The process by which information encoded in a gene is converted into a protein or functional RNA, resulting in or contributing to a phenotype.
2
votes
1answer
54 views
Optogenetics - How do microbial opsins work?
I'm just introduced to the optogenetics method and am having some trouble grasping the genetics (of the optogenteics) part of things.
So we have Retinal and Opsin that form Rhodopsin molecule that ...
4
votes
1answer
27 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
votes
2answers
97 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 ...
2
votes
1answer
45 views
What is the mechanism of regulation of PER /CRY genes?
I've read multiple descriptions of biological/circadian clocks and they all mention PER, CRY and CLOCK genes. While I kinda get how they are connected, what interests me is how these actually regulate ...
1
vote
1answer
62 views
Manipulation of gene expression using VP16 fusion and engrailed fusion to a transcription factor?
Today, a presenter briefly mentioned that gene expression in sea urchins during development might be manipulated using VP16 and engrailed fusions.
On a slide, it said that expression might be ...
2
votes
0answers
37 views
Where to put the gene after eukaryotic promoter for best expression levels?
As far as I know there is an optimum distance between a promoter and the gene for the best expression levels. What is that distance for common promoters like CMV, SV40? If you have a first hand ...
1
vote
1answer
79 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, ...
6
votes
1answer
70 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 ...
2
votes
1answer
52 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 ...
0
votes
1answer
20 views
Complexity in creating transgenic animals (e.g., mice)
Many papers I have seen describing transgenic rodent models (and presumably applicable to other model organisms) involve the knock-in, or modification to, a single gene, possibly two genes. With ...
4
votes
2answers
69 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 ...
3
votes
1answer
74 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 ...
2
votes
1answer
32 views
Confusion related to the DAVID tool
I am trying to use the DAVID tool to do some gene analysis. I have some probe set intensities for some cancer cell lines. I found this link in the DAVID tool http://david.abcc.ncifcrf.gov/tools.jsp. I ...
1
vote
1answer
31 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 ...
6
votes
3answers
101 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 ...
3
votes
2answers
40 views
What do breeders call the effect when a breed resists modification?
It is impossible to breed a blue rose or a cat with a bulldog shape. This is because breeding is limited by gene variations in the population.
What do breeders call this effect?
UPDATE
I guess ...
7
votes
2answers
93 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. ...
4
votes
2answers
64 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 ...
6
votes
1answer
37 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
votes
1answer
173 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 ...
5
votes
1answer
95 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 ...
1
vote
1answer
65 views
Expression of an ancesteral gene
Why would the expression of an ancestral gene and comparing the product to a modern protein give misleading conclusions about heredity?
Update:
By ancestral gene I mean a gene which was used by an ...
2
votes
1answer
49 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 ...
4
votes
1answer
165 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 ...
7
votes
1answer
83 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 ...
6
votes
2answers
125 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 ...
8
votes
2answers
424 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 ...
6
votes
1answer
72 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? ...
4
votes
1answer
71 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?
5
votes
1answer
59 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 ...
9
votes
1answer
125 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 ...
13
votes
2answers
194 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 ...
7
votes
3answers
285 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 ...
12
votes
2answers
268 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 ...
9
votes
1answer
164 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, ...
8
votes
1answer
80 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 ...
16
votes
2answers
154 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 ...
