Questions tagged [gene]

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

Filter by
Sorted by
Tagged with
1
vote
1answer
30 views

Differential gene expression analysis of time series with replicates

I have a dataset that has two groups, perturbed vs control. Each group has 3 replicates. Each replicate has 8 time points. How do we do Differential gene expression analysis to find significantly ...
0
votes
1answer
32 views

How to find genes whose expression vary the most in time-series?

Hi I am reading this paper and trying to analyse the same datasets in my work: dynGENIE3: dynamical GENIE3 for the inference of gene networks from time series expression data In this paper, the ...
0
votes
1answer
28 views

Annotating gene names or gene IDs to a dataframe containing SNPs?

I have a large data-frame (excel file) of SNPs with genotyping data. I need to filter the data to get SNP information of a specific gene alone. The list is too long to do it manually. I was wondering ...
1
vote
2answers
71 views

What is the best way to programmatically convert Ensembl ids from one release to other? e.g. transcript ids from release 75 to 100

3 solutions that I had to unfortunately rule out. Potential solution #1 As far as I know, the conventional way is to do this is by using CCDS ids (e.g. using biomart). However, the issue is that, as I ...
1
vote
1answer
42 views

How to identify genes from a genome assembly of C. Elegans?

I have two full genome assemblies for C. Elegans samples collected from two different geographical areas that I found on WormBase. These are in fasta format. I want to go gene-by-gene and compare the ...
0
votes
1answer
26 views

Dataset showing evolution of gene

As a way to exemplify how the hierarchical clustering of particular DNA sequences can be used to derive phylogenetic trees, I'm looking for a (even very small) dataset of the same genes (or other ...
0
votes
0answers
19 views

going from probe sequence to hgnc gene symbol

I have a bunch of (human) Agilent probes (both probe ID and the actual sequence, some custom array), and I would like to get the hgnc gene symbol based on the actual probe sequences, rather than the ...
0
votes
0answers
62 views

Convert DNA raw data between a different formats [duplicate]

I have .vcf file with partly decoded genome provided by some service. How can I convert this file into other popular formats which may be used in other services? I'...
0
votes
1answer
30 views

How to determine a correct promotor sequence? (Bisulfite sequencing - uni assingment)

aspiring bioinformatician here, I'd like to ask you for help with an university assignment. First let me post the entire question: ...
0
votes
1answer
28 views

Retrieving all genes for a gene ontology term

I'm looking for an easy way to retrieve all the genes in a list that are associated with a certain GO term, preferably using R/Bioconductor packages. I'm not interested in under/overrepresentation or ...
0
votes
0answers
14 views

How to merge several microarray-based gene expression datasets while not excluding genes that are not present in all datasets?

In integrative gene expression analysis when two expression matrices from different datasets are merged together, they are usually merged by common genes in both expression matrices while all other ...
1
vote
0answers
26 views

10x Single-cell RNA-Seq - Updating gene symbol with latest ensembl release - Ensembl IDs missing

I am trying to update the gene symbols provided by the 10x human precompiled reference (2020-A), using the mapping Ensembl ID to gene symbol provided in release 102. However, I found out that 56 of ...
0
votes
1answer
53 views

Align the HIV-1 Gag protein with the Gag protein of Visna virus

Align the HIV-1 Gag protein with the Gag protein of Visna virus Background Visna virus is a lentivirus causing encephalitis in sheep The problem is align the follow two protein Gag of viruses HIV-1 (...
1
vote
1answer
24 views

Mapping protein refseq to Gene ID

I have a protein refseq (eg, NP_000029). How can I get the corresponding gene ID (ag, APC) from NCBI using an R package?
0
votes
0answers
34 views

Finding a gene of similar length

I would like to find a few genes that are similar in length to a gene of interest, and by that I mean the total length of a canonical transcript including introns. This is proving to be surprisingly ...
0
votes
0answers
12 views

? What meaning do positive and negative values have in the centroid plot for genes?

I was working with a dataset containing genes. The central plot of the model after using "shrunken centroid" is like the following picture: I noticed that they can all be negative ...
1
vote
1answer
41 views

how to train a gene dataset with a nearest shrunken centroid classifier?

I have a data file named "geneexp.csv". the data contains information about gene expression of three different cell types (CD4 and CD8, CD19) I want to classify cells by performing the ...
1
vote
1answer
37 views

Is there a Python program that is able to show convergent and divergent evolution on a phylogenetic tree?

I was wondering if there was a Python program that detects convergent and divergent evolution on a tree. I am also curious if it is just better to look at a phylogenetic tree and conclude what is ...
1
vote
2answers
40 views

Multiple Alignment cost application

Is there any biological application/case where someone would be interest in the estimated total cost of the alignment between a set of sequences (genes or amino acids) without the aligned sequence ...
3
votes
1answer
70 views

What are the coordinates of the extended major histocompatibility complex (xMHC) in GRCh38?

Is there an accepted boundary of the extended major histocompatibility complex (xMHC) in human? Specifically, I am interested in the boundary coordinates for Genome Reference Consortium Human Build 38 ...
0
votes
0answers
42 views

tissue cross talk using gene expression data

I am studying about tissue cross-talk using gene expression data. My first goal is to identify the genes responsible for communication signaling(cross talk). Let say the tissues are fat and muscle. ...
0
votes
1answer
39 views

gene-gene correlation from two different Tissues

I am stuck on how to do correlation for two independent data sets with common row and column names. A and B are datasets that contain as many rows as genes and as many columns as samples. The rows in ...
0
votes
2answers
19 views

Easy way to create gene plot in gviz?

I would like to create a simple plot of a given human gene containing the main features, e.g. exons, introns, ORFs, transcripts etc. I understand that gviz is a ...
0
votes
1answer
90 views

Choosing Fisher's Exact or Binomial test for overrepresentation in PANTHER

The PANTHER website offers a tool to obtain the GO-based overrepresentation of a gene list (the analyzed list) versus a reference gene list. After entering both these lists, the tool asks to choose ...
0
votes
0answers
34 views

GTF parser returned Empty DataFrame

I used the following script to retrieve for RPKM and cov value for each transcript. ...
0
votes
1answer
36 views

How to annotate gene length to a list of gene symbols using UCSC data?

I have a list of HGNC gene symbols, I am looking to get the gene length of each gene. Although I also describe these genes with lots of UCSC datasets as features, so I am wondering if there is a ...
1
vote
1answer
63 views

How to compact variant data to their genes without bias?

I have a dataset of genes I am trying to collect data on from public databases, to use as features in machine learning. I am trying to take some features from UCSC genome browser (e.g. number of CpG ...
0
votes
1answer
58 views

Seurat DE t.test

I am new to the Seurat package and was looking at the tutorials on the Seurat website and am just curious to know if there is any way to perform a t.test for the expression of a specific gene between ...
0
votes
0answers
10 views

How to get the gene names corresponding to genes in a module in R?

On doing module extraction, I get the module as a text file containing the index number of the gene and not the gene names. I have saved the gene names from the original gene expression file in a ...
1
vote
1answer
34 views

Comparing gene abundances between metagenomes

My workflow until now: Find fragments of a marker gene in unassembled metagenomes > download and assemble metagenomes > recover the gene neighborhood / gene set of interest Right now I have a ...
3
votes
2answers
117 views

How can I obtain a list of all NCBI gene ID's along with their full name, symbol, and also known as symbols?

I would like to do two things: (1) Obtain a list of all NCBI (Entrez) gene ID's. (2) Obtain the "Official Symbol", "Official Full Name", and "Also known as" fields from ...
-2
votes
2answers
113 views

Problem with merge data while trying to convert gene names in R

I've been trying to code (in R) a way to convert gene accession numbers to gene names (from RNAseq data). I've looked at all the related questions and tried to modify my code such, but for some reason ...
0
votes
0answers
35 views

How can I obtain gene lengths programmatically for genes in Wormbase?

I would like to programmatically, in R, obtain gene lengths (excluding introns) of genes of c. elegans given their Wormbase identifier (for example: WBGene00000004). How can I do so?
0
votes
0answers
103 views

haplotype network analysis in R

it has been a few days that I am struggling to generate haplotype network analysis for a gene plays important role in pesticide renitence. I am trying a R package "pegas" which seem pretty ...
0
votes
0answers
20 views

Determining a Gene's Unknown Function

I'm a beginner in this field (so pardon my rudimentary knowledge/explanation) trying to understand ways on how I could potentially identify genes of unknown function. I am trying to get as close as I ...
1
vote
1answer
40 views

How can I convert codon coordinates to genomic position?

I am looking for a given mutation in IGV, which accepts coordinates in the form of chr<X>:<Y> Where X is the chromosome number and Y is the base ...
1
vote
0answers
29 views

miRNA dataset for prediction experiments

I am from the field of Computer Science and I want to perform some experiments related to miRNA and mRNA prediction.I have been searching for datasets in this area and found one called mirWalk ...
2
votes
4answers
74 views

Separate multiple sequence into different file, one sequence per file

I have a file contain multiple sequence, and I want to separate them by "gene:" into different file. example: example.fa ...
0
votes
0answers
27 views

How do I generate a list of post-synaptic gene markers that will guide me in my search for these markers in intestinal stem cells?

I would like to generate a list of gene markers that represent post-synaptic related genes. I will then use this list to search through single cell sequencing data, in order to assess whether certain ...
1
vote
1answer
24 views

Map gene IDs to protein structure if exist

I want to map some gene ids to their proteins structures if they exist. The genes are rows of this CSV. There are other information that may help also such as Product description but that may lead to ...
0
votes
0answers
27 views

Finding regions between ORFs

I'm doing work on mRNA and need to get predicted mRNA sequences from a genome. I'm working with this genome https://www.ncbi.nlm.nih.gov/nuccore/U00096.3 (E. coli k-12 mg1655). So have a genome ...
0
votes
1answer
221 views

How to map gene names to ensembl Ids in R

I am trying to convert a list of gene names into Ensembl IDs but I'm having a bit of trouble. I've tried using the EnsDb.Hsapiens.v86 package but I always get LRG-ID values returned as well, even ...
2
votes
1answer
33 views

Assemble reads for a specific gene

I have a lot of unassembled sequencing data and I want to build phylogeny for some genes from these data. I can retrieved the sequene by mapping reads to a reference sequence but if the two species ...
0
votes
0answers
22 views

Free, user-friendly software for visualizing and comparing gene clusters?

I'm looking for a tool to do the job listed in the title. I've come across Gene Graphics (https://academic.oup.com/bioinformatics/article/34/8/1406/4708234), but never used it and I was wondering if ...
1
vote
1answer
57 views

Available phenotype data from GTEx

I am using gene expression data from the The Genotype-Tissue Expression (GTEx) project, available here: http://gtexportal.org. I would also like to use phenotype data for each sample (especially age, ...
1
vote
1answer
48 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 ...
0
votes
1answer
45 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 ...
0
votes
1answer
47 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 ...
1
vote
1answer
19 views

Scooping and GeneMatcher

A colleague has uploaded about a dozen candidate disease genes to GeneMatcher, described here and here and located here, with excellent success. However last year and again recently he has ...
0
votes
1answer
288 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 ...