The study of genomes (the entirety of the hereditary information) of organisms.
6
votes
2answers
123 views
Effect of single-gene overexpression in the cell's response
Which are the factors that modify the overall gene differential expression by introducing a vector for single-gene overexpression?
If you overexpress a gene for a protein involved in signal ...
2
votes
0answers
27 views
What does conditional analysis of a SNP in a GWA study entail?
I am familiar with the use of tag-SNPs in genome-wide association studies to identify gene loci involved in complex traits, but I keep seeing the term "conditional analysis" used without any ...
3
votes
1answer
57 views
How might gene clusters like the lac operon evolve?
The obvious answer for a gene cluster is gene duplication and mutation of one or both genes. But the genes in the lac operon seem not be so functionally/structurally similar (as compared to the Hox ...
1
vote
1answer
46 views
How are geneticists able to isolate gene functions?
As an example, this Scientific American article describes a known area in the dog genome that metabolizes carbohydrates.
How is it that researchers are able to determine specific functions such as ...
0
votes
0answers
57 views
What are usable Sum formulas for Proteins?
I'm looking for something like this: $C_{13}H_{25}O_7N_3S$
. Obviously it's not about knowing the exact shape or composition of a specific protein, but knowing the relative contents of major chemical ...
4
votes
2answers
67 views
Combining gene expression data from two species
I currently have two sets of gene expression data. The first is a dataframe of genes identified by Annotation id CG numbers (for example "CG10005") in one column and a numerical variable of interest ...
4
votes
1answer
82 views
Can forensic DNA analysis be used to generate a visual approximation of a suspect?
In light of the current US supreme court case, I'm curious if enough information can be teased out of a DNA sample to get a "reasonable" approximation of the suspect (never mind the legality). I ...
9
votes
2answers
302 views
What is the difference between SOLiD, 454, and Illumina next-gen sequencing?
I've started teaching myself about next-generation sequencing in preparation for a new job, and I'm wondering what the main differences are between the 454, SOLiD, and Illumina/Solexa machines, in ...
1
vote
1answer
57 views
What is the best way to read and normalize large amounts of Agilent data into R? [closed]
I have a large amount of Agilent data (580 text files that are ~200 MB in size each) that I'd like to normalize. I've run into a problem in that my machine (with 8 GB of memory) still runs out of ...
10
votes
4answers
192 views
What can you tell about a person, having only their whole genome as information?
Well, the question is in the title, no explanation need.
3
votes
1answer
47 views
Is copy number variation dynamic?
Is there any evidence showing that copy number variation changes over time? I'm wanting to model interactions in expression level as a dynamic bayesian network, but an assumption my approach will need ...
6
votes
3answers
84 views
How to map the Gene name to its Gene Symbol?
I am learning in Gene data lately so I apologize for the silly questions in advance. I read a paper for a cancer on human which found some important genes. For example, the paper listed one of genes ...
0
votes
0answers
99 views
Text Book on Cancer Genomics/Biology [closed]
Could anyone of you suggest few of the best text book(s) for Cancer Genomics/Biology from basic to advance level.
7
votes
1answer
61 views
Do antisense transcripts have different names than their sense strand transcripts?
I want to find which genes in the human genome can potentially be complementary to a transcript that could act as antisense transcript inhibtion? Are cis-NATs (naturally occuring anti-sense ...
3
votes
0answers
59 views
Comparative cost of RNA-seq vs sequencing full length cDNAs
I am in the process of assembling and annotating the genome of a non-model organism, using almost exclusively short read (paired-end Illumina) data. Throughput is one obvious benefit of these data ...
4
votes
1answer
87 views
Which way to run BLAST?
I have a set of scaffolds from a genome assembly, and I want to align a collection of proteins from various species to it. I can do this using BLAST in two ways:
Create a BLAST database of the ...
2
votes
2answers
60 views
Microbiome Data
How is it possible to access microbiome data like that found here? I'd like to perform analyses on similar type of data, but cannot find OTU data like that at the Human Biome Project. Thanks for any ...
6
votes
1answer
163 views
Does DNA contain information beyond protein synthesis?
It's well known that genetic information is stored in DNA. As far as I know, DNA only has information at the protein level. What about higher levels, such as organelles, cells, tissue, organs? Is ...
3
votes
2answers
209 views
Transcript(omics) terminology: cDNAs, ESTs, RNA-seq, etc
I've worked pretty frequently with genome and transcriptome data for several years now, but I'm still not 100% sure I understand the proper usage for certain terminology related to transcripts and ...
6
votes
2answers
212 views
What distinguishes “coding” and “noncoding” DNA from each other?
I've been reading a bit about "junk DNA" and how much of our genome consists of this "non coding DNA" in comparison to "coding DNA".
I'm just an interested layperson but I thought all combinations of ...
11
votes
1answer
188 views
What are the limitations to current nucleotide sequencing technologies?
Using the Illumina platform, it is cheap and (relatively) easy to sequence huge amounts of DNA or RNA. There are various other platforms out there (Roche/454, SOLiD, PacBio, Ion Torrent) each with ...
11
votes
4answers
192 views
Why did high A+T content create problems for the Plasmoduim falciparum genome project?
The main paper for the Plasmodium palciparum genome project (Gardner et al., 2002) repeatedly mentioned that the unusually high A+T content (~80%) of the genome caused problems. For example they imply ...
2
votes
1answer
104 views
Which part of a female mantises's DNA causes her to be a few times larger than a male mantis?
Which part of a female mantises's DNA causes her to be a few times larger than a male mantis?
Do other species have that part of DNA?
5
votes
1answer
77 views
Assembly of metagenomic data
I'm trying to assemble metagenomic data that comes from termite guts. The sequences comes from SOLiD and no paired, so the reads are extremely short (25bp).
I have tried multiple assemblers (CLC, ...
9
votes
2answers
141 views
Shortest strings not present in the human genome
What length are the shortest strings of DNA not present in any known person's genome, and what are they?
And is there a database online by which I could find this out?
5
votes
1answer
147 views
Computational/mathematical models for predicting phenotype from genotype
Karr, Sanghvi, et al. (2012) propose a whole-cell computational model for predicting phenotype from genotype in Mycoplasma genitalium. Their model simulates myriad cell processes such as DNA ...
5
votes
1answer
61 views
DNA methylation and genome size
Is there any relationship between DNA methylation as a level of stability to epigenetic states and genome size? For example, it is claimed that DNA methylation is not required for epigenetic stability ...
5
votes
1answer
137 views
What is the relative power of GWAS studies in different species?
I would like to know of any publication studying the relative power of GWAS studies in different species. For example, I've seen reports that say genotyping and GWAS in dog breeds is much more ...
2
votes
0answers
111 views
Too few transcripts from transcriptome assembler Oases
I am trying to run Oases for transcriptome assembly. The result is far from expected, so I would like to ask whether I am running it in a right way? Thanks.
Here is my running command:
...
13
votes
2answers
188 views
Percentage of genome devoted to regulating gene expression
Recently I've been studying the p53 tumor suppressor gene as a model for regulation of gene expression. It's amazing how many different post-translational modifications are known to regulate p53 ...
7
votes
1answer
43 views
Which functional annotations could be useful?
Analyzing a genome, for a generic gene, which functional annotations (e.g from Gene Ontology) can help understanding its meaning/function or, at least, provide helpful informations?
Annotations of ...
8
votes
2answers
185 views
Are there differences in DNA between humans of today and humans from 2000 years ago?
Are there any significant differences in our genome compared to the genes of our ancestors from 1000-2000 years ago?
And if there are significant differences, do they result in significant ...
8
votes
3answers
128 views
How is the sequenced genome of a person useful to him in practice, now?
Currently it is possible and not so expensive for a person to have his genome. This is useful in general for understanding how life works. But, in practice, how is this useful for the specific person ...
10
votes
1answer
299 views
Sequencing the genomes of polyploid organisms
I've done some transcriptomics work in the past with a polyploid organism, and this presented some unique challenges in the data processing and analysis. Since then, I have been brainstorming about ...
7
votes
2answers
112 views
Is it possible to trace of the ancestry of a person by only using his/her genetic information?
Is it possible to trace the descent of a person only using his/her genome sequence?
10
votes
2answers
150 views
Overlapping genetic information in eukaryotes
In my research, I look at a lot of gene predictions / annotations. Frequently, I see loci where multiple gene models overlap. I haven't taken a systematic approach to analyzing these cases, but I do ...
