Questions tagged [tcga]

TCGA (The Cancer Genome Atlas) is a biology-oriented project for understanding the genomics of different types of cancers.

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How to find essential genes by differential expression from TCGA 3rd level CNV data?

I have two types of data one have normal patients copy number variation (CNV) data and another have tumor patients CNV data. In each file there are three columns one contain patient ID, second ...
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795 views

What does probe number and segmentation mean in copy number variation (CNV) data

In TCGA Copy number variation (CNV) data there is a column with title Num_Probes. What is the meaning of probe number with respect to the sample data below? ...
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Open databases for copy number variations similar to TCGA

The Cancer Genome Atlas(TCGA) has open data for copy number variation(CNV) from at least 10k different cancer patients. They offer two types of data, CNV data from tumor and CNV data from normal ...
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325 views

How do I find samples/patients in TCGA (the cancer genome atlas) that had radiation therapy?

I want to correlate the expression of a gene (for sample the KRAS gene) with survival and if the patient received radiation therapy using any suitable TCGA (the cancer genome atlas) dataset. However, ...
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How can I download histological slide from Cancer Digital Slide Archive

Could you tell me if it possible and how to download images data from http://cancer.digitalslidearchive.net ? Thank you.
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1k views

How to compute CNV from TCGA data

TCGA provide CNV data for each cases like this. I want to know, how can I calculate CNVs from this data? What are standard algorithms and methods used?
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488 views

How to preprocess htseq counts for gene expression (TCGA)

I want to prepare a matrix of gene expression to analyse TCGA LAML data. The required data is available at TCGA LAML - Gene expression quantification. The following is an example of the kind of data ...
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483 views

Where do I find microsatellite instability annotation for TCGA data

I have searched through the TCGA data portal but I was unable to find MSI annotation for TCGA Colon Adenocarcinoma (COAD) and Rectum Adenocarcinoma (READ) datasets. I am searching for the annotation ...
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365 views

Deciding a reasonable threshold for copy number variation in a CNV (SNP array) TCGA dataset

Is there a methodology to select a reasonable threshold for copy number variation in a CNV (SNP array) TCGA dataset, to define when there is a significative alteration? Can I download CNV data for ...
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3k views

How copy number variation thresholds are defined in GISTIC

I am having trouble trying to understand how GISTIC discretize copy number variation to values -2, -1, 0, 1, 2. I am using TCGA copy number variation for ColoRectal Adenocarcinoma. In cBioPortal FAQ ...
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Y Chromosome in Ovary Cancer Data

I have been analyzing TCGA Ovary Cancer data. In Somatic Mutation data, there is data of mutations in all the chromosomes (1-22 and X), but amazingly, I have found one (just one) row of Y Chromosome ...
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622 views

Relative microRNA comparison from from TCGA data?

I have a conceptual question that I was hoping someone could answer. Can I say that microRNA A is expressed x-fold greater than microRNA B directly from the TCGA miRseq data? Can I do this after ...
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546 views

How to select genes before log2 ratio on a RNASeq gene expression matrix, based on signal median

I want to transform a TCGA mRNA expression matrix (in linear data format) to log2-ratios and then run a feature (gene) selection, selecting the 1000 most variant genes (genes with higher standard ...
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530 views

Where can I find mutation datasets for cancer?

My lab has been using TCGA data (somatic mutations and clinical data) to develop panels of genes and of mutations we expect to see in certain cancer populations. We'd like to validate our panels by ...
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280 views

How TCGA CNV values are calculated?

When I download CNV SNP array data for ovarian cancer from TCGA data portal, I see some very small numbers like -5, -6 in the "Segment_Mean" column of the segmentation data files. I am very new to ...
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945 views

Using RNA-seq to compare gene expression across patients instead of between Control and Experimental conditions

I am working with RNA-seq data from the Cancer Genome Atlas TCGA and I have been reading about how people have compared gene expression levels measured by RNA-seq. Many of the papers I have read talk ...
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267 views

Classify chemotherapy drugs?

I'm studying a TCGA dataset trying to find correlations between gene expression and clinical data which might shed light on some pathways. One column of the clinical data provides a list of ...
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2k views

TCGA gene expression data are missing matched normal

I'm trying to use the TCGA data portal to get gene expression data for cancer tissues, but I'm not sure what "Tumor matched normal" means. It is unclear to me if the values are already compared to a ...
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508 views

Best way to automatically link Gene Entrez ID with Gene Symbol in TCGA

I am trying to figure out how to link Gene Entrez ID with Gene Symbol, for TCGA dataset. So far, I have found this ftp directory with Gene info updated daily. But, for Entrez ID 728661, I have found ...
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363 views

Mapping a mutation to known SNP, 3' UTR, miR

I've parsed out a very large TCGA cancer ssm (single mutation file) file to give me the essential information. The ssm is in the following format: ...
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972 views

TCGA data, and bioinformatics design questions for SNP/ mirna analysis

It's my first time posting to this forum but was looking for some help on the data aspects of this project. My tools of choice would be in python/R . Goal: I'm looking to create a disease specific ...