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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155 views

Can the environment affect genes and adaptation in offspring?

I recently read several articles that believe that environment can affect gene expression and this change will transfer down to the children. Some theorists believe that random mutations are more rare ...
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Can proteins structure change depending of alimentation of an organism? [closed]

In my understanding protein are built using information caring by RNA. So a given protein should always have the same structure in a given organism has the DNA of this organism does not change. I'm ...
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Why don't cells double gene expression after S-Phase?

In the cell cycle (G1-S-G2-M), all of the DNA is replicated during the S or Synthesis stage. The cell may then spend some considerable time in the G2 phase before splitting in the M phase. Since there ...
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Can gene-gene interactions result in gene expression?

I am building a project on Inferring Gene Regulatory Networks using ARACNE and PCA-CMI algorithms, and the input to these algorithms is taken from the DREAM3 challenge. The format of the input data ...
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Low cost cell free expression system

I am a graduate student looking to incorporate some protein engineering into my training. I have been reading a lot about E coli lysate based systems, but they still require 3rd party additives like ...
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Mathematical representation of "gene signatures"

According to Wikipedia's definition, "a gene signature is a group of genes in a cell whose combined expression pattern is uniquely characteristic of a biological phenotype or medical condition." ...
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Finding targets of transcription factors

I'm trying to find an easy way to get a list of putative targets of a particular transcription factor (for example, STAT1). I'm interested in targets determined using both experimental and ...
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120 views

When does genetic randomization happen?

When two parents (regardless of species) reproduce in sexual reproduction each offspring is generally a random combination of genetic traits from each parent. Their developed traits then depend on the ...
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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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178 views

Pseudoautosomal regions of the X chromosome showing heterozgyosity

I've always had questions for myself about sex differentiation, mostly on account of an unusual history & puberty. I won't go into details, but needless to say it was unique. My question is... I ...
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3k views

What is the difference between gene expression and protein synthesis? [closed]

I have no idea what I'm supposed to do. Can someone please help me? What is the difference between gene expression and protein synthesis?
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Is it possible to artificially select for flight in pigs?

After reading this rant by Fodor, as a layperson, I was idly wondering whether it would be possible to artifically select for flight in pigs. Of course by that time the porcine lineage will probably ...
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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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Overexpression by integration of an additional copy vs promoter exchange

In Becker et al (2011), the authors increase the expression of several genes through different methods. For some genes (e.g., lysA, ddh), they achieve overexpression by integrating an additional copy ...
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Are there differences between the activation proteins of Eukaryotes and those of Prokaryotes

I'm in BIO 203 (for reference to my skill level), and I noticed the textbook makes a whole section out of transcriptional activator proteins, their function and applications in eukaryotes, but in ...
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What determines the differences between differentiated cells?

Given two multi-cellular species with obviously different phenotypes. The reason for the different phenotypes reflects their different DNA. However two types of cells in an adult organism may have ...
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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 ...
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which exact mechanism triggers the first cell differentiation after n divisions?

I would like to understand which mechanism triggers the first cell differentiation after n divisions. I read previous articles on SE and Wikipedia articles on cellular differentiation and ...
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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 ...
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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
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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
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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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
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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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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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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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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
193 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
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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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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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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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2answers
857 views

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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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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1answer
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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
310 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
417 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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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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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 (...
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1answer
992 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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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
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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
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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
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
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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1answer
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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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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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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 ...
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547 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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Could miniaturization be used to protect endangered large species? [closed]

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 ...

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