Questions tagged [gene]
Use this tag to refer to the gene sequence/coding part of the sequence.
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Is GEPIA reliable for gene expression prediction?
After I obtained the hub genes related to AML disease, I checked their expression in GEPIA. I got in problem for explain my gene expression. for example, the expression of PTEN, which is a tumor ...
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answer
24
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Edge table on cytoscape won't show gene name on the shared name pp interaction column
Could you help me solve this problem?
So, basically both shared name and name column on this edge table not showing the gene name. It just show like this picture.
How can I change the name in the name ...
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1
answer
31
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Stringapp failed to start in cytoscape
Hello, I encountered a problem of stringapp failed to start. I already reinstall string app 3x but still unable to use string app for creating network of genes.
Thank you
Vania
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1
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26
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"BLASTx for miRNA Annotation: Mature vs. Primary miRNAs as Query Sequences"
I am doing miRNA annotation of a plant genome. I have two files - one containing all the predicted mature miRNAs and another containing all the predicted primary miRNAs. I want to find out which are ...
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1
answer
23
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StringApp installed on Cytoscape, But does not added to IMPORT/Network from Public Database
I have different versions of Cytoscape in different PCs. one is 3.10.1 and the other is 3.10.2. for both I installed StringApp but in 3.10.2, It is not added to "import/network from public DB&...
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Find most abundant transcript isoform of a gene across different tissues in long read RNA-Seq data
I want to understand which is the most abundant variant of a gene of interest across different tissues by looking at different publicly available databases (mouse/human). I have deduced from ...
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2
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What is difference between gene and CDS in the gff file?
I'm investigating bacterial genome.
In GFF file, it includes gene, CDS, tRNA or something like that in region fields.
What is the difference between gene and CDS?
Thant you in advance.
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Best reference book for basic concepts when working with bioinformatics
I'm starting to study Bioinformatics, I already have basic knowledge of Biochemistry and Genetics, but I want to buy a reference book, to use when I forget a concept (I'm a Computer Science student, ...
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What is it about gene names starting with "LOC"?
I was struggling to use AnnotationDbi to change my ensemble ID to gene name, for datasets of three different species (human, canine, mouse). Among gene names for all three species there are genes with ...
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51
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Gene ensemble vs Hugo id
Hi
I have been recently struggling with the gene annotations and changing gene ID to ensemble ID. While I was doing that there were some genes for the same species that had the same gene ID but ...
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71
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conducting a ttest on a board of 1000 genes in 50 peope divided into to groups(A and B). pvalues are different each time
I am struggling in conducting at test on a board of 1000 genes in 50 individuals divided into to groups (A and B). I have a dataset of 1000 genes of two groups of people (total individuals=50)
group A ...
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77
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Convert genotyping results to vcf or other plink formats
I used a Genotyping software called T1K to generate KIR genotyping, the output file contains genes and alleles for each sample, how can i convert the results to a vcf file or other formats which can ...
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31
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Need to make circos plot from Enrichment data
I have a list of genes and their associated pathways. The data was generated using Partek. The data looks like this -
Gene_in_list
Gene_set
Description
Enrichment score
P.value
Gene1
hsa
Disease C
...
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2
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1
answer
70
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How to rearrange gene ontology obo file?
I have a gene ontology obo file, and would like to rearrange the obo format file in a single column to a text file in three columns comprised of 'parent (id:GO:xxxxxxx)', 'child (is_a: GO:xxxxxxx, ...
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54
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Gene Set Comparison Without Expression Data
I have been looking all over the web to find some answers to my problem but unfortunately, I was unsuccessful. I wish to determine whether an a priori defined set of genes in my case genes associated ...
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