Questions tagged [gene-expression]

The process by which information encoded in a gene is converted into a functional protein or RNA, resulting in or contributing to a phenotype.

Filter by
Sorted by
Tagged with
-1
votes
0answers
13 views

Does a whole exome sequence include whole genome data?

I am trying to learn more about epigenetics, and ways in which DNA can be sequenced. I am still confused about the different ways exomes are sequenced vs how genomes are sequenced. I believe I fully ...
0
votes
0answers
14 views

What are the effect of P. Falciparum on gene expression in humans? Do they have an effect in the first place?

I am looking for names of genes which are affected (if any) and how are they affected, I mean whether the expression levels are lower or higher?
1
vote
1answer
30 views

What prevents mRNAs that are localized to a specific part of the cell from being translated before they reach their destination?

One of the methods of mRNA localization, for example, is random diffusion of mRNAs where the mRNA binding proteins are localized to a certain part of the cell. However, I was taught that the ribosome ...
0
votes
1answer
49 views

How to design a permanent vaccine to cholera using CRISPR?

I know that Vibrio Cholerae infects the body through the GM1 ganglioside. So, would it be possible to engineer a CRISPR gene editing tool to prevent Vibrio Cholerae from getting into our cells? ...
3
votes
2answers
51 views

Can a bacterium express a virulence gene and not produce toxins and what may be the cause of this?

I am preparing a seminar on viable but non-culturable (VBNC) state in bacteria, mainly foodborne pathogens and I just saw this line in a journal article by Lothigius et al that "the expression of the ...
1
vote
0answers
40 views

How can we say that a gene is spacio-temporally regulated?

Gene expression is depending on the space and time of the cell. How can we distinguish the function of a gene without a chance of changing its expression? And also how is it possible to find the exact ...
0
votes
0answers
26 views

Study on Introns?

I am curious whether there has been a study done on the effects of removing introns. Specifically, what happens if you genetically edit a eukaryote genome to no longer contain introns? Or maybe just a ...
3
votes
1answer
58 views

Why are protein-coding regions rich in GC?

I have been searching for an answer for this question and have some possible solutions, but I am not sure. GC regions are more stable as there are 3 hydrogen bonds instead of 2 with AT, however I am ...
0
votes
0answers
38 views

Linker DNA and Genetic Expression

So I was reading on linker DNA, and the textbook only describes it in terms of structure. I was wondering if linker DNA can ever contain genes, and if it can, whether it will always be expressed or ...
-1
votes
1answer
32 views

Where to find a list of genes coding for protein in human

I have raw read counts extracted by htseq from STAR alignment I have both data with both Ensembl IDs and gene symbols, but I need only a latest list of protein coding genes in human; I googled but I ...
0
votes
1answer
26 views

Which one is better to use for water stress experiment GWAS or RNASeq?

This is my first time in this area of research. I am working on 95 varieties of bambara groundnut. I have done the agromorphological characterization of these varieties as well as the genetic ...
1
vote
1answer
33 views

Question about alternative polyadenylation

I know that alternative polyadenylation creates different transcript isoforms. My question is whether alternative polyadenylation ever results in differences in the terminal/last exon? The only case I ...
0
votes
0answers
12 views

How to find essential genes by differential expression from TCGA 3rd level CNV data?

I have two types of data one have normal patients copy number variation (CNV) data and another have tumor patients CNV data. In each file there are three columns one contain patient ID, second ...
0
votes
0answers
42 views

For how long is the gene expression altered in tenocytes' nuclei following changes in mechanical load, and which genes are affected?

I read in {1}: The matrix is far more conspicuous than the cells. However, it is now widely recognised that the cellular elements hold the key to understanding development, repair and the ability ...
0
votes
1answer
36 views

Studying the epigenetic variability, can I use SNPs?

So, I'm trying to study the effects of epigenetic variability on the brain structure. Can I use SNPs associated with a gene's higher expression to compute the likelihood of that gene being expressed ...
1
vote
2answers
29 views

Is there natural occurrence of induced pluripotency / expression of Yamanaka factors and what is the evolutionary explanation of that?

Is there natural biological processes in which the full (full reprogramming into pluripotent state) or partial (partial reprogramming, stopped before point-of-no-return, preserving the functional ...
2
votes
2answers
46 views

Is complete dominance actually a genotypic process?

An example often stated for codominance is blood groups, where both alleles version of the protein is expressed and can be found in the cell membrane. An example of incomplete dominance often given ...
0
votes
1answer
54 views

x-linked recessive inheritance and correlation for males

I was inspired by a discussion in this thread. Wikipedia lists a number of disorders linked to recessive genes on the x-chromosome. One typical example is red-green color blindness. Now wikipedia says ...
0
votes
0answers
32 views

How do introns code for proteins? [duplicate]

The reason I am asking this is because my textbook states that: Some introns may themselves encode proteins, and some may become short non-coding lengths of RNA involved in gene regulation. Some ...
1
vote
3answers
230 views

Why are there three stop codons but only one start codon?

I was wondering whether there is any specific reason that there are three stop codons but only one start codon in prokaryotic and eukaryotic cytoplasmic mRNAs.
2
votes
0answers
122 views

Why do BRAF mutations appear more in skin cutaneous melanoma?

When looking at the tissue expression of the BRAF protein it seems that BRAF is regularly expressed in almost all of the tissues. There is elevated expression in tissues like the Testis and the ...
3
votes
0answers
190 views

Regulation of LBD33 genes Arabidopsis. If LBD 33 gene is up-regulated by auxin then why does expression decrease when increasing auxin concentration?

I have a question regarding the regulation of lateral boundary domain genes in Arabidopsis (specifically LBD33). I am an undergraduate student trying to understand the results of a lab where I measure ...
0
votes
1answer
51 views

Is there a data base, tool or method I can use to find out which of my genes code for cytokine receptors?

I have a list of over 600 differentially expressed genes from my single cell RNA seq data analyses. I want to proceed to find out which of my genes code for cytokine receptors so that I can show on a ...
0
votes
1answer
34 views

X linked traits expression in females

We all know that females have an inactivated X chromosome (Most of its genes are inactivated). Consider a female who is a heterozygous carrier of an X linked abnormality, If the inactivated X was that ...
0
votes
0answers
17 views

Data base or computational tool to help predict if two predicted interacting surface proteins are located on separate cells or on the same cell?

Is there any computational method or database with the help of which one could predict if two interacting cell surface proteins are located on separate cells or are located on the same cell surface?
0
votes
0answers
46 views

Given a list of cell surface genes, is there a computational possibility to predict their interaction partners on the surface of another cell?

After performing differential expression analyses with the Seurat package on my single cell RNA sequencing data from ILC2s of mouse origin, I generated a list of differentially genes. I afterwards ...
0
votes
1answer
39 views

Element of promoter responsible for expression power of gene

I know that there is a classification of promoters like: strong, medium and weak. This shows how a promoter affects gene expression levels. So my question is: what part of the promoter affects it? ...
1
vote
0answers
26 views

Is bi-allelic gene expression random?

Supposing we have the genotypes “Aa”, “AA”, and “aa”... which are not mono-allelic (not imprinted and not X-inactivated). Does the dominance of the “A” allele over “a” allele affect which gene is ...
1
vote
1answer
62 views

What do the haploinsufficiency scores in the clinVar database represent?

I understand that haploinsufficiency occurs when one of the two copies of a gene is mutated to the point of being unusable, and the single copy remaining is unable to cope with the cell's demands for ...
2
votes
1answer
28 views

What are mutator genes which cause copying errors in other genes?

Reading Dawkins' book "The Selfish Gene," I came across this line: "There are even genes--called mutators--that manipulate the rates of copying errors in other genes." (The context is his argument ...
1
vote
0answers
34 views

How can the same transcription factor be both an activator and suppressor of the same gene?

For example, hunchback in moderate concentrations is an activator of kruppel, but a suppressor of kruppel in large concentrations. From what I've seen in literature, that's because the kruppel's ...
2
votes
0answers
75 views

Is there a mechanism of timing or delaying the expression of gap genes?

Summary Gap genes are expressed in presence of the right combination and amount of transcription factors. But is there any additional mechanism of timing the expression of the gap genes to ensure ...
0
votes
1answer
25 views

Cloning a coding gene into a non-expression vector

Does it make any sense to clone a CODING gene into a NON-expression vector? doing this will only give us multiple copies of the gene, while we could run PCR instead (Let's say we know the gene ...
-1
votes
1answer
63 views

Are modern gene-editing techniques capable of creating genetically-superior versions of humans? [closed]

Can we alter the DNA in, say, a small-framed, low muscle mass male to those of elite bodybuilders? Can we alter the DNA sequence that stops balding and hair loss? How about the genes responsible for ...
0
votes
1answer
20 views

Question: What is CINWntUp and CINnormL?

What is CINWntUp and CINnormL? I read a paper that uses this two things as classes but Im not sure what they represent. I imply that CIN is referring to Chromosomal instability but I don't know what ...
0
votes
1answer
27 views

Gene expression: which allele is considered?

For human beings, we have two copies of each gene inherited from the parents. The question is, when referring to gene expression, which copy (or allele) is considered?
2
votes
1answer
76 views

Is there a resource to query gene expression similarity? Stratified by sex?

We developed such a resource. The editors of "Bioinformatics" (at OUP) rejected the paper on the grounds that we did not run a comparison with "state-of-the-art" [similar] resources. Can someone help ...
0
votes
1answer
41 views

How is the timing of gene expression controlled in developing embryo? [closed]

I understand how cell differentiation works in general (gradients of homeobox proteins etc), but how is timing controlled? Why do some genes switch on at a very specific moment of development and then ...
0
votes
2answers
52 views

identification of differentially expressed genes in RNA-seq analysis [closed]

I am using four different packages (viz. EBSeq, DESeq2, edgeR, LPEseq) for identification of differential genes. Now I am confused whose fold change value should I take for further downstream ...
4
votes
2answers
341 views

How does transcription end?

In rho-dependent termination in prokaryotes, how does RNA polymerase “know” that it has reached the end of a gene and that it has to stop so that the rho-factor can bind mRNA’s rut site? Is there a ...
0
votes
1answer
27 views

About Frameshift Mutation

I am coding a DNA translater, based on the homosapiens genome, & i knowing that the data provided from NCBI is surely not 100% precise (there may be some base changes / removes etc...) , & i ...
1
vote
1answer
62 views

What is the role of CRISPR-dCas9 in gRNA-dCas9 transcription regulator complexes?

In this paper1, I read that mutant versions of Cas proteins such as a deactivated Cas9 (dCas9) are used alongside a guide-RNA (gRNA) to form variants of CRISPR tool that can function as transcription ...
2
votes
0answers
22 views

Preprocessing microarray data to detect increased male expression variance due to dosage compensation?

I am currently working with a dataset from a large microarray experiment where one of the aims is to look for evidence of the predicted doubling of variance in expression on the X chromosome in ...
2
votes
2answers
51 views

What happens to the complementary base when the other undergoes a base substitution mutation?

From what I know only the base pairs A and T/U, or G and C can occur due to hydrogen bonding. So if a base substitution mutation occurs, say an A is replaced by a C on the strand, does it affect only ...
2
votes
0answers
45 views

How are animal patterns encoded in the dna?

After seeing the patterns on the feathers of a argusianus argus pheasant (shown below), I am curious where is the information that encodes a pattern for a particular bird, and what form is this ...
1
vote
0answers
45 views

qPCR: Huge variation in fold change of genes between biological replicates

I am trying to validate my RNAseq data by doing qpcr for which I am looking at the fold change of few genes across various timepoints of treatment conditions. I am getting huge amount of variation (in ...
-1
votes
1answer
96 views

Can the environment affect genes and adaptation in offspring?

I recently read several articles that believe that environment can affect gene expression and this change will transfer down to the children. Some theorists believe that random mutations are more rare ...
2
votes
1answer
40 views

Why don't cells double gene expression after S-Phase?

In the cell cycle (G1-S-G2-M), all of the DNA is replicated during the S or Synthesis stage. The cell may then spend some considerable time in the G2 phase before splitting in the M phase. Since there ...
2
votes
2answers
73 views

Can gene-gene interactions result in gene expression?

I am building a project on Inferring Gene Regulatory Networks using ARACNE and PCA-CMI algorithms, and the input to these algorithms is taken from the DREAM3 challenge. The format of the input data ...
3
votes
0answers
37 views

Low cost cell free expression system

I am a graduate student looking to incorporate some protein engineering into my training. I have been reading a lot about E coli lysate based systems, but they still require 3rd party additives like ...