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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R Tool and analysis of Gene Expression data from NCBI GEO datasets [migrated]

When i execute this code in "R" i het answers for this gset <- getGEO("GSE51808", GSEMatrix =TRUE) if (length(gset) > 1) idx <- grep("GPL6244", attr(gset, "names")) else idx <- 1 gset <- ...
3
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16 views

Why introduction of an extra copy of a gene related to pigmentation causes RNA interference in Petunia?

RNAi became famous after Fire and Mello experiment in C.elegans; however, it had been observed before. In the 80's, Jorgensen was trying to increase pigmentation of Petunia flowers by introducing ...
6
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2answers
44 views

Can molecular genetics make a boolean variable from a continuous variable?

In the same kind of idea than this question. Gene expression are regulated through complex interactions. The concentration of enhancers and repressors is an important aspect that dictate the level of ...
2
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1answer
34 views

Comparing gene expression levels between control and disease at different time points

I have a data set with expression levels of a list of genes, measured in replicate at two different time points between two groups; a control group and a disease group. I want to identify the changes ...
6
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1answer
55 views

Do DNA repressors exist?

I know about enhancers and the mechanism that lead them to increase the gene expression of their targets but I was wondering if similarly DNA repressors exist. I know about protein repressors but I am ...
3
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32 views

“Enhancers” of enhancers?

I am looking for examples (if any) of genomic regions which regulates the activity of enhancers, either augmenting or reducing it. Essentially some kind of enhancers (or repressors) of enhancers to ...
1
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1answer
20 views

How to correlate the pattern by which CAP activator from E.coli binds to DNA and its mechanism of action?

The catabolite activator protein (CAP) activates the expression of more than 100 genes involved in secondary sugar metabolism in E.coli. Apparently, it always binds in sites that are away from -10 and ...
6
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3answers
44 views

Mechanism by which $lacI^{d}$ is a dominant mutation, impairing the function of normal copies of the Lac Repressor

Jacob-Monod model for the lac Operon was based on experiments using two strands of bacteria which constitutively expressed $\beta$-gal: $I^{c}$(mutation in the gene lacI , which encodes the repressor) ...
1
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1answer
49 views

How does alternative splicing work?

I am trying to find out what controls what exons are spliced out, and I keep coming across the term cis regulator, but I cannot seem to find a clear explanation of what happens... Thank you in ...
0
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1answer
45 views

What are microRNA, siRNA and antisense RNA?

From what I understand, microRNA binds to proteins which can cut certain mRNA strands do that this protein is not synthesised. This seems like gene silencing to me, however I have also come across the ...
0
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7 views

What is the control level of activation in Paradigm?

I am trying to use Paradigm for pathway analysis on mRNA expression data. In Sample-Specific Cancer Pathway Analysis Using PARADIGM it is written that Each entity can take on one of three ...
1
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0answers
17 views

Which data format for mRNA expression matrix is necessary to run pathway analysis with Paradigm?

I am running Paradigm on a matrix of mRNA expression. I read Vaske, Charles J., et al. "Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using ...
4
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2answers
79 views

Name two reasons why it is impossible to determine a gene's nucleotide sequence from the amino acid sequence of the polypeptide

I can only think of one reason, which is because different codons can specify the same amino acids. However I am having trouble thinking of another reason.
4
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2answers
94 views

How does optogenetics work?

I am aware of the post here 'Optogenetics - How do microbial opsins work?' however it is a bit too technical for me. I am struggling to understand how the neurons can be genetically engineered to ...
3
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1answer
53 views

meaning of the “reads” keyword in terms of RNA-seq or next generation sequencing

I'm an undergraduate student at computer science and currently, I'm interested in bioinformatics. Today, I've started to read a paper about clustering and classification of non-coding RNAs can be ...
2
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1answer
30 views

What network motifs or other mechanisms can make the expression of a gene invariable to the environment?

Next to double positive feedback loops and chromatin modification, which other mechanisms can make a gene susceptible to a certain environment in one cell-type but not in another?
0
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1answer
34 views

Two heterozygote mice for skin color are reproduced. Find the probability that in 3 children 2 will be dark and one white

Two heterozygote mice for skin color are reproduced. Black is dominant to white color. Find the probability that in 3 children 2 will be dark and one white. How did you do the ordering. Well I found ...
0
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1answer
75 views

How to select genes before log2 ratio on a RNASeq gene expression matrix, based on signal median

I want to transform a TCGA mRNA expression matrix (in linear data format) to log2-ratios and then run a feature (gene) selection, selecting the 1000 most variant genes (genes with higher standard ...
2
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2answers
245 views

Why people fear GMOs? Can't we map a plant composition?

My main question is can we map what a fruit is made of? For instance apples are made of 0.0002% of protein X, 0.00001 of protein Y, 0.001% of amino acid Z... etc... If we can, then my next question ...
3
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1answer
24 views

IPTG and lac operator with e coli for foreign gene question

We did an experiment were we have e coli with a plasmid with a gene from another bacteria in it, and we put in IPTG in for induction. Will after looking up more about IPTG online I see it's related to ...
0
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0answers
6 views

In insects, does the Alanine repeat occur on the homeodomain sequence of the abdomen or does it occur on a different sequence?

By "Alanine repeat", I am referring to the suppression of the formation of extra insect legs due to Ubx gene suppression through Distal-less repression.
5
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1answer
57 views

Plasmid in the nucleus and gene expression

If we insert a plasmid into a human nucleus that contains exact copy of gene and all relevant promoters to produce some human protein, will the cell create functional protein from that plasmid only ...
1
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1answer
20 views

Why does a tumour's genome change depending on the environment?

According to the book "Primer of The Molecular Biology of Cancer" by Vincent, Theodore and Ateven, the tumour cell is changed depending on its environment. performed genome-wide analysis on three ...
4
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1answer
23 views

Can methylation of a promoter induce gene expression in some rare cases?

Can methylation of a promoter induce gene expression in some rare cases? I've read somewhere that methylation of an intron can induce gene expression (eg. Igf2). How is that even possible? Thank ...
2
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0answers
25 views

Why are riboswitches mostly present in bacteria and not in eukaryotes?

Riboswitches are a rather elegant way to regulate gene expression without any additional machinery. A small ligand binds to the mRNA and directly influences transcription or translation. Most of the ...
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1answer
38 views

Multi-modal distribution for gene expression data

Why would some genes have more than two modes in their expression distribution? What external factors would cause this anomaly? I'm referring to the expression distribution of a gene across different ...
4
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2answers
489 views

Father with mutated gene for mtDNA- why isn't his offspring at risk?

Mothers transmit their mitochondria (and therefore mtDNA) to their offspring and fathers don't. Lets assume that father had a mutation of the gene that encodes mtDNA, would then be his offspring at ...
5
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2answers
67 views

Balanced vs Maximized Codon Optimization

I have worked with the optimization of several viral proteins, from different viruses/families, with different results. When Menzella, 2011 was published I tried that method. I found quite the ...
8
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1answer
89 views

How to validate the regulatory interactions inferred from gene expression data?

My algorithm learns regulatory interaction between genes using Bayesian Network approach from gene expression data. After the algorithm has converged to a network of interacting genes, how to validate ...
0
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1answer
24 views

If gene differs between chromosome pair does individual get a mixture of protein shapes?

Do diploids such as humans end up with a mixture of two different shaped proteins where the appropriate gene is expressed differently in the two halves of a chromosome pair or is there some governing ...
0
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1answer
49 views

Why we do not use RNAi to control ebola?

As you know using RNAi we are able to prevent gene expression. so why we do not use it to stop viral genes expression?
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45 views

Word denoting genetic state

Is there a single word, or brief phrase, that denotes the state of the total genetic machinery (genome + transcriptome + proteome + ...) of a cell or organ or organism at a particular point in time?
4
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42 views

Mechanisms of genotype*sex interactions [on hold]

I'm looking for suggestions of the mechanistic level at which genotype*sex interactions can occur. These give different phenotypes from the same genotype dependent on the sex they are expressed in. ...
3
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1answer
44 views

What does it mean for the signals for transcription and translation to be “conserved”?

I was reading this article: "Overview of vector design for mammalian gene expression." for an explanation of why mammalian cell lines are used for expressing cloned genes, and one of the reasons ...
2
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45 views

Imperfect dosage compensation

Dosage compensation is used to make up for different copy numbers of the major sex chromosomes in males and females (One X or Z chromosome in one and two in the other). Two main mechanisms of dosage ...
1
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1answer
60 views

Gene Therapy for Cystic Fibrosis

I have another question regarding cystic fibrosis. I understand that gene therapy is currently being talked about in the cure for cystic fibrosis. I know that Eric Alton at imperial college London is ...
4
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1answer
77 views

Redundancy of the genetic code

One particular codon codes only for one amino acid, but an amino acid can be coded for by several different codons. Now according to the genetic code, the codon UUU ...
0
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1answer
33 views

Cell targets of Glybera

So we know that there is a first gene therapy drug in the market out there called Alipogene tiparvovec to address lipoprotein lipase deficiency (LPLD) at a genetic level. Does this genetic drug ...
2
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1answer
119 views

Why do our epiphyseal plates close up in our late teens or early twenties?

What causes our epiphyseal plates close up in our late teens or early twenties? I realize that one's genetics plays the main role in this. I assume there is a gene that controls the epiphyseal plates ...
1
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1answer
105 views

Are there anatomical differences between male and female mammal brains before action of hormones?

is there any evidences of these differences during development stages prior to hormone driven sexual differentiation? mice studies ?
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11 views

How to automate this custom gene expression microarray chip?

I have 16 gene sequences that I am interested in their detection in clinical samples. I already measured their RNA levels by using RT-qPCR technique and their benefit has already been proven to help ...
1
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1answer
31 views

How to identify the genes that distal enhancers pair?

I am writing a project proposal and I have to talk about this problem: how to identify the genes that distal enhancers pair? I am really new to this topic and I don't know what it is all about. I ...
2
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1answer
199 views

Using RNA-seq to compare gene expression across patients instead of between Control and Experimental conditions

I am working with RNA-seq data from the Cancer Genome Atlas TCGA and I have been reading about how people have compared gene expression levels measured by RNA-seq. Many of the papers I have read talk ...
2
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1answer
184 views

Why does the pET- expression vector contain a LacI gene additionally to the one in the genome?

The pET plasmid is used for protein expression with T7 promotor in expression strains, such as E.coli BL21(DE3) It contains a lacI gene which codes for the lac repressor protein, a protein of ...
2
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0answers
67 views

How to track and describe the evolution of a gene?

So I have a project student (undergraduate) who has been assigned a project to study the evolution of a gene (and possibly related genes) through species. I am not an evolutionary biologist, and hence ...
2
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2answers
40 views

regarding genetic disorders related to protein production

I am not completely familiar with biology, but i had a genetics course in college along with practicals. Forgive me if there is something wrong with my question. Is there a genetic disease which ...
0
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1answer
103 views

what is the biggest known functional distance between an enhancer and its target gene (TSS) in cis?

since the title seems self explanatory; It would be nice if anybody could provide a reference. I'm looking for a paper that I belive stated around 1.5 Mb but anything above will be cordialy welcomed. ...
2
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2answers
43 views

Valid comparison of gene expression between several genes in several cell lines

We have gene expression data (Affimetrix mRNA gene expression results) for several cell lines, over a set of genes. Our goal would be to be able to compare relative gene expression for genes over the ...
1
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2answers
105 views

Gene perturbation, what is it used for, explain to computer scientists? [closed]

I am trying to build a gene regulation network, and I need some basic knowledge of it. So, in gene research, we perturb genes. Such as knock down them? Can people tell 2 or 3 experiment methods to ...
2
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1answer
19 views

Question regarding 2 constructs of tobacco plant

Six independent transformation experiments of tobacco leaf explants were carried out using two different constructs - (1) construct I containing only a Hygromycin-resistance gene $(HYG^R)$ as a ...