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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.

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In theory, how would genetic engineering of certain genes affect morphology/phenotype of individuals in adulthood? [on hold]

Say we get to the point where we then can identify all of the correct genes/combination of genes and etc. that are responsible for things like zygoma, maxilla, mandible, frontal bone, etc. shape (...
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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 ...
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1answer
25 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 ...
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28 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 ...
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3answers
92 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.
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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 ...
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180 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 ...
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1answer
48 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 ...
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1answer
29 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 ...
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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?
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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 ...
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1answer
31 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? ...
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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 ...
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1answer
17 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 ...
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1answer
26 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 ...
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32 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 ...
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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 ...
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1answer
23 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 ...
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1answer
54 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 ...
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1answer
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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 ...
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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?
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1answer
73 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 ...
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1answer
40 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 ...
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2answers
50 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 ...
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2answers
296 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 ...
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1answer
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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 ...
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1answer
40 views

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

In this paper, 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 ...
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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 ...
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2answers
41 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 ...
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Increasing my PCR efficiency to be able to better visualise my bands

I run an electrophoresis in agarose gel and my expected bands are extremely week, is even hard to see them. It looks I need to increase my PCR efficiency. I have read about a Hot start setp, which ...
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0answers
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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 ...
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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 ...
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1answer
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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 ...
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1answer
38 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 ...
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2answers
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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 ...
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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 ...
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30 views

X-inactivation in kleptons

Kleptons have additional sets of chromosomes from a host species. How do they deal with the pluritude of X chromosomes? Assuming a triploid individual (e. g. of the edible frog from an all-hybrid ...
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2answers
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When does genetic randomization happen?

When two parents (regardless of species) reproduce in sexual reproduction each offspring is generally a random combination of genetic traits from each parent. Their developed traits then depend on the ...
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1answer
76 views

Pseudoautosomal regions of the X chromosome showing heterozgyosity

I've always had questions for myself about sex differentiation, mostly on account of an unusual history & puberty. I won't go into details, but needless to say it was unique. My question is... I ...
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1answer
2k views

What is the difference between gene expression and protein synthesis? [closed]

I have no idea what I'm supposed to do. Can someone please help me? What is the difference between gene expression and protein synthesis?
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1answer
70 views

How can individual strands of coat hair have only a single color when considering codominance?

I understand how codominance works. We have two (or more) alleles for one gene, neither having dominance over the other. They are both expressed independently, which means that different phenotypes ...
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1answer
40 views

Are there differences between the activation proteins of Eukaryotes and those of Prokaryotes

I'm in BIO 203 (for reference to my skill level), and I noticed the textbook makes a whole section out of transcriptional activator proteins, their function and applications in eukaryotes, but in ...
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1answer
109 views

Overexpression by integration of an additional copy vs promoter exchange

In Becker et al (2011), the authors increase the expression of several genes through different methods. For some genes (e.g., lysA, ddh), they achieve overexpression by integrating an additional copy ...
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3answers
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Is it possible to artificially select for flight in pigs?

After reading this rant by Fodor, as a layperson, I was idly wondering whether it would be possible to artifically select for flight in pigs. Of course by that time the porcine lineage will probably ...
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2answers
225 views

Which information can be extracted from time course RNA-Seq Data?

So I am very new to the area of biology so I am sorry if this is a stupid question. I have RNA-Seq data carried out over a span of 100 days and I have gene expression data in the following format. ...
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0answers
73 views

What determines the differences between differentiated cells?

Given two multi-cellular species with obviously different phenotypes. The reason for the different phenotypes reflects their different DNA. However two types of cells in an adult organism may have ...
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1answer
42 views

Can proteins structure change depending of alimentation of an organism? [closed]

In my understanding protein are built using information caring by RNA. So a given protein should always have the same structure in a given organism has the DNA of this organism does not change. I'm ...
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2answers
57 views

Finding targets of transcription factors

I'm trying to find an easy way to get a list of putative targets of a particular transcription factor (for example, STAT1). I'm interested in targets determined using both experimental and ...
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2answers
129 views

Mathematical representation of “gene signatures”

According to Wikipedia's definition, "a gene signature is a group of genes in a cell whose combined expression pattern is uniquely characteristic of a biological phenotype or medical condition." ...
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How does a gene “know” what to change to?

Excuse my ignorance but I've always been curious about this... For example, a frog is red, but it starts living in a green forest. Over time the frog becomes green to camouflage. But a gene can't see ...