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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219 views

What is the reason behind choosing the reporter gene when experimenting on your gene of interest?

I noticed within example experiments in class that different reporter genes are chosen to be inserted near your gene of interest to prove whether or not the gene is being expressed. For example, you ...
13
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2answers
242 views

Percentage of genome devoted to regulating gene expression

Recently I've been studying the p53 tumor suppressor gene as a model for regulation of gene expression. It's amazing how many different post-translational modifications are known to regulate p53 ...
12
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2answers
446 views

Which is more important for protein expression mRNA structure or codon optimization?

The field seems extremely divided on the debate. On one hand, artificial experiments have suggested that synonymous mutations don't correlate with gene expression but rather, the mRNA 5' structure is ...
10
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1answer
239 views

Does the genetic expression of specific physical traits ever correlate to behaviour?

Over at skeptics, there were a couple questions asked as to the correlation of specific physical traits in relation to personality/behaviour. For instance, the simian line as well as red hair. Now, ...
9
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2answers
774 views

Databases for gene regulatory network graphs?

What databases are available for gene regulatory network graphs starting from a given gene? For example, starting from p53 gene, where can I find a gene regulatory network image that can be exported ...
9
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1answer
190 views

How are there alternative initiation codons?

According to wikipedia and the original complete sequence of the K-12 genome, there are multiple non-AUG start codons such as GUG and UUG. How is this possible? I'm particularly curious about the ...
9
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1answer
88 views

Time from stimulus to gene expression

My understanding is that gene expression, in response to some stimulus, generally occurs on the order of minutes. I'm curious about the extremes...the quickest and the slowest cases. What is(are) the ...
8
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1answer
272 views

Does DNA contain information beyond protein synthesis?

It's well known that genetic information is stored in DNA. As far as I know, DNA only has information at the protein level. What about higher levels, such as organelles, cells, tissue, organs? Is ...
7
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2answers
110 views

A mathematician's confusion regarding parametric $t$ tests for gene expression data

I'm a mathematician trying to test some things on gene expression data, and I'm thus skimming over various articles such as Sotiriou et. al. to understand what is typically done with such data sets. ...
7
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3answers
550 views

Determining potential protease sites within a recombinant protein

My expressed proteins are frequently truncated and I'm trying to figure out which bands are which. The first thing to come to mind is using PeptideCutter from ExPASy but there is just a data deluge of ...
7
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1answer
137 views

Is the function of adjacent genes correlated?

Do genes that occupy a similar locus on the genome have correlated function, specifically in human beings? It is my understanding that adjacent genes are inherited together, and so location plays a ...
7
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1answer
45 views

circulating microRNAs are functional?

In plasma and other body fluids, miRNAs can be found. They not only originate from dying cells but also from active secretion and are usually 'packed' into vesicles/lipo-proteic structures (i.e. ...
6
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2answers
265 views

Why do we assume that the first humans were dark-skinned?

According to the article Dark skin and blue eyes: How Europeans once looked: It is widely accepted that Man's oldest common forefather was dark skinned, and that people became more pale as they ...
6
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3answers
512 views

How to map the Gene name to its Gene Symbol?

I am learning in Gene data lately so I apologize for the silly questions in advance. I read a paper for a cancer on human which found some important genes. For example, the paper listed one of genes ...
6
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1answer
256 views

How much does the distance between a transcription factor binding site and a promoter influence transcription?

Assume we have a synthetic construct with a minimal (inducible) promoter that requires activation for significant transcription to occur. Realistically, how important is the distance between an ...
6
votes
1answer
102 views

Bicoid regulation of hunchback

I'm learning about development via the example of Drosophila embryogenesis. I understand that bicoid regulates hunchback, among other genes. My question whether the regulation is direct or indirect? ...
6
votes
1answer
166 views

What is the best way to express two proteins in a mammalian cell?

I have two proteins and I will be preparing a vector with both genes for stable transfection. Each protein will have their own promoter and I will use piggyBac vector to insert a single cassette with ...
6
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2answers
159 views

Effect of single-gene overexpression in the cell's response

Which are the factors that modify the overall gene differential expression by introducing a vector for single-gene overexpression? If you overexpress a gene for a protein involved in signal ...
5
votes
3answers
122 views

What are some examples of genes that code for multiple proteins?

The title pretty much says it all. It is widely taught that a gene in a eukaryotic system could produce more than one protein due to post-transcriptional modification, but I do not believe I have come ...
5
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2answers
132 views

How is gene expression estimated?

I'm reading this fantastic article on estimating body time: Molecular-timetable methods for detection of body time and rhythm disorders from single-time-point genome-wide expression profiles and one ...
5
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2answers
84 views

Average number of gene products in (a) eukaryote(s)

Due to alternative RNA splicing, it isn't uncommon to ultimately find multiple gene products expressed from one gene in eukaryotes. I'm looking for a reference value for the average number of final ...
5
votes
2answers
89 views

How extensive is CD47?

CD47 aka the "don't eat me" signal has recently been claimed to be expressed on all tumor cells. This doesn't seem to corroborate with other cell-biology experiments. On what other cells is CD47 ...
5
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1answer
67 views

How are the various classes of E coli genes determined?

Looking at some more detailed codon usage tables, genes may be further clustered into three gene classes: Metabolic genes, highly expressed genes during exponential growth, and horizontal gene ...
5
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1answer
41 views

Is there are practical lower limit to gene length in E. coli?

Question is rather self-explanatory. Putting aside other post-transcriptional factors like rate of degradation of transcript, what is the smallest gene ever reported to have successfully been ...
5
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1answer
260 views

Where can I find the tissue-specific protein expression levels for hTERT (telomerase subunit)?

I find a number of contradictory sources regarding the tissues in which hTERT - the protein - is expressed. Does anybody know some resource that authoritatively (as authoritative or widely-accepted as ...
5
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0answers
126 views

Cytoplasmic determinants - protostomes and deuterostomes

Cytoplasmic determinants are spread unevenly in the egg, and so when embryo starts forming (cells start dividing), the determinants are also unequally divided between cell. This unequal distribution ...
4
votes
1answer
111 views

What is benjamini

I was doing some gene expression analysis using this tool http://david.abcc.ncifcrf.gov/summary.jsp. However, I have a confusion about what benjamini is. I fed it some gene list and it gave me some ...
4
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1answer
107 views

What exactly is meant by the expression “differentially expressed”?

As far as I've seen, this expression is almost always used in relation to gene expression profiling. Unfortunately, I have no background in this area. Can someone please explain this in layman terms?
4
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1answer
45 views

What is meant by “alien” probe in a microarray?

In my lab we did a microarray to analyze differential gene expression in S. cerevisiae treated with UV irradiation. We are now analyzing the results and one of the up-regulated genes is labeled ...
4
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1answer
56 views

What is the relation between plasmid concentration and mRNA levels?

Suppose a simple synthetic construct, consisting of a constitutive promoter and a single gene: One of the simplest ways to model GFP transcription is to use an ODE: $\frac{d [GFP_{mRNA}]}{dt} = a - ...
4
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2answers
109 views

How does the colinearity of the HOX genes determine the body plan of an organism?

I was recently reading about colinearity in the HOX genes that give an organism its high-level body plan (where the order of the HOX genes on the chromosome follow the head-to-tail order of body ...
4
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1answer
27 views

Is the regulation of lactose operon different between Gram + and Gram -?

I know that in E. coli the lactose operon is shut down by CAP protein when binding cAMP. Is this true also for Gram positive bacteria?
4
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2answers
86 views

Combining gene expression data from two species

I currently have two sets of gene expression data. The first is a dataframe of genes identified by Annotation id CG numbers (for example "CG10005") in one column and a numerical variable of interest ...
4
votes
1answer
52 views

Where can I find histograms and tables of prevalence of mutations in cancer?

At some point in the past I found a cancer portal site which had aggregated data for the relationships between various mutations and their prevalence in cancer types and tumor data. The data was ...
4
votes
1answer
19 views

What are the effect of microtubule or microfilament inhibition on yeast expression profile?

I was wondering whether anyone has looked at what are the expression changes in yeast when the microtubule or the microfilament polymerization is inhibited? Have there been whole-genome studies?
4
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1answer
292 views

T7 promoter leakiness

Can a gene be expressed under the T7 promoter in an E. coli strain (e.g. DH5 alpha), which does not have the T7 polymerase gene encoded in its genome? In other words, is T7 promoter leaky? To be ...
4
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0answers
124 views

Genetic expression in interspecific hybrids

Referring to interspecific hybrids, I have the following two questions:- Quoting from wikipedia:- The offspring of an interspecific cross are very often sterile; thus, hybrid sterility ...
3
votes
2answers
81 views

How can CI repressor both activate and repress $P_{RM}$ promoter found in $\lambda$ phage?

I'm reading a paper where the authors constructed a toggle switch that uses bidirectional $P_R/P_{RM}$ promoter found in the $\lambda$ phage. There are 3 binding sites - $O_R1$, $O_R2$, $O_R3$ - ...
3
votes
1answer
201 views

Negative value on linear gene expression in microarrays

I am starting to use microarrays and maybe this is a dumb question: Using Illumina microarrays, linear gene expression can be negative? Or maybe some artefacts have been introduced? And, in this ...
3
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0answers
60 views

Data analysis of transcriptome sequencing data

I want to learn more about the data analysis and statistics on transcriptome sequencing data. I would like to read some important papers of the field and books and maybe some MOOCS, if they are ...
3
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0answers
56 views

Could miniaturization be used to protect endangered large species?

In some animals (like dogs) size seems like it's controlled mostly by just a few genes (IGF1, and the genes that repress it). I'm curious: (1) Does other miniaturization takes a similar route (for ...
2
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1answer
49 views

Expression of bidirectional promoters

How are bidirectional promoters expressed ? (Won't RNA Pol have to go in 3'-5' direction?) Why are they more commonly found in eukaryotes than prokaryotes?
2
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2answers
172 views

Promoter in the lac operon

Here is the question: Suppose an experimenter becomes proficient with a technique that allows her to move DNA sequences within a prokaryotic genome. If she moves the promoter for the lac operon to ...
2
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1answer
36 views

What is mRNA expression level?

I cannot find clear explanation of what is mRNA expression level, and how to measure it. I would appreciate if someone explained it or gave a reference. Thanks!
2
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1answer
94 views

How can a continuous RNA be transcribed in the lac operon?

The lac operon has 3 genes: lacZ , lacY and lacA. I have seen that the m-RNA transcript of these genes has stop codons in between. So, how can the RNA be made continuously? Won't the RNA Pol detach if ...
2
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1answer
88 views

Confusion related to a term probe-by-background interaction

I was reading a paper related to bioinformatics where it uses the drug response on the cancer cells and the gene expression of the individual cells are studied to find any useful insights. Specially, ...
2
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1answer
159 views

One flybase gene number (FBgn), many Affymetrix Id's

I am trying to convert a set of Affymetrix ID's, like this one 143053_at_3745, to Flybase Gene Numbers (FBgn) like this one FBgn0000015. I have downloaded the Flybase file required to do so (as ...
2
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1answer
124 views

How to determine the direction of regulation of a gene by comparing gene expressions?

I am just learning about the gene expressions and regulation. Several researches focus on finding the genes of altered gene expressions on a microarray to claim that they have a correlation to a ...
2
votes
1answer
60 views

variation in expression accounted for a SNP — what's a usual percent?

I am reading a GWAS paper that found a SNP associated to predisposition to colon cancer and was assessed for gene expression of the nearby gene. They found that the genotype accounted for 55% of the ...
2
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2answers
28 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 ...