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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Can a gene-expression or epigenetic 'user-history' be found in the body?
(EDITED - a lot of what I am saying is implicit and simplified. I'm not looking to recreate the numerous textbooks and scientific papers on how DNA works).
As far as I can understand it, an ...
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What do the intervals between groups of arrays in microarray gene expression data images mean?
This can be a dummy question, but I am not familiar with microarray experiments at all. In this image, what does each of 16 big squares mean, and what are the black intervals between them are? I know ...
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Gene vs. Protein Expression Assays
Are the terms gene expression assays and protein expression assays used interchangeably in molecular biology? Or is it expected of you to differentiate between the two terms.
For example, if I ...
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RNA-Seq library normalization and experimental setup
I'm working on an RNA-Seq project and I am trying to figure out library normalization. I'm aware of using the geometric means (e.g. cuffdiff) of the fpkm for the normalization.
However, I was ...
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Do housekeeping genes vary between tissues
I am working on an RNA-Seq project, and I am aware that some researchers use housekeeping genes as a method of normalization. My project has several different tissues, and I was wondering if ...
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Collecting virgin fruit flies [closed]
Suppose that you place P generation wild type males and mutant virgin females in a vial and allow them to mate. You leave this vial undisturbed in the incubator for 12 days. Could you collect F1 flies ...
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Gene expression for mathematicians: where to start?
I am a PhD student in mathematics, and I will be involved on a project that aims to cluster (i.e. automatically group) people according to their gene expressions.
Well, the project looks very nice, ...
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Is it possible to identify a particular gene sequence from next gen sequencing techniques (especially RNA-seq )?
I have to check the expression of a gene in a fish whose sequence is not known in the fish in question. Sequence is known in an another fish (zebrafish) but the gene has 10 isoforms. The genome of ...
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What is the gene corresponding to MIR382 RNA molecule? [closed]
Where can I find information such as this?
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How can there be a one-to-one correspondence between RNA and genes?
From what I know, multiple strands of DNA make up a gene, so how can for each gene there can only be one RNA corresponding to it and vice versa? Is my knowledge incorrect?
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Can the brain influence gene expression?
A neuroscientist told me (according to my hazy memory) that the brain/nervous system can have an epigenetic function, ie directly regulate gene expression.
I'm not a biologist, but she talked me ...
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house keeping gene variation under treatment
I am injecting BCG in mice ears to measure the local inflamation response in the infection side, one ear in the same mouse is kept as control by injecting PBS, in the other one, BCG is injected. When ...
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Validation by PCR of a lowly expressed gene in microarray
I am interested in validating the precence of a gene (FETUB) whose expression is in the lower quartile of the microarray (see figure in link).
https://drive.google.com/open?id=...
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How many co-expressed genes would be expected in a tissue?
I am working with gene expression microarrays of tumor tissues and I want to use a program to find the clusters of co-expressed genes in order to know if some particular genes are co-expressed with ...
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What is a cognate enhancer sequence?
What is a cognate enhancer sequence?
While reading a paper (1) presented at a journal class in graduate school, I encountered this sentence:
HIF-1 binds to its cognate enhancer sequence, the ...
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How to specify a promoter in de novo gene synthesis service?
I am trying to use a de novo gene synthesis service (Genscript) and one part confuses me:
Where do I pick the choice of promoter? Or is the promoter choice automatic based on my plasmid choice?
e.g....
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How to put a gene under the control of a regulable promoter?
Suppose I have a hetrologous (eukaryotic, plant) gene sequence that I want to express in E Coli under the control of a regulable promoter (say the lac promoter induced by IPTG) how exactly does one ...
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Are the subordinate genes of a repressed operon really "turned off"?
Operons are often described using all or nothing language. A repressor binding to the operator is usually presented as "turning off" the regulated genes. Case in point, Scitable at Nature.com says:
...
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Current state of Gene Therapy [closed]
I am interested in learning about attempts to treat adult individuals suffering from a genetic disease in which the underlying changes in the DNA of the gene are understood.
(i) Are there approaches ...
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Mutating a protein without mutating the gene?
Is it possible to mutate a region of a protein (says about 300 amino acids long) without actually mutating the gene?
One possible way that I can think of is to use RNAi and specifically block that ...
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Multiple start and stop codons in mRNA and pre-mRNA [duplicate]
I have a main question that will lead to further questions depending upon the answer.
In the process of transcription, will there be multiple start and stop codons in one sequence of pre-mRNA? If ...
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What is the most appropriate way to normalize gene expression data?
This question comes because reading a paper about normalization of gene-expression data, is not clear if the method for normalize the data is just for RNA-Seq data or could be applied also for ...
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What is the role of TATA box in transcriptional regulation? [closed]
I know what is the TATA box, but I wish to know whether it has specific roles in transcriptional regulation.
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Why does pETDuet-1 only have one T7 terminator but two T7 promoters?
Why does pETDuet-1 only have one T7 terminator but two T7 promoters (vector map below)? Is there any advantage of having only one terminator? There are going to be two mRNAs transcribed from this ...
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How big advantage had a trait have to bring to evolve in the human evolution? [closed]
Yes, I've heard that we have evolved from the common ancestor with primates as intesively, as the chimpanzees. Sometimes I read about some enormously complex traits, evolutionary psychologists think ...
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How do biologists quantify "gene expression" in experiments?
I've read papers which contain statements such as "control of gene expression is critical in biological processes".
How exactly does one quantify "gene expression"? Isn't gene expression an umbrella ...
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Genes that exist in old Affymetrix platform but not in the newer one
I am using two gene expression datasets from an Affy U95Av2 platform and an Affy U133 Plus 2.0 platform. When I map the Affy probe names to HUGO gene names, there are thousands of genes which exist in ...
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What further research can the result of gene variation detection be used for [closed]
We do a research on a particular cancer (for e.g. breast cancer). Now, we have a result for the gene variation detection (VCF file). What next steps do we need to do? We don't have a clear picture ...
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Is the increased/decreased enzyme activity (tyrosinase) caused by an environmental factor (UV radiation) considered to be gene expression?
My AP Bio assignment asks that I research the effects of UV radiation on melanin production, but the directions and questions suggest that UV radiation influences gene expression. From what I could ...
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How much time do the different mechanisms of gene regulation need to take effect?
I am thinking of the major regulatory mechanisms, like general transcription factors, activators, repressors, and RNA interference.
If non-active regulator genes using each of the different ...
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What's the difference between CREs and DHSs?
I would like to know what's the difference between cis-regulating elements and DNase I–hypersensitive sites, in order to produce a meaningful segregation of non coding elements affecting gene ...
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Does a zygote express all genes?
If a zygote has all the cytoplasmic determinants and all the specific transcription factors, does that mean that all genes in the genome are expressed?
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Is the zygote the only totipotent cell?
I’ve been told that the unfertilized egg contains cytoplasmic determinants (e.g. proteins, transcription factors, mRNAs) that are divided unevenly during the early stages of cell division in an embryo....
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Using PGAL10 promoter to overexpress specific yeast genes: How to?
I was reading a poster about expression boosting for Artemesinin production in yeast and it had this line:
PGAL1
and PGAL10 have been used for the
overexpression of all genes from the ...
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Are all genes transcribed in differentiated cells?
My textbook tells me that it’s specific transcription factors that allow for a different set of genes to be expressed in different cells (differential gene expression). My book gives the example of ...
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Pooling for qPCR
I am comparing miRNA expression levels in 3 different groups but I am low on money and time. I have to get some preliminary results to get the actual research going so I decided to pool my samples and ...
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From DNA to final traits of microorganisms? [closed]
From the answer of this topic, could someone indicate me a book or article about how DNA set the phenotype of microorganisms? For example, showing how DNA changes the shape of such a cell or how DNA ...
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How to Download the broadpeak files from the encode chip-seq experiment matrix? [closed]
I have tried the SqlDatabase of Encode opened it trough R ,i have tried other packages in R, i have tried the ENCODExplorer package but none of them seems to do what i want. I have an app that asks ...
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differentially expressed genes of the treated with estradiol samples
I did differential analysis on samples treated (G1E-ER4) with estradiol (differentiation induced by estradiol) and control (G1E).
The genes that I gor as differentially expressed in G1E-ER4 showed ...
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cell specialisation and their location
When we create new cells, how come they are of the 'right' type at the 'right' place?
For example, when I make a new cell on my lips, it's obviously not the same as a new one in my kidneys.
Is the ...
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What determines whether the maternal or paternal allele is expressed?
I am taking cell biology and have this question:
During the process of gene expression, it is possible to express either the maternal allele or the paternal allele.
When and how is the determination ...
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Why don't housekeeping genes have TATA Box regions in their promoter sequences?
Housekeeping genes are genes that are continuously transcribed. Like all other genes they have promoter sequences, but they don't have TATA box sequences that are used to specify from where ...
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Transcription of Genes: Are Specific Transcription Factors + Enhancers Necessary?
I learned about transcription in my AP Biology class and we discussed how transcription occurs, but I was wondering whether transcription always requires the enhancers, activators (specific ...
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What is the instructional language of DNA?
DNA carries most of the genetic instructions used in the development, functioning and reproduction of all known living organisms and many viruses (Wikipedia).
Is it already know how ATCG's sequences ...
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Can genes be expressed sequentially?
As I understand it, any gene on an exposed/unpacked region of a chromosome is continuously being expressed. Regulatory genes may increase or decrease the amount of protein synthesised due to its ...
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Lac operon: How can lactose enter the cell in the absence of lactose permease?
My textbook states that
lactose permease...transports lactose into the cell
and
When lactose is added to the growth medium, the lactose molecules bind to the other site on the repressor protein
...
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Animal gene in plants
Usually only microbes, specifically bacteria are used to express genes of other species for various functions. But, it is possible to try and express an animal gene into a plant. Bacteria like ...
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Plasmid Expression Vector [closed]
If I am going to transform a plasmid into a bacterium, which will then be fed to a C. elegans, the expression vector needs to be bacterial correct? The other option is to have a worm expression vector,...
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Organ secretions
If an animal secrets an enzyme from an organ that is entirely dedicated for the same secretion, can one or cannot one just use the gene coding for that protein to obtain the protein in vitro. How much ...
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Question about cutting gene in Plasmid
I am designing a researching proposal for the class. Because it uses microinjection to up-regulate the gene in C. elegans, the plasmid pCFJ104 - Pmyo-3::mCherry::unc-54 sequences has been chosen. But ...
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