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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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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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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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Transcription of Multiple RNAs on One Section of DNA in Eukaryotes

When RNA Polymerase moves along the template strand it bind to the promoter and moves along in a 3'-5' fashion on the template strand. Can RNA Polymerase also move along the coding strand of this ...
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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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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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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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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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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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identification of differentially expressed genes in RNA-seq analysis

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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Meting temperature of PCR products and product expected size

I know the Melting temperature of my primers but I would like to know if the melting temperature of my product match with the melting temperature I get in the melting curve when doing a qPCR, in order ...
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RET Gene mutations and HSCR

I'm writing an essay about RET oncogene and it's affects on Hirschprung's disease. I have found out that RET gene and it's receptor plays major role in developement of neural cells (that are missing ...
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How does RNA get from the nucleus to a ribosome?

How does a strand of mRNA get from the nucleus to a ribosome? Does it just float around waiting to bind to one? I know that RNA-binding proteins exist to supposedly modify and guide RNA, so if these ...
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What percentage of differentialy expressed genes associated with complex disease are located in the susceptibility region?

To uncover the mechanism of complex disease, GWAS and high-throughput gene expression analysis were performed. The former method will provide many disease-associated candidate sites on the genome, ...
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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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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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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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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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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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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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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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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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How to find the UTR sequences in yeast?

Since it is know that the promoter say for example GAPDH promoter does not contain 5'UTR sequences, so from where we can take the UTR sequences of any gene????
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Can agouti signalling peptide inhibit MC1 and MC5 production in the body?

I read a comment on reddit where someone said that its impossible to use ASIP to inhibit those two. And that it will be difficult for the peptide to reach MC1 and MC5, and that the chances of it ...
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Why doesn't Pax6 expression in the pancreas lead to eye formation in the pancreas?

Researchers have been to induce ectopic eye structures in fruit flies using the Sey/Pax6 from mouse. But since Pax6 is also expressed in the pancreas, why is there a different phenotype?
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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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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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How do cells reproduce more slowly in the later stages of the human pregnancy?

I’m a 5th grader learning human reproduction and both my father and teacher told me that in the later stages of pregnancy the cells reproduce more slowly. What are the regulating mechanisms? Is it ...
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247 views

One-sample t-Test for mean fold change

I want to see if there is down-regulation of some hypermethylated genes. I have the mean fold change values from qPCR and have decided to use the one-sample t-Test to see if the changes are ...
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1answer
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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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How can a hypermethylated gene be upregulated?

I treated MCF-12A cells with an endocrine disrupting compound resulting in hypermethylation of a DNA repair gene. However, when I measured the expression levels of the gene, I found the gene to be up-...
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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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Which chromosome carries gene of sugar diabetes? [duplicate]

As we all know, sugar diabetes or diabetes mellitus is genetic to a great extent. Now my question is, which chromosome: X or Y - carries gene of this disease? I'm asking this in order to gauge ...
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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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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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Translation in prokaryotic cells

For translation to occur in the mRNAs of prokaryotic cells, the presence of ribosome binding sites (RBS) for each Open Reading Frame (ORFs) is required. How does translation occur in prokaryotic cells ...
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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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Making sense of the Gene Expression Omnibus datasets

I have no experience in genomics but need to use a few datasets from gene expression omnibus data repository for a project. I am starting with reading the datase GSE 3431(https://www.ncbi.nlm.nih.gov/...
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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
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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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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
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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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Downstream Promoter Element’s Role

The promoters‘ role is to bind polymerase to get started transcription. And in fact: by Wikipedia “Like all core promoters, the DPE plays an important role in the initiation of gene transcription by ...
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2answers
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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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What does having no consensus symbols in a ClustalX2 alignment mean?

I have completed a full sequence alignment of 30 tyrosinase sequences using ClustalX2, yet there are no consesus symbols above the data like there normally is. I think it has run correctly, but am not ...
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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 might the distance from the transcript start site affect genetic interactions?

How might the distance from the transcript start site affect the extent to which a nearby noncoding variant may vary the level of expression at a coding variant? My guess would be that a greater ...