PubMed The Cancer Genome Atlas Cancer Cell Line Encyclopedia Genie ICGC Data returned |
Clinical
Molecular
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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.
This analytical module allows to visualise DNA copy-number alterations (CNAs) for the whole-genome. |
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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. |
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Sample of interest |
The expression of selected gene(s) across both the samples and the groups are presented
This analytical module allows to visualise changes in gene expression, for the whole-genome. |
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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. |
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Sample of interest |
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.
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.
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. |
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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. |
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Sample of interest |
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.
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 name | Description | Tumour purity |
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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)
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Interaction score threshold |
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Gene set for the analysis |
Experimental group |
Run analysis |
Here we present the oncoprint, a way for visualising the top mutated genes as well as the type of mutation in cancer samples
General
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This module aims at mapping a list of mutations to the TCGA samples
This analytical module allows to screen user-defined gene for mutations identified across all samples.