TCGA Marker Papers

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Contents

Overview

In addition to metadata from the original TCGA project, OmicSoft extracts data from publications from the TCGA working group and in 2018, the PanCancerAtlas publications. Here, users can browse sample level clustering information or categorical attributes from TCGA publications. These variables are grouped into several categories based on phenotypes, molecular subtypes, gene signatures, etc. under Clinical Data | TCGA Marker Paper. This page describes the source of this data. Users can also use the tool tips when browsing the data in Land to get a Pubmed ID (PMID) for the paper from which the data was curated:

ToolTip.png

TCGA Marker Papers

Below is a table of all TCGA working group papers and PanCancerAtlas (2018) papers curated by OmicSoft in TCGA_B37 and TCGA_B38:

Column Name PMID Link
ACC_CancerCell2016 PMID: 27165744 https://www.ncbi.nlm.nih.gov/pubmed/?term=27165744
BLCA_Cell2017 PMID: 28988769 https://www.ncbi.nlm.nih.gov/pubmed/?term=28988769
BLCA_Nature2014 PMID: 24476821 https://www.ncbi.nlm.nih.gov/pubmed/?term=24476821
BRCA_Nature2012 PMID: 23000897 https://www.ncbi.nlm.nih.gov/pubmed/?term=23000897
CESC_Nature2017 PMID: 28112728 https://www.ncbi.nlm.nih.gov/pubmed/?term=28112728
CHOL_CellReports2017 PMID: 28297679 https://www.ncbi.nlm.nih.gov/pubmed/?term=28297679
COADREAD_Nature2012 PMID: 22810696 https://www.ncbi.nlm.nih.gov/pubmed/?term=22810696
ESCA_Nature2017 PMID: 28052061 https://www.ncbi.nlm.nih.gov/pubmed/?term=28052061
GBM_Cell2013 PMID: 24120142 https://www.ncbi.nlm.nih.gov/pubmed/?term=24120142
HNSC_Nature2015 PMID: 25631445 https://www.ncbi.nlm.nih.gov/pubmed/?term=25631445
ILC_Cell2015 PMID: 26451490 https://www.ncbi.nlm.nih.gov/pubmed/?term=26451490
KIRC_Nature2013 PMID: 23792563 https://www.ncbi.nlm.nih.gov/pubmed/?term=23792563
LGG_Cell2016 PMID: 26824661 https://www.ncbi.nlm.nih.gov/pubmed/?term=26824661
LGG_NEJM2015 PMID: 26061751 https://www.ncbi.nlm.nih.gov/pubmed/?term=26061751
LIHC_Cell2017 PMID: 28622513 https://www.ncbi.nlm.nih.gov/pubmed/?term=28622513
LUAD_Nature2014 PMID: 25079552 https://www.ncbi.nlm.nih.gov/pubmed/?term=25079552
LUSC_Nature2012 PMID: 22960745 https://www.ncbi.nlm.nih.gov/pubmed/?term=22960745
Pan12_Cell2014 PMID: 25109877 https://www.ncbi.nlm.nih.gov/pubmed/?term=25109877
PanCan_Cell2018_Ding PMID: 29625049 https://www.ncbi.nlm.nih.gov/pubmed/?term=29625049
PanCan_Cell2018_Hoadley PMID: 29625048 https://www.ncbi.nlm.nih.gov/pubmed/?term=29625048
PanCan_Cell2018_Liu PMID: 29625055 https://www.ncbi.nlm.nih.gov/pubmed/?term=29625055
PanCan_Cell2018_Malta PMID: 29625051 https://www.ncbi.nlm.nih.gov/pubmed/?term=29625051
PanCan_Cell2018_Sanchez PMID: 29625050 https://www.ncbi.nlm.nih.gov/pubmed/?term=29625050
PanCan_Immunity2018_Thorsson PMID: 29628290 https://www.ncbi.nlm.nih.gov/pubmed/?term=29628290
PCPG_CancerCell2017 PMID: 28162975 https://www.ncbi.nlm.nih.gov/pubmed/?term=28162975
PDAC_CancerCell2017 PMID: 28810144 https://www.ncbi.nlm.nih.gov/pubmed/?term=28810144
PRAD_Cell2015 PMID: 26544944 https://www.ncbi.nlm.nih.gov/pubmed/?term=26544944
PRCC_NEJM2015 PMID: 26536169 https://www.ncbi.nlm.nih.gov/pubmed/?term=26536169
SKCM_Cell2015 PMID: 26091043 https://www.ncbi.nlm.nih.gov/pubmed/?term=26091043
STAD_Nature2014 PMID: 25079317 https://www.ncbi.nlm.nih.gov/pubmed/?term=25079317
THCA_Cell2014 PMID: 25417114 https://www.ncbi.nlm.nih.gov/pubmed/?term=25417114
UCEC_Nature2013 PMID: 23636398 https://www.ncbi.nlm.nih.gov/pubmed/?term=23636398
UCS_CancerCell2017 PMID: 28292439 https://www.ncbi.nlm.nih.gov/pubmed/?term=28292439
UVM_CancerCell2017 PMID: 28810145 https://www.ncbi.nlm.nih.gov/pubmed/?term=28810145

Categories of Metadata

Categories Metadata.png

Curated metadata from the papers described above can largely be found here under the TCGA Marker Paper category. Metadata is further broken down by the sample attributes curated from each paper.

Category Description
Other This category contains additional information attributed to samples from the given publication. For example, users can browse additional histological characterization, microsatelite instability status, and Genomic alteration status.
mRNA Samples clustered into subgroups in publications using the mRNA expression can either be filtered or grouped using these cluster identities for further analysis in OmicSoft Land.
Copy Number Similar to mRNA, samples clustered into subgroups in publications using the CNV status can either be filtered or grouped using these cluster identities for further analysis in OmicSoft Land.
Methylation Similar to mRNA, samples clustered into subgroups in publications using the methylation status can either be filtered or grouped using these cluster identities for further analysis in OmicSoft Land. Global hypermethylation can also be examined here.
miRNA Similar to mRNA, samples clustered into subgroups in publications using microRNA expression can either be filtered or grouped using these cluster identities for further analysis in OmicSoft Land.
RPPA Similar to mRNA, samples clustered into subgroups in publications using the RPPA quantification results can either be filtered or grouped using these cluster identities for further analysis in OmicSoft Land.
Virus Users can filter or group samples based on viral load for the indicated tumor type.
Mutation Sample Data dealing with mutation status can be found here, including mutation rates from PanCancerAtlas and mutation status of indicated genes.
Immune Indications of percentages of distinct immune cell types defined by PanCancerAtlas studies
iCluster Clustering of ~10,000 Tumor samples using iCluster as part of PanCancerAtlas
Clinical Clinical attributes defined by https://www.ncbi.nlm.nih.gov/pubmed/?term=29625055
Stemness Stemness attributes defined by https://www.ncbi.nlm.nih.gov/pubmed/?term=29625051
Fusion Fusions identified by https://www.ncbi.nlm.nih.gov/pubmed/?term=29625050
lncRNA Cluster attributes based on lncRNA expression
Bacteria Users can filter or group samples based on bacterial load for the indicated tumor type.

Additional PanCancerAtlas Metadata - Survival

In addition to the cluster and categorical attributes described above, metadata attributed to survival has been updated in 2018. Specifically, Thorrson et al. and Liu et al.

PanCan survival.png

Users can filter to samples that have this metadata attributed to them, and generate Kaplan-Meier Survival Plots to visualize varying survival categories, such as Disease-Free Survival.

Survival PanCan.png

Example Usage of PanCancer Information

Recent publications from the PanCancerAtlas (2018) have examined a number of features across TCGA tumor samples, including immune cell composition, neoantigen information, and clustering of samples across all tumors. Users can browse all this data and use it to group samples based on these characters. For example, grouping all tumors by iCluster:

ICluster.png

Coloring the clusters by Tumor Type, users can identify samples across tumors that have similar character by iCluster:

PanCancer iCluster.png

Within Lands, users can identify features within these clusters using some of the Analytic tools, such as Analytics | Report Top Mutated Genes:

ReportTop.png

Here you will now see the top mutated genes in each cluster:

ResultSet.png