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17

The first modern humans evolved about 200.000 years ago in Africa. When they lost their body hair (or at least most of it), they needed some other protection of their skin from the sun - otherwise they are prone to develop melanoma. Melanin is such a protection, and the rate of melanoma is much lower in dark skinned people. There is also a nice correlation ...


14

This language is called the genetic code. But before talking about this specific code, it is important to talk about how the code is read. Please note that the below answer is a simplification of the reality. Mechanism by which the code is read To make things easier (reality is a little more complicated), DNA is "formatted" into RNA which is then "...


13

Different genes will serve different purposes. For example, if you want to perform colocalization studies, then fluorescent genes like eGFP and DS-Red (or any variation of those, namely Emerald, mCherry, etc) will be quite useful, since you can use different filters on your microscope for the various fluorophores. For morphological assessments, perhaps a ...


12

According to wikipedia, "comparisons between known skin pigmentation genes in chimpanzees and modern Africans show that dark skin evolved along with the loss of body hair about 1.2 million years ago and is the ancestral state of all humans." This is several million years after after the time estimated for the last common human-chimpanzee ancestor, but at ...


11

This is an excellent question! To my knowledge, there hasn't been a definite answer yet. Recently, I did tons of research on which factors influence protein expression and you should definitely check out the following questions which I asked: What is the criticality of the ribosome binding site relative to the start codon in prokaryotic translation? What ...


11

...would then be his offspring at risk? Why? No. Generally speaking, fathers do not pass on their mtDNA (Mitochondrial DNA). Why? Because the mitochondria present in oocytes (egg cell) is the mother's, as every oocyte directly inherits the mother's mitochondria when they are made in the reproductive organs. The mitochondria that the sperm from the father ...


10

What a timely question. Does DNA contain information beyond protein synthesis? Yes. In fact, protein-coding genes only constitute a tiny part – less than 2% – of the whole DNA. There are of course many other genes which aren’t protein coding: there are genes for ribosomal RNA and we find more and more genes which code for small RNAs, such as tRNA. But ...


10

For a free resource, try GenMAPP. Commercial products like Ingenuity Pathway Analysis do the same thing with prettier graphics and a curated approach to network-building, but access can be expensive if you're not affiliated with an institution that will foot the bill.


10

You can validate the interactions by knockding down (KD) or overexpressing (OE) a gene and checking the change in expression levels of the downstream nodes. You can do this in a high throughput fashion using microarray or RNAseq. For protein you can do an LC-MS. However this method cannot help you in: Differentiating direct vs indirect interactions Finding ...


9

Actually, the start codon, no matter whether it is AUG or GUG/UGG, always encodes for Met. So the translation is initiated by tRNAfMet (prokaryotic translation). The 30s ribosome subunit binds to the Shine-Dalgarno sequence and then it scans the dowstream mRNA sequence for AUG and the tRNA loaded with Met, which has the CAU anticodon form the most stable ...


9

Okay, I'll take this out of the comments and put in an answer for all of us to work on. To directly answer your question: "Is there an estimate for the percentage of these genes whose primary function is related to regulation of gene expression?" It depends on how you define "gene expression." And what cellular processes you want to include in ...


9

Yes, these sequences exist and they are called "silencers" (surprising, right?). There are different mechanisms by which this silencing of genes can happen. In the "classical" way the silencer is bound by a transcription factor which either passively suppress the gene by hindering the binding of specific transcription factors or by actively preventing the ...


8

I can think of at least 3 reasons in addition to the one you gave: 1: As mentioned in the comments, RNA splicing takes place on most messenger RNA encoding proteins in eukaryotes. Sections of the mRNA may be spliced out, therefore multiple mRNAs with different codon sequence can encode the same gene. 2: Translation is a stateful process, since it depends ...


7

If you can't afford ingenuity, KEGG has branched out into regulatory networks as well. Here's the link to their version of the pathway. http://www.genome.jp/kegg/pathway/hsa/hsa04115.html Its free to use as a reference and for academic research.


7

Although each cell of your body essentially contains the same DNA and the same genes, cells in different tissues express (turn on) different genes under different conditions. Measuring differential gene expression involves looking at the amount of expression for a gene (or set of genes) in two contrasting scenarios. The contrast could be across different ...


7

Yes, look at FANTOM and their work. There are about 2000 transcription factors and co-factors in the human genome. These are proteins, of course. If you add a couple (or few?) thousand microRNAs and a few dozen anti-sense transcripts, although small in size, you inch that percentage upwards. With some 70% of the human genome transcribed, by some estimates, ...


7

The fastest I know of is the heat shock locus in Drosophila. The transcription factor (HSF) accumulates within about 30 seconds, and RNA Polymerase can be seen to start accumulating within 3 minutes. Katie L. Zobeck, Martin S. Buckley, Warren R. Zipfel, John T. Lis. 2010. Recruitment Timing and Dynamics of Transcription Factors at the Hsp70 Loci in Living ...


7

I understand this in the following way: For each probe you have two sets of measurements, one for ER+ and one for ER-. What you do is a T-test (to my understanding is that the "parametric" just emphasizes that T-test is a parametric test) on these two sets, testing if their mean is significantly different (they refer to this as "separated"). You repeat this ...


7

It is a Benjamini-Hochberg q-value, similar to a p-value corrected for multiple hypothesis testing using the false discovery rate.


7

The technique described here is called microarray. Your question has given me an opportunity to put forth one of my opinions about certain problems of gene expression studies. Gene expression is a measure of the activity of any gene. If the gene performs its activity in the form of a protein, then its expression should be a measure of the protein. If a gene ...


7

If you transfect cells with plasmid then these plasmids need to go into the nucleus (otherwise they wouldn't be transcribed). Getting the plasmid either happens during cell division (when the nucleus is not present) or by adding a signal sequence to the plasmid which induces the import into the nucleus through nuclear pores. The SV40 sequence is an example ...


7

Introductory textbooks will not get into the details of the lac operon. Basically, the operon is expressed constitutively at a low level that means that Beta Galactosidase and Lactose Permease are expressed at low levels by the bacterium. This is because it takes a little bit of time to build up the concentration of LacI in the cell before it can start to ...


6

In bacteria, this is often true. This is because more than one gene is often transcribed onto a single RNA. This grouping of genes is called an operon. It is usually true that these have a related function because they are being translated to protein in very much the same proportion - a convenient way to regulate the function as a whole. Once you get ...


6

Aldridge et al. (2011) show a correlation between facial phenotypes and autism spectrum disorders (ASD) in a sample of 8-12 year old boys. They studied two groups of boys, 65 that had been diagnosed with ASD and 41 who had not. They collected 3D images of the faces and looked for similar patterns among the two groups. They found a significant association ...


6

That really depends on your system. At least for yeast the difference influences the strength of the activation ("Analysis of Transcriptional Activation at a Distance in Saccharomyces cerevisiae"). For bacteria such long distance regulations have recently been identified. Before that it was thought that this does happen only in eukaryotes. See the paper: "...


6

There are some databases in which you can search for E.coli gene expression data: GenExpDB: E. coli Gene Expression Database Many Microbe Microarrays Database (M3D): A resource of microbial gene expression data Stanford MicroArray Database (use the search tool to find relevant organisms) Colombos (COLlection Of Microarrays for Bacterial OrganismS) ...


6

People often imprecisely say that type of regulation takes place on the order of many minutes to hours, and that may be as precise as you can get given the variable kinetics of any given pathway. Also, all genes in eukaryotes require general transcription factors, but basically all of them also require activators to act first to recruit the GTFs and ...


5

Unfortunately, protein and gene name mapping is one of the most annoying problems in modern computational biology. There is no surefire way of doing this. Especially from hopeless gene names as the one in the paper you cite. Here are a few services you can try though: General, text search, useful if you have a gene description (as in the case described in ...


5

It's a probe to detect external 'Alien' RNA standard, a synthetic mRNA commercialized by Stratagene/Agilent. The Alien RNA transcript is a ~500-nt, polyadenylated RNA molecule that is synthesized by in vitro transcription. The Alien RNA transcript is nonhomologous to all known nucleic acid sequences currently in public databases, as determined ...


5

I'm not personally familiar with Illumina arrays, but I can give some notes here. This link is a paper which describes the array quality controls specifically. This presentation describes the calculation of the intensities in bioconductor. The answer is yes: you will find negative numbers sometimes. They should be rare. The Intensities numbers from from ...



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