Episode #125 of the Stack Overflow podcast is here. We talk Tilde Club and mechanical keyboards. Listen now

Questions tagged [gene]

Use this tag to refer to the gene sequence/coding part of the sequence.

Filter by
Sorted by
Tagged with
0
votes
1answer
39 views

correlation between transposon and gene

I have two matrix identical in N° of rows and columns. In the first matrix rows indicate transposable elements and columns indicate samples. the matrix show the degree of expression of each element ...
0
votes
1answer
29 views

Download protein structure from gene name

I have a list of gene name, I want to download and save each protein 3D structure corresponding to each gene name.
0
votes
1answer
43 views

From ensembl id to protein structure

Forgive me if this question is too trivial. I have a list of ~700 Ensembl ID. I need to extract the protein structures of each Ensembl id. How can I do this? Is there any script(python, R) so that ...
1
vote
2answers
136 views

How can I find out if my gene of interest is duplicated?

To identify homologous genes, I performed tBLASTn analyses against my genome of interest resulting in sequences of a closely related species. Using this method, I found two (and in some cases up to ...
1
vote
1answer
55 views

Are there any resources for calculating / representing evolutionary relationships within gene clusters?

I am working with a gene cluster found in several species. The genes involved are pretty much the same, with the odd insertion, but they can be often found in different orientations. So, I can't just ...
1
vote
2answers
77 views

How to efficiently get human gene names from NCBI based on a large list of SNPs

I found a good answer related to my question here: How to get a list of genes corresponding to the list of SNPs (rs ids)? But it says about small number of SNPs. I want to get gene names based on ...
0
votes
0answers
17 views

How to order grouped elements in Gviz

Gviz is useful for visualization of gene transcripts by genomic coordinates. I'm using it to show the difference between splice variant transcripts. However, it seems that the ordering of transcript ...
1
vote
0answers
55 views

Visualizing Ortholog and Paralog genes

I ran PorthoMCL but I could not find an explanation about the output format and I would like to visualise the results, maybe as a circos plot. PorthoMCL produces two output files: Orthologs sample ...
1
vote
2answers
175 views

CDS length for each human gene

Does anyone know where and how could I download a list of all human genes and the length of the coding sequence for each gene? Is it possible to do this on the NCBI site, ensembl?
1
vote
0answers
37 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 ...
2
votes
0answers
33 views

How can `limma` be used to determine genes predictive of a given phenotype?

Using limma and lmFit on gene expression data, I can perform a series of regressions ...
1
vote
1answer
154 views

Clustering of gene co-expression network by igraph R package

I have constructed a gene co-expression network from RNA-seq data. The network has more than 10000 nodes and more than 1 million edges. The network file as an edge list format of memory around 1gb ...
0
votes
1answer
48 views

How do I get the adjacency matrix from gene similarity network?

I am exploring application of Graph convolution network on gene similarity network. I am trying to explore genemania.org and https://string-db.org/ Please let me know where can I find the data for my ...
2
votes
1answer
62 views

How to interpret UniProt allele patterns?

In creating a parser for the UniProt flat file uniprot_sprot.dat (directory) in the manual for the comments POLYMORPHISM there ...
1
vote
2answers
36 views

Strategies to disentangle the effect of two genes on phenotype

I am analyzing the effect of one putative tumor suppressor (and its loss) on a specific cancer phenotype. This putative tumor suppressor is known in literature to have an effect on the growth of ...
2
votes
1answer
60 views

How can I interpret gene expression data from Bioconductor packages?

I am currently looking at microarray data from a bioconductor microarray dataset. Specifically, I have data (a snippet) which looks like the following: ...
2
votes
3answers
696 views

How to quantile normalization on RNA seq counts

I have a read count data (RNAseq) and want to perform quantile normalization. Could you please help me how to do it. I tried some scripts in R but it didn't work. I want the result output in matrix ...
2
votes
1answer
25 views

Linking of MeSH terms and genes

Is there an alternative to mesh2gene for linking MeSH terms to genes? The http://www.ncibi.org/gene2mesh.html site appears to be down for months now (click on "Launch Gene2MeSH via gene2mesh.ncibi....
0
votes
1answer
38 views

How to create a graph of multi column gene dataset?

well, I'm new to Bio. what I'm going to do is create a network/graph of a dataset related to the genes I think. here's the sample of the nodes dataset with CSV format named lung-nodes : and this is ...
1
vote
0answers
47 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) ...
6
votes
3answers
158 views

Fast filtering of intervals not falling within a certain distance from known genes

I would like to filter a bed file with intervals, ie. in the format of: chr1 13800 14301 chr1 15500 16001 chr1 19400 19901 chr1 22800 23301 ...
3
votes
1answer
3k views

Converting Gene Symbol to Ensembl ID in R

I'm trying to convert ~20,000 different human gene symbols to ensembl IDs. I've been trying to use biomaRt to do this, but continue getting the following error ...
1
vote
1answer
69 views

TagReadWithGene missing when using latest version of Drop-seq_tools

I am using Drop-seq_tools to analyze scRNA-seq in a similar way of this paper. I am using the same data (GSE97930) to get used to Drop-seq_tools. On the GEO repo the authors provide the relevant code ...
1
vote
0answers
16 views

Finding gene name from human genome using SP1 transcrition factor binding site from Postion Weight Matrix

I have a list binding site motif of SP1 transcription factor which collects from PWMScan tools. Actually this tool scan whole human genome and give the entire binding motif list. From that list of ...
4
votes
3answers
298 views

Finding gene length using ensembl ID

I want to find the length of a list of genes, of Homo sapiens, that is reported in the GEO database. I have gathered the ensembl id's of those genes. I understand this information can be parsed from ...
0
votes
2answers
57 views

Comparing the gene expression data

I'm trying to compare the gene expression data reported in the studies documented in GEO for a specific gene expressed in a tissue of my interest in Homo sapiens. I compared the values reported in 4 ...
2
votes
0answers
41 views

Hemoglobin subunits genes in scRNA-seq

In one scRNA-seq sample I encountered the genes: Hbb-bs, Hba-a1 and Hba-a2. These genes appear on top of the list of the highest expressed genes but having up to the 75% percentile of cells having ...
7
votes
2answers
109 views

Are gene names same across species?

I have a bunch of gene names of Apis mellifera (specifically 194). I used these gene names as an input on STRING database to create a network for Drosophila melanogaster. 54 of those genes were also ...
1
vote
1answer
65 views

To find p-value of compounds (pairwise)

I have next SNPs data.frame structure ...
0
votes
1answer
98 views

How to calculate Moreau-Broto autocorrelation, Moran autocorrelation, Geary autocorrelation from protein (amino acid) sequences?

I want to code Moreau-Broto autocorrelation, Moran autocorrelation, Geary autocorrelation in Python 3.6 from the scratch for amino acid sequences without using any package. Unfortunately, I have not ...
2
votes
0answers
38 views

How to visualize genome track of gene in specific cell-lines?

I'm trying to make a plot showing genome tracks of specific genes in specific cell-lines of RNA-seq and Chip-seq data. It should look something like this I have recently seen this encode, but in ...
0
votes
0answers
34 views

Find Dataset of human genes in GEO datasets

I am trying to build model to predict relation between diseases and genes using genes features. I have a list of genes that I am interested in. I need to get gene expression of specified genes from ...
1
vote
1answer
194 views

Get Gene Expression Matrix from GEOquery

I am trying to get gene expression matrix for a list of genes I have for my list: Gene ID, Gene Symbol How can I get for each gene corresponding expression as array?? I suppose that I will have ...
3
votes
2answers
54 views

Associating SNP and GENE

Assuming I have SNPs data using hg19, how can I know which SNP belongs into which Gene? The data looks like: chr10_103577643 chr10_124712463 and so on. I ...
3
votes
1answer
29 views

Is there a way to tell which chromosome a gene is on, by looking at the “Chromosome/scaffold name”

I recently got a data set, from which I need to figure out which chromosome a gene is from, but the head of the data reads like: ...
2
votes
0answers
38 views

Correcting for noise in RT-qPCR gene expression data

I have a training set of RT-qPCR gene expression data (not run in triplicate) for a batch of samples with two phenotypes $A$ and $B$ on which I've trained a logistic regression classifier. I also ...
0
votes
3answers
225 views

How to find correlation between two specific genes in same dataset?

I would like to plot the correlation between two specific genes in my data. I have a matrix with genes in rows and samples in columns, with read counts data. If I want to look at the correlation ...
4
votes
3answers
189 views

Expression of a gene in different groups

I would like to check the expression of a gene in different groups like Disease vs Normal samples. I want to make a plot out of that to check whether it is significant or not. From this paper lncRNA ...
3
votes
2answers
97 views

How can I find the chromosomal location of a list of genes?

I have a list of genes nearly 20000: gene name (column1) and coordinates (columns 2 and 3) ...
1
vote
2answers
82 views

obtaining identifier from plot of sequence GC%

I was looking at this script from http://biopython.org/DIST/docs/tutorial/Tutorial.html#htoc297 and wanted to use it to determine outliers for tentative Horizontal gene transfer. The data set is ...
2
votes
1answer
110 views

What's “signal” in gene expression?

I'm exploring gene expression on public available databases. RefExa is one of the databases I've been studying. When I searched something there, the website reported the expression value unit as "...
8
votes
3answers
831 views

How to identify gene expression signatures from gene expression data?

I have TCGA gene expression data. I'm interested in identifying gene expression signatures using the data. I would like to know whether there are any tools or R packages for identifying gene ...
5
votes
3answers
220 views

A good tool for gene locus visualization

Does anyone know of a good tool for visualizing gene loci? Basically, I'd like to show how a group of genes look in different strains of a bacteria. I have annotation of course, I just need a tool to ...
4
votes
1answer
214 views

How to get results from Homo.sapiens package in bioconductor for a specific reference

I want to use the Homo.sapiens package in Bioconductor to retrieve the chromosome location start and end for each gene symbol in a specific reference (e.g. hg19 or hg38). Right now, I am using the ...
3
votes
1answer
127 views

How to download gene expression data from NCBI gene database

In the NCBI gene database, I can add the expression tracks (circled in picture blow) through 'Tracks' button, but How I can download the expression data directly, not just look the picture?
3
votes
1answer
45 views

How to read gene regulatory network edge list files?

The following is an excerpt from an edge list file from the Gene Regulatory Database, YeastNet v3 ...
4
votes
2answers
109 views

Writing a perl script to holding information for two genes

Basically I have a perl script in which I have an array (where each element of the array references a hash) and need to be able to print the array with a dumper function. Thus I need to be able to ...
2
votes
1answer
30 views

Link to UCSC gtexGene track description page for selected gene symbol

I have this link that comes up when I am in the browser window and click on the gene name, which leads me to description page about the gene (in this example it is BOK gene). How can I generate that ...
2
votes
2answers
43 views

When working with Bioconductor and the curatedOvarianData dataset, what are the unit values of the expression data?

I am wondering how to interpret values inside the gene expression levels contained within Bioconductor. For example, if we have the following commands via R, we get:...
3
votes
1answer
74 views

Combine multiple species trees

I have five species trees run using starBeast and Beauti. Here is a link to the paper discussing both, http://journals.plos.org/ploscompbiol/article/file?type=supplementary&id=info:doi/10.1371/...