Questions tagged [gene]

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

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1answer
47 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
186 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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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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51 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
30 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
22 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
81 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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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
40 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
32 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
55 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
164 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
85 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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29 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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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
322 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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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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34 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
234 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
78 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
64 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
37 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
34 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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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
198 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
6k 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
95 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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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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3answers
475 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
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 ...
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0answers
45 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
117 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
65 views

To find p-value of compounds (pairwise)

I have next SNPs data.frame structure ...
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1answer
128 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 ...
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0answers
50 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
250 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 ...
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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
30 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 ...
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3answers
251 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
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3answers
244 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 ...
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2answers
183 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) ...
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2answers
102 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 ...
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1answer
112 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 "...