Hot answers tagged gene-expression
10
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 ...
10
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 ...
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
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 ...
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
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.
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, ...
6
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 ...
6
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 ...
5
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 ...
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 ...
4
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.
4
LC-MS is certainly quantitative and will give you a definitive answer, but it is costly and requires access to such a machine.
I presume you're analyzing your protein based on western blotting.
The first thing you should always do is verify your DNA sequence is coding for the protein product you want. Once you're sure of this, the western blot will give ...
3
I read through the paper. The author starts by stating that as of the time of writing, two different classes of codon usage profiles were known (or at least putatively so). All 782 unique CDS sequences used were subjected to a two-step classification method. In step one, each CDSs was broken down into a 61-dimensional vector representing each of the 61 ...
3
Consider mRNA primary structure in terms of uORFs, upstream open reading frames. These can cause ribosome pausing or slowing and even disassociation from the mRNA.
I agree that a definite answer is not known (+1). For different mRNAs, under different cellular conditions (eg, low levels of a given charged tRNA), the balance or interplay between structure- ...
3
eQTLs (expression quantitative trait loci) are variants that affect the expression of one or more genes.
There have been several 'genome-wide' studies of SNPs that directly affect expression. The actual effect sizes are hard to pin down in most of them, but in the supplementary data for this paper is a list of the SNPs with the largest effects and ...
3
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 ...
3
I can answer this - I may not have time to dig though the file you are pointing to... but here's some explanation - lmk if you need more.
The shorter names (123456_at) are the original names for the probe sets that Affymetrix gave. The file you area asking about has been extended for FlyBase's purpose and I'm only dimly aware of its existence. It looks ...
2
One way to learn more about how your protein is being processed/degraded is to add two different tags on either end of your protein. Express your protein, then blot with the two antibodies for your tags. The most likely scenario here is that one end or another is being cleaved and then degraded - you'll be able to tell which end by what tag epitope remains. ...
2
You could also try induction at lower temperatures to minimize chances of protein degradation. Cells such as Arctic cells (http://tinyurl.com/arcticecoli) are optimized for low temperature expression although BL21 works just as good for the proteins we express (upto 140kDa in size)
2
These two papers[1] [2] argue that bcd is a direct activator of hb, although be aware that this does not rule out downstream events feeding back to further activate hb. (In fact, given the complexity of the embryonic gene network, it is likely that both mechanisms have a role.)
Struhl G, Struhl K, Macdonald PM. 1989. The gradient morphogen bicoid is a ...
2
See papers by D Bianchi for reports of miR levels in blood of pregnant humans, both of maternal and fetal origin.
A review by Steer and Subramanian offers a number of examples pertaining to your question.
Lastly, Vickers, Palmisano, et al. (2011) show that some miRs are present in the HDL-cholesterol particle and that those levels differ between normal and ...
2
This isn't the answer you're probably looking for, but I'd recommend not bothering with what they mean about their test in particular ... maybe they were really using a mann-whitney but their software (SPLUS) labeled it as a "non-parametric t test" for the non-formally-trained-statistical-end-user
[update]: I misread the text and thought you (and the ...
2
One answer can be found in the UniProt FAQ:
What is the human complete proteome?
In 2008, a draft of the complete human proteome was released from
UniProtKB/Swiss-Prot: the approximately 20,000 putative human
protein-coding genes were represented by one UniProtKB/Swiss-Prot
entry, tagged with the keyword 'Complete proteome'. This
...
2
Its a bit confusing, but DAVID uses the term Gene List as a generic term.
Looking at Step 2, you can submit many kinds of lists to DAVID, including actual gene symbols, Ensembl or RefSeq Accessions, etc... actually nearly 30 kinds of terms including 'not sure' which probably looks at your list and tries to guess.
Affymetrix or Illumina probe set IDs are ...
2
If you have control expression values $c$ and e.g. disease expression values $d$, you take the ratio: $\frac{d}{c}$. If this is greater than one, it's up-regulated. Usually, the log-ratio is computed: $log\frac{d}{c}$. Now, if this is positive, the gene is up-regulated.
Gene expression values are usually measured genome-wide and then normalized before ...
2
This is the FlyBase page for the example gene: Dsim\GD10095. There, you have a section "orthologs", linking to OrthoDB. So my suggestion is: Find the list of synonyms for D. simulans on FlyBase (perhaps here?), download the Drosophila section of OrthoDB, and finally find the 1:1 orthologs.
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