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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8answers
5k views

How does a gene “know” what to change to?

Excuse my ignorance but I've always been curious about this... For example, a frog is red, but it starts living in a green forest. Over time the frog becomes green to camouflage. But a gene can't see ...
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1answer
61 views

How can cancer preventing genes from animals be transferred to humans? [closed]

I recently read this non-peer reviewed article that states that the prevalence of cancer in crocodiles or elephants is really low, much lower than humans. It is said below A team of researchers in ...
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1answer
193 views

Can DNA methylation induce breast cancer? [closed]

What is the role of DNA methylation in breast cancer? DNA methylation is a process by which methyl groups are added to the DNA molecule. In the September 2015 paper The Role of Methylation in Breast ...
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1answer
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Optimization of Signal Peptides

We are looking at modifying the signal peptide of a receptor in a common immortalized human cell line. The cell line already expresses an unusually high amount of the protein, but much of it is not ...
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1answer
223 views

Methods to evaluate gene expression [closed]

I was wondering what method should i use if i want to evaluate if a gene is being expressed or not. The first method that came to my mind was Western blot , but i don't know if i could use others. I ...
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0answers
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What is the difference between “dysregulation” and “deregulation” of miRNA?

I've started to study the role of miRNA in cancer. Wikipedia says: Just as miRNA is involved in the normal functioning of eukaryotic cells, so has dysregulation of miRNA been associated with ...
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0answers
55 views

Can elementary alternative splicing events be combined in more complex events?

I'm a computer scientist who is trying to understand alternative splicing. As the title says, I'm here to ask you if, from a biological point of view, elementary/basic alternative splicing events (...
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1answer
337 views

How do I find samples/patients in TCGA (the cancer genome atlas) that had radiation therapy?

I want to correlate the expression of a gene (for sample the KRAS gene) with survival and if the patient received radiation therapy using any suitable TCGA (the cancer genome atlas) dataset. However, ...
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1answer
192 views

Cell type that expresses 90% of the genome

Cells that are differentiated express the genes that are necessary for their own usage. I've heard that some cell type expresses about 90% of 30,000 proteins that are encoded in the genome. Can ...
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1answer
53 views

What is allele-specific gene expression?

I read somewhere that the two different alleles which we (and other species) inherit from our parents are not expressed equally in our cells. Which genes show allele-specific expression? How and why?
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1answer
213 views

How exactly are genes swapped during the process of recombination?

I am studying recombination in Meiosis and the idea of crossing over doesn't make sense. My understanding is that 46 chromosomes in our germ-cell (23 from mom + 23 from dad) line up next to each other ...
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why should someone study mRNAs instead of miRNAs as a biomarker

why should someone study mRNAs instead of miRNAs as a biomarker from liquid cell-free biopsy like from exosomes? Is it wrong to do it? Does it offer you something different? Thank you in advance
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2answers
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What are the pros & cons of site-directed mutagenesis? What are the alternatives?

For a lab course we have been assigned to "remove a stop codon, using mutagenesis, that is in the middle of a gene in order for the full gene to be expressed. This will then fluoresce." To do this we ...
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1answer
106 views

Copy number regulation & CNV

I have some genes which showed copy number loss between two groups. Now I want to see the copy number regulation of those genes. I really don't know about this concept. Can anyone please tell me ...
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1answer
416 views

What is the difference between differentially expressed genes and deregulated genes?

Can anyone explain clearly what is the difference between differentially expressed genes and deregulated genes?
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1answer
6k views

Can Blood Types Change?

I recently heard a radio show where two callers claimed that their blood types had changed. One caller claimed that he was born O-, but recent tests said he was A+. Another caller claimed to change ...
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0answers
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How are oncogenes targeted for therapy?

How would oncogenes be targeted for therapy and are there any examples of existing therapies for such cancers if the gene was upregulated (i) as a result of copy number variation and (ii) due to ...
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0answers
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Are RNA transcripts always synthesised from the same DNA strand? [duplicate]

The DNA is read 3'->5' (and RNA synthesized 5'->3'). But due to the DNA strands having to be complementary, it seems to me that the origin can only appear on the correct side of the ORF on one of the ...
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1answer
66 views

Validation of houskeeping genes in a mixture of cDNAs of two species

I have a parasite sample (mixed with host blood) and I need to check gene expressions of parasite using relative quantification (RT_qPCR). For this, I need a good housekeeping gene. I chose 10 genes (...
5
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1answer
239 views

Left-handedness and Right-handedness - Are they genetic?

I have a biology book that states that whether a person will be left-handed or right-handed is determined by the genetic constitutional makeup. Is this true? As far as I knew, these traits depend on ...
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1answer
73 views

In microarray normalization, why is the normalization factor this?

I am working on analysis of a huge number of microarray files. I was trying to understand the need for normalization in microarray data and was going through this paper by John Quackenbush(2002). In ...
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1answer
138 views

How do I read an RNA expression pattern?

When reading about diseases one can find links to proteins and their associated genes, an example of which is here. I'm wondering how to decode/read the following graph as a non-specialist in this ...
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0answers
585 views

How to preprocess htseq counts for gene expression (TCGA)

I want to prepare a matrix of gene expression to analyse TCGA LAML data. The required data is available at TCGA LAML - Gene expression quantification. The following is an example of the kind of data ...
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1answer
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Query for gene upregulation in cBioPortal

there! Could anyone help me with some biostatistical problems using cBioPortal. We are looking for cell lines with upregulation of certain genes on cBioPortal. My supervisor is teaching me to use ...
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1answer
306 views

Multiple transcripts matching same gene in de novo assembled RNA-seq data, but FPKM values vary?

I have a data set of de novo assembled RNA-seq datasets across different sample types. When BLASTing, many of the matches of the individual transcripts match to the same gene on the reference genome. ...
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1answer
493 views

Sex linked genes?

I am learning about genetics and sex-linked traits. All of the X-linked traits we have considered (eye colour in Drosophila, Duchene Muscular Dystrophy to name a couple)follow the rule that, a female ...
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1answer
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Why are most mutations recessive? [duplicate]

Why are most of deleterious mutations recessive in nature? I understood that if it's recessive then one reason may be that the mutant gene doesn't code for a functional protein and so there is no ...
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0answers
538 views

What's the best wat to combine biological replicates in qPCR gene expression analysis? (2^(-∆∆Ct) method; one-way anova, turkey's test)

I am measuring the levels of gene x after transfection of cells with a plasmid and I want to compare them to the levels in mock-transfected cells. I did three different transfection experiments, in ...
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2answers
66 views

Division of proteins

This textbook states Proteins determined by a single gene may divide to form different proteins with various physiological actions. First how do proteins divide? Second if it's just fragmentation ...
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0answers
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Why is the total length of Introns greater than the total length of exons?

I have just been reading that typically the total length of the Exons of a split gene is very much smaller than to total number of its Introns. Could anyone please explain why this is the case if its ...
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2answers
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Do all polygenic traits involve epistasis?

Consider the following statement All polygenic traits involve epistasis. I think its true because polygenic traits involve several genes interacting together to result in a certain phenotype and ...
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1answer
90 views

Do any RNAs directly inhibit transcription

In eukaryotes, microRNAs and small interfering RNAs, as part of protein complexes, can attack specific messenger RNAs with complementary sequences, thereby inhibiting translation. However, RNA can ...
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0answers
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Gene products of recessive/mutated alleles

I probably would not cite a specific example, but some recessive allele work by encoding for the non-functional form of an enzyme. While the dominant allele encodes for sufficient levels of functional ...
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1answer
51 views

Proteome patterns between treated and control cells

We did 4 experiments to compare the amount of certain proteins in treated and untreated cells. Each experiment was done separately. Because of the high cost of experiment, we were able to perform only ...
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1answer
997 views

Why is aneuploidy usually lethal?

So, I was reading about aneuploidy and how a zygote with one extra or less chromosome usually would not survive to full term. I suppose this happens because aneuploidy leads to some kind of protein ...
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1answer
975 views

Asymmetric volcano plot

Nearly all volcano plot I've seen tend to be roughly symmetric around the y-axis, with a fairly equal number of up- and down-regulated genes. What are the potential reasons for a volcano plot that is ...
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1answer
138 views

How to determine continental ancestry group (race) with transcriptome data obtained with RNA microarray?

Say I have a whole genome expression data (transcriptome) for some sampled human tissue. Is this data sufficient to find out the continental ancestry group of a donor?
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1answer
1k views

Rescue cell lines function

I'm reading in a paper in which the authors have made three cell lines to study the function of a gene of interest (Mbd3): The one is knocked out for the gene of interest [Mbd3 -/-], the other is ...
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4answers
2k views

How can both strands of DNA code for proteins with similar functions?

It's not clear from the question but for example: AAAAAAA TTTTTTT The top strand would create a different protein than the bottom, and with the huge amount of nucleotide in a gene, I think it's ...
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2answers
265 views

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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1answer
30 views

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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2answers
3k views

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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0answers
52 views

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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2answers
146 views

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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1answer
976 views

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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3answers
197 views

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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2answers
74 views

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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1answer
48 views

What is the gene corresponding to MIR382 RNA molecule? [closed]

Where can I find information such as this?
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2answers
202 views

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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1answer
481 views

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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