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Questions tagged [cancer]

An abnormal growth of cells that can threaten an individual's life. Cancerous cells are very proliferative and can spread to other parts of the body, creating metastases.

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How to perform meaningful Gene set erichment analysis or otherwise find broader themes/functions in different cell populations?

(For context: I'm somewhat new to bioinformatic analyses but am mostly comfortable with R) I have identified transcriptomically and morphologically different cancer cell populations within a patient (...
immunoLogical's user avatar
3 votes
1 answer
64 views

How to prove correlation between gene expression and functions using omics data in bioinformatics?

I am new to bioinformatics, coming from a background in mathematical biology. I am currently participating in a project where the Principal Investigator (PI), who is a biologist, has tasked me with ...
LOVEMATH's user avatar
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Suggestion for way foward with upregulated genes

I am working with single cell RNA data- control and treated. I analyzed and got a list of upregulated genes. Upon doing pathway analysis all the genes were of apoptotic pathway. But these genes can ...
subhiksha sundaram's user avatar
4 votes
0 answers
80 views

MergeBamAlignment error

I doing the alignment of samples following the GATK pipeline, and doing the MergeBamAlignment,like this: ...
Rita Soares's user avatar
2 votes
1 answer
57 views

How to identify a low proportion cell subpopulation in the single-cell RNA-seq data?

The cell subpopulation that I am interested in only accounts for around 1.2% of the total cells. I have previous FACS experiments that sort out the subpopulation from the samples (using markers CD166+ ...
Wang Ming's user avatar
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1 answer
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how to download all metadata for a single TCGA dataset and link to data file UUIDs?

I've been able to download specific data types from the TCGA portal (https://portal.gdc.cancer.gov/) using the Manifest files and the GDC Tool. But it's not clear to me how to download the metadata (e....
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1 vote
0 answers
18 views

Experimental data on searching for breast cancer

In addition to the Wisconsin breast cancer (diagnosis) can be found in UCI machine learning library for breast cancer datasets, what websites can you find similar breast cancer datasets?Or which ...
Red bean's user avatar
2 votes
1 answer
224 views

Where to find database for breast cancer phenotype?

Where can I find databases for breast cancer mutations (SNPs & indels) phenotype, with chromosome, position, ref, alt, gene, clinical significance. So far, I have only found the Clinvar database. ...
Maryem Life's user avatar
1 vote
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Drug indication data for only cancer phenotype from Chembl

I am interested in getting the drug indication data for all drugs in the database using sqlite. I used following step to get this ...
Megha's user avatar
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2 votes
1 answer
147 views

Querying The Cancer Genome Atlas (TCGA) for gene expression

The UCI gene expression cancer RNA-Seq ​dataset (https://archive.ics.uci.edu/ml/datasets/gene+expression+cancer+RNA-Seq) consists of 5 types of cancers (BRCA, KIRC, LUAD, COAD, PRAD) and gene ...
fuad021's user avatar
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1 answer
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How to interpret the Copy Number from pseudocount depmap portal file?

This question has also been asked on Biostars How do I convert the Copy Number (CN) file into useful information such as HOMDEL and AMP? This is an already normalized file with pseudo count + 1. In ...
flavinsky's user avatar
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1 answer
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What are Dummy fastqs?

I had to do a file transfer for in our system to run from fastqs and I came across the term "dummy fastq", not sure what exactly it means and what is the purpose of it in the workflow. Can ...
Navya's user avatar
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1 answer
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building complex drug-dna for AMBER software

I will appreciate if you can please clarify some of my doubts about drug-DNA complex. I want to study the drug-DNA simulation using AMBER. I did go through all the tutorials video on youtube but ...
dnalectronics's user avatar
3 votes
1 answer
40 views

Is there any database about the abundance of proteins in urine of healthy patients?

I have a dataset about adundance of urine proteins from cancer patients. I would like to compare these abundance levels to healthy patients' urine proteins. However I don't have any data with healthy ...
rev.peter's user avatar
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2 answers
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Using grep to get lines from a file (.tsv) that contain specific samples listed in a sample file (.tsv)

So I have a file, let's call it pcawg.tsv. It's formatted like the one down below. ...
Michelle Yang's user avatar
2 votes
1 answer
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Important genes beyond PAM50 for breast cancer classification

Note: this question has also been asked on Biostars I am currently trying to complete a Breast Cancer Classification task using Neural Networks. I have experimented with using my full dataset of gene ...
Udb 's user avatar
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Ccle miRna data units

Does anybody know what units the mirna expression data on ccle is in? I saw the pipeline in the original paper but it doesn't mention units. Original paper: https://www.nature.com/articles/s41586-019-...
n232's user avatar
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Clusters in scRNA of Glioblastoma

There is a scRNA dataset on Glioblastoma from 10xgenomics. Unfortunately, there seems to be no research paper related to that data. Question 0 : May be there is paper ? How to find it ? I am not ...
Alexander Chervov's user avatar
2 votes
1 answer
238 views

Survival analysis using CoxPH - Effect of covariates

Hi and sorry for the long post in advance, I'm doing a survival analysis of lung cancer patients using Python's lifelines package. According to the documentation, the function ...
beerzy's user avatar
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0 votes
1 answer
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Comparing AUCs: Discrimination of same Control from different Test Group - paired or unpaired? miRNA

I want to compare two AUCs using a bootstraping method from pROC package (roc.test). I have done a classification using Logistic Regression and Serum miRNAs as prediction factors. The Controls are in ...
Mischa's user avatar
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1 vote
2 answers
108 views

Bacterial DNA at the tail of transcriptome reads. What does that mean?

I am assembling a transcriptome obtained from the Internet. The transcriptome was extracted from a human cancer tissue that had been previously grafted into a mouse. I have detected that many ...
juanjo75es's user avatar
1 vote
0 answers
439 views

How to aggregate multiple MAF files together?

I have cancer genomic data (tumor/normal whole exome sequencing) from 50 patients that received the same type of treatment, half of whom responded. These come in the form of 50 .maf files, along with ...
Kyle Weise's user avatar
1 vote
0 answers
32 views

Portals besides the National Cancer Institute GDC Data Portal for downloading histology slides

I am downloading sample slides (in svs format) from the GDC Portal for a convolutional neural network model, but I also need normal tissue slides to perform classification. There are some normal ...
Arthur Frankel's user avatar
1 vote
1 answer
45 views

Are there databases or resources that contain expression of proteins or genes before and after cancer treatment?

Are there databases that contain information about gene or protein expression before and after targeted therapy or chemotherapy? I am curious about different cancer cell lines or cancer types. Any ...
0x90's user avatar
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3 votes
0 answers
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Patient-sample mapping in GSE72056 dataset

I want to use the single-cell data from the following expression profiling which concerns the RNA-seq of metastatic melanoma: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE72056 The data was ...
hadi's user avatar
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2 answers
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Can we use GTEx data as control data for TCGA data?

I am using Recount2 TCGA data and was wondering is it right to use GTEx data as control data for this. I would really appreciate your views on this?
Priya's user avatar
  • 351
3 votes
1 answer
63 views

Database for germline copy number variations in cancer

I am interested in looking at germline copy number variations in individuals that are at high risk of developing cancer. Are there any databases where I can look, if a CNV seen in our test case has ...
Aprasad's user avatar
  • 31
1 vote
0 answers
39 views

Building cancer gene database

I am trying to build a database of different cancer genes i.e lung cancer, throat cancer etc. Searched through NCBI website by searching for nucleotide sequences, but I am unable to find appropriate ...
Prabhuraj Metipatil's user avatar
0 votes
1 answer
43 views

Finding genes especific to microenvironment

I have RNA-seq .bam files for 3 patients, tumour and its matched derived model, namely organoid, but I don't have any matched normal sample. Differentially expressed genes between a tumour and its ...
Zizogolu's user avatar
  • 2,148
2 votes
2 answers
2k views

How to interpret fish plot in R

I am working on subclonal evolution of multiple myeloma. After literature survey, I found people use Fish plot to represent tumor evolution. The example of fish plot can be found here. But I am not ...
Lot_to_learn's user avatar
1 vote
2 answers
808 views

Why the t-test for a specific gene shows different value compared to differential analysis?

I have RNA-Seq data for LUNG cancer. 370 tumor and 50 Normal. For differential analysis initially I did some filtering and kept approx. 19k genes for further analysis. I used edgeR. With a FC > or &...
beginner's user avatar
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1 vote
0 answers
54 views

How transcription factor influence gene expression?

I am studying about gene regularity network(GRN). I'm interested to work on cancer detection to find start reasons of this particular illness. I'm trying to find out how the transcription factor(TF) ...
Mohammad Heydari's user avatar
0 votes
2 answers
240 views

GDC data portal cancer subtype

I need to use Gene Expression quantification data (using HTSeq-FPKM-UQ) for breast cancer data on the gdc portal (https://portal.gdc.cancer.gov/repository) to classify breast cancer subtypes (luminal ...
ImAUser's user avatar
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2 votes
0 answers
156 views

Meaning of category in MutSigCV

I am trying to understand the working of MutSigCV. But I am not sure about some terms used in MAF file format which is category. According to MutSigCV, every mutation can be divided into the following ...
Lot_to_learn's user avatar
1 vote
1 answer
138 views

Tumor sample and heterozygous SNVs: what is the genotype of the normal cells?

In the following picture, you can see that in normal cells (yellow) we have two copies of each gene, while in tumor cells (violet), we just have one copy due to a clonal mono-allelic deletion. I do ...
wrong_path's user avatar
4 votes
2 answers
99 views

Use of heterozygous SNPs in cancer research: why?

When reading about allelic fraction (AF) and SNPs in cancer research, they always mention the fact that they're using heterozygous SNPs (informative SNPs). Why is this? Why can't we use homozygous ...
wrong_path's user avatar
3 votes
1 answer
105 views

Difference between copy number neutral reads and active reads

In this paper, the authors talk about copy number neutral reads (as reads that equally represent parental chromosomes) and active reads (as reads from only one parent chromosome): We reasoned that ...
wrong_path's user avatar
3 votes
1 answer
589 views

Is there a publicly available tumor-normal sample?

I am looking for a publicly available matched tumor-normal sample. I need Illumina fastq reads (or an aligned bam file, since I could extract the reads from it) from a tumor and a matching, non-tumor ...
terdon's user avatar
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0 votes
1 answer
106 views

Information about control data

I am putting this question because I did not find any useful information from internet because of limited access. My question is related to control (or normal) data that we use for somatic mutation ...
Lot_to_learn's user avatar
2 votes
1 answer
88 views

COSMIC Genotypes and Phenotypes

I'm trying to find files containing genotypes and phenotypes for cell lines in COSMIC. On their downloads page I found links for mutation data, which I guess could be converted to genotypes, but I ...
Greg's user avatar
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1 vote
1 answer
459 views

What would be a reasonable healthy data set/control group to compare with a cell line from TCGA?

Assume I want to run a simple machine learning of healthy/non healthy classification, how can I use TCGA where it has only data of people with cancer. What do usually people do for example for study ...
0x90's user avatar
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3 votes
2 answers
105 views

EMT/EMT-like processes in bioinformatics to study cancer progression

First I am not sure why, but it seems EMT can be used to infer the status of cancer progression. What kind of databases are there for the EMT process in the context of cancer? I saw this book which ...
0x90's user avatar
  • 1,437
6 votes
3 answers
2k views

Somatic tumor only variant calling?

I'm evaluating possibilites for somatic tumor variant calling without paired-normal samples. I'm aware of the consequences without a normal sample. All the popular variant calling tools such as ...
SmallChess's user avatar
  • 2,699
5 votes
1 answer
541 views

How can I calculate loss of heterozygosity (LOH) in NGS sequencing data?

I'm analyzing a tumor sample and a healthy sample from the same patient. I want to use sciClone to look at tumor clonality. One input is the genomic regions that need to be excluded due to LOH. I have ...
story's user avatar
  • 1,573
3 votes
1 answer
312 views

Database of copy number alterations in different cancer types

Is there a database of somatic copy number alterations (CNAs) in different cancer types? That is, annotations of which CNAs are more commonly seen in different cancer types.
719016's user avatar
  • 2,324
2 votes
0 answers
30 views

Working with the additional cell lines in NCI-60

NCI-60 has additional cell lines, but when I get results from CellMiner they are not included in there. Namely, the genes such as: DLD-1(Colon), ...
0x90's user avatar
  • 1,437
2 votes
2 answers
72 views

Using data mining of papers in order to derive genomic connections [closed]

Are there any examples of researchers data mining articles and papers (e.g., from pubmed or google scholar) in order to derive relations between genes and diseases?
0x90's user avatar
  • 1,437
4 votes
1 answer
239 views

How are PDO and PDX used in computational and predicative models for tumour biology?

There are wet methods: Patient-derived models: Patient Derived Xenograft (PDX) and Patient Derived Organoids (PDO) to reflect tumor biology. Are there any databases or computational tools that use ...
0x90's user avatar
  • 1,437
6 votes
2 answers
717 views

Searching for gene expression data by cell line

I have two cancer cell lines (OCI-Ly18 & riva) that I want to find gene expression data for, but I'm not aware of many gene expression databases that allow searching by cell-line without searching ...
JSneathThompson's user avatar
7 votes
3 answers
501 views

GRCh38 vcf file with common cancer mutations

Is there a vcf file on the GRCh38 assembly with common cancer mutations I can download somewhere? Maybe from one of the big international cancer genomics consortia? By common, I mean whichever ...
719016's user avatar
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