924.01A PDAC 79.93
TCGA.XN.A8T5.01A PDAC 23.15
TCGA.2J.AABH.01A PDAC 92.47
TCGA.FB.AAPY.01A PDAC 41.2
TCGA.HZ.A4BH.01A PDAC 41.88
TCGA.2L.AAQM.01A PDAC 96.73
TCGA.3A.A9I5.01A PDAC 96.74
TCGA.F2.A44H.01A PDAC 24.31
TCGA.IB.8126.01A PDAC 37.12
TCGA.HV.A5A3.01A PDAC 96.45
TCGA.3A.A9I7.01A PDAC 50.42
TCGA.3A.A9IZ.01A PDAC 95.31
TCGA.OE.A75W.01A PDAC 69.78
TCGA.IB.AAUW.01A PDAC 62.54
TCGA.FB.AAQ0.01A PDAC 98.72
TCGA.2J.AAB4.01A PDAC 75.31
TCGA.HV.AA8X.01A PDAC 99.8
TCGA.XN.A8T3.01A PDAC 71.72
TCGA.US.A77G.01A PDAC 99.8
TCGA.XD.AAUH.01A PDAC 32.1
TCGA.2J.AABI.01A PDAC 78
TCGA.3A.A9IR.01A PDAC 99.89
TCGA.IB.AAUS.01A PDAC 0
TCGA.LB.A9Q5.01A PDAC 46.35
TCGA.FB.AAPS.01A PDAC 1.97
TCGA.HZ.7289.01A PDAC 99.99
TCGA.FB.A4P6.01A PDAC 57.48
TCGA.Q3.A5QY.01A PDAC 11.83
TCGA.3A.A9IC.01A PDAC 65.4
TCGA.IB.7646.01A PDAC 47
TCGA.HV.AA8V.01A PDAC 51.42
TCGA.HZ.7922.01A PDAC 55.23
TCGA.IB.AAUN.01A PDAC 90.99
TCGA.YB.A89D.01A PDAC 22.59
TCGA.HZ.7926.01A PDAC 81.7
TCGA.F2.7276.01A PDAC 29.46
TCGA.FB.A4P5.01A PDAC 0
TCGA.IB.7651.01A PDAC 38.52
TCGA.HZ.8002.01A PDAC 40.74
TCGA.2L.AAQE.01A PDAC 93.77
TCGA.HZ.7920.01A PDAC 46.66
TCGA.IB.A5SO.01A PDAC 12.74
TCGA.2J.AAB6.01A PDAC 79.8
TCGA.HV.A5A4.01A PDAC 74.39
TCGA.HZ.7919.01A PDAC 75.11
TCGA.FB.A5VM.01A PDAC 66.8
TCGA.2J.AAB1.01A PDAC 70.23
TCGA.RB.AA9M.01A PDAC 96.08
TCGA.IB.A6UF.01A PDAC 99.46
TCGA.IB.A5SQ.01A PDAC 39.53
TCGA.HV.A7OP.01A PDAC 99.48
TCGA.3A.A9IN.01A PDAC 92.81
TCGA.FB.AAPU.01A PDAC 100
TCGA.IB.7891.01A PDAC 17.2
TCGA.2J.AAB9.01A PDAC 58.17
TCGA.IB.7890.01A PDAC 51.51
TCGA.IB.A5SS.01A PDAC 51.55
TCGA.3A.A9IX.01A PDAC 20.69
TCGA.3A.A9IV.01A PDAC 98.11
TCGA.3A.A9IU.01A PDAC 94.28
TCGA.HZ.8005.01A PDAC 58.15
TCGA.2L.AAQA.01A PDAC 97.44
TCGA.IB.7886.01A PDAC 56.01
TCGA.IB.AAUQ.01A PDAC 81.69
TCGA.RL.AAAS.01A PDAC 19.49
TCGA.3A.A9IS.01A PDAC 98.61
TCGA.IB.7645.01A PDAC 0
TCGA.3A.A9IH.01A PDAC 98.82
TCGA.3A.A9IB.01A PDAC 59.94
TCGA.2J.AABU.01A PDAC 82.76
TCGA.3E.AAAY.01A PDAC 20.31
TCGA.IB.7654.01A PDAC 75.7
TCGA.HZ.8637.01A PDAC 17.36
TCGA.S4.A8RM.01A PDAC 92.68

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