Questions tagged [gene]

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

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1answer
41 views

what is the concept of N-channel geneChip?

I can understand two-color and one-color(Channel) gene chip; but there is another type of gene-Chip called "N-channel chips" ; I do not know how can several (> 2) samples be hybridize in one chip. I ...
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26 views

Will using smaller kmers help get larger contigs? If not, then what?

I've been using MEGAHIT to assemble metagenomes, with particular focus on specific genomic areas. Sometimes all I get is gene fragments or pathway fragments (eg. if I know that genes A, B, C, D and E ...
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1answer
100 views

Algorithmic investigation of viral proteins for vaccine design [closed]

I wish to investigate how a virus could be attenuated through targeted mutagenesis by investigating its protein mutations in order to produce an efficacious vaccine. Are there examples where the ...
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1answer
24 views

HTSeq-count is returning 0 for every gene, instead of expression value

(Ported from stack overflow) I'm trying to summarize gene count using htseq-count; and it's returning 0 counts at every gene. I'm not sure what I'm doing wrong; I think it has to do with the gene ...
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10 views

Scooping and GeneMatcher

A colleague has uploaded about a dozen candidate disease genes to GeneMatcher with excellent success. However last year and again recently he has encountered the case wherein a case was uploaded and a ...
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1answer
53 views

vcf file to gene annotations and or genes

Is there some tool that will convert a vcf/bcf file to some gene annotation, based on the fact that I have the gene annotation of the already exsisting reference genome. Or some tool that will give me ...
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3answers
197 views

What are the different kinds of bioluminescent genes?

I know of the common green glow gene but I forgot the name and I also know that some algae glow blue. There are so many types of bioluminesent organisms, so I am wondering what species have which ...
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0answers
16 views

How can I find genes of fundamental metabolic processes for an organism?

I want to find genes of fundamental metabolic processes in the Phytophthora cinnamomi genome. I'm using the genome sequence deposited in the NCBI and I'm searching ORF by ORF, using the ORF finder (...
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0answers
53 views

How to get the GO information for all the human genes?

I would like to find a list of all the human genes and their proteins’ functional classification. The Gene type attribute on ensembl.org is not specific enough, ...
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1answer
32 views

tp53 example in Momand's book

I am new to bioinformatics. While reading Momand's 'Concepts in Bioinformatics and Genomics' , I understood clearly that each codon translates to a specific amino acid. But then, he talks about the ...
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1answer
24 views

How to Convert From Gene Location to SNP Location

I am new to this. I have an SNP array composed of digits [0,1,2] for chromosome 21. How do I find the start:end locations for the region that is "21q22.11" step by step?
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1answer
87 views

Any user friendly way to find rare mutations in whole genome raw?

Is there any user friendly way to find rare mutations in the individual human whole genome sequencing raw data? (from Dante, 30x coverage). To be more specific, I want to find mutations from this ...
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0answers
28 views

How to check the distribution of gene expression across the genome?

I have a group of genes with the same functionality belonging to 3 different families. I would like to see how their expression is distributed across the genome: do they tend to be expressed in a kind ...
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0answers
21 views

Gene size and power of detection in sequence divergence analyses

I want to look at violation of the strict molecular clock and compare dn/ds ratio to test differences in evolutionary rates in a set of genes. Some of these genes are really short (30AA), is it likely ...
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1answer
42 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 ...
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1answer
33 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.
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1answer
65 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 ...
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2answers
166 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 ...
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1answer
62 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 ...
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2answers
87 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 ...
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0answers
33 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 ...
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0answers
61 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 ...
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3answers
374 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?
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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 ...
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0answers
36 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 ...
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1answer
257 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 ...
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1answer
90 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 ...
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1answer
68 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 ...
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2answers
39 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 ...
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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: ...
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3answers
1k 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
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1answer
37 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....
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1answer
43 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 ...
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0answers
48 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) ...
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3answers
206 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 ...
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2answers
7k 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 ...
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1answer
102 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 ...
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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 ...
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4answers
570 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 ...
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2answers
60 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 ...
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0answers
46 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 ...
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2answers
118 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 ...
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1answer
66 views

To find p-value of compounds (pairwise)

I have next SNPs data.frame structure ...
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1answer
132 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
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0answers
53 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 ...
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0answers
35 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 ...
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1answer
272 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
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2answers
55 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
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1answer
31 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: ...
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0answers
41 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 ...