functional_enrichment_new - Baliga Lab at Institute for Systems
... # generate a summary of the enrichment analysis > results.table <- GenTable(GOdata.BP, results, topNodes = length(results@score)) # How many GO terms were tested? > dim(results.table)[1] # reduce results to GO terms passing Benjamini-Hochberg multiple hypothesis ...
... # generate a summary of the enrichment analysis > results.table <- GenTable(GOdata.BP, results, topNodes = length(results@score)) # How many GO terms were tested? > dim(results.table)[1] # reduce results to GO terms passing Benjamini-Hochberg multiple hypothesis ...
Structural organization of the malaria mosquito heterochromatin
... gambaie genome, we physically mapped genes to the polytene chromosomes: 16.6 Mb of the mapped portion in the An. gambiae genome has been identified as heterochromatin. Unlike Drosophila, Anopheles possesses three large regions (0.7, 0.8, and 2.9 megabase pairs long) of intercalary heterochromatin. T ...
... gambaie genome, we physically mapped genes to the polytene chromosomes: 16.6 Mb of the mapped portion in the An. gambiae genome has been identified as heterochromatin. Unlike Drosophila, Anopheles possesses three large regions (0.7, 0.8, and 2.9 megabase pairs long) of intercalary heterochromatin. T ...
cystic fibrosis
... As long as we're drawing blood from you today, Nancy, would you consent to participate in one of the genetics studies we're conducting here at People's Best Hospital?" Dr. Kwin prided herself on putting her patients at ease, but her question caught Nancy a little off guard. "What would that entail, ...
... As long as we're drawing blood from you today, Nancy, would you consent to participate in one of the genetics studies we're conducting here at People's Best Hospital?" Dr. Kwin prided herself on putting her patients at ease, but her question caught Nancy a little off guard. "What would that entail, ...
portable document (.pdf) format
... in some but not all samples in a disease group. The detection of DE genes has become increasingly useful in cancer studies, where oncogenes are only activated in a minority of samples. Since there are not many discussions about detecting DE genes in multi-group microarrays, we are in need of more ap ...
... in some but not all samples in a disease group. The detection of DE genes has become increasingly useful in cancer studies, where oncogenes are only activated in a minority of samples. Since there are not many discussions about detecting DE genes in multi-group microarrays, we are in need of more ap ...
Phylogenomics: improving functional predictions for uncharacterized
... present an outline of one such phylogenomic method (see Fig. 1), and I compare this method to nonevolutionary functional prediction methods. This method is based on a relatively simple assumption—because gene functions change as a result of evolution, reconstructing the evolutionary history of genes ...
... present an outline of one such phylogenomic method (see Fig. 1), and I compare this method to nonevolutionary functional prediction methods. This method is based on a relatively simple assumption—because gene functions change as a result of evolution, reconstructing the evolutionary history of genes ...
second of three for Chapter 8
... mutant phenotype. • If two working copies of a gene are required for normal gene function, only havinog one is a problem. • ‘Cri du Chat’ syndrome in humans: – Deficiency of a part of chromosome 5 ...
... mutant phenotype. • If two working copies of a gene are required for normal gene function, only havinog one is a problem. • ‘Cri du Chat’ syndrome in humans: – Deficiency of a part of chromosome 5 ...
Journal of Advanced Computing (2012) 1
... knowledge vector and contains a gene identifier for each node. For example, the entries may be the Human Gene Nomenclature Committee (HGNC) identifiers or UniProt protein identifiers. 4) A file containing a root node set. This is a list of r genes specified using the gene identifiers described in 3) ...
... knowledge vector and contains a gene identifier for each node. For example, the entries may be the Human Gene Nomenclature Committee (HGNC) identifiers or UniProt protein identifiers. 4) A file containing a root node set. This is a list of r genes specified using the gene identifiers described in 3) ...
![Exam 3 ANSWER KEY Page 1 [10] 1. The proBA genes are required](http://s1.studyres.com/store/data/022831268_1-65a27ab890c110d79900531dcea4fd6a-300x300.png)
Exam 3 ANSWER KEY Page 1 [10] 1. The proBA genes are required
... a. Briefly describe the difference between an IS element and a transposon. ANSWER: Both IS elements and Transposons can transpose to new sites on the chromosome in a recA independent manner. Both IS elements and transposons produce direct repeats of chromosomal DNA at the insertion site. Both IS ele ...
... a. Briefly describe the difference between an IS element and a transposon. ANSWER: Both IS elements and Transposons can transpose to new sites on the chromosome in a recA independent manner. Both IS elements and transposons produce direct repeats of chromosomal DNA at the insertion site. Both IS ele ...
A SNP in ASAP1 gene is associated with meat quality and
... Regitano, L.C.A.) who found an association of this gene with marbling, SF, and hot carcass weight in Bos taurus beef cattle. We have to considerate that the SNP effect on trait variation could be biased by the small sample size analyzed, so including more animals in these analyses can help to confirm ...
... Regitano, L.C.A.) who found an association of this gene with marbling, SF, and hot carcass weight in Bos taurus beef cattle. We have to considerate that the SNP effect on trait variation could be biased by the small sample size analyzed, so including more animals in these analyses can help to confirm ...
The ApoE gene fact sheet
... people and the impact that these differences may have on our health and risk of disease. At the University of Reading, we are interested in how these variations affect people’s response to foods. For this reason, in some of our studies we ask you to provide a blood sample that we use to determine wh ...
... people and the impact that these differences may have on our health and risk of disease. At the University of Reading, we are interested in how these variations affect people’s response to foods. For this reason, in some of our studies we ask you to provide a blood sample that we use to determine wh ...
8 MOSAICISM—Complex Patterns of Inheritance 3 FACT SHEET
... This Fact Sheet discusses another example of complex patterns of inheritance, where the genetic change is not present in all the cells of the individual. Instead, they have a mixture of cells containing the correct genetic information, and cells containing the changed information. This situation is ...
... This Fact Sheet discusses another example of complex patterns of inheritance, where the genetic change is not present in all the cells of the individual. Instead, they have a mixture of cells containing the correct genetic information, and cells containing the changed information. This situation is ...
A single-nucleotide polymorphism tagging set for human drug
... Carlson, C.S. et al. Selecting a maximally informative set of single-nucleotide polymorphisms for association analyses using linkage disequilibrium. Am. J. Hum. Genet. 74, 106−120 (2004). ...
... Carlson, C.S. et al. Selecting a maximally informative set of single-nucleotide polymorphisms for association analyses using linkage disequilibrium. Am. J. Hum. Genet. 74, 106−120 (2004). ...
BioOntologies2007_jb.. - Bio
... Total experimental GO annotations - 388,633 Total proteins with manual annotations – 80,402 ...
... Total experimental GO annotations - 388,633 Total proteins with manual annotations – 80,402 ...
Background concepts for sequence analysis Ana, homo
... The claim that two sequences are homolog thus results from an inference, based on some evolutionary scenario (rate of mutation, level of similarity, !). The inference of homology is always attached to some risk of false positive. Evolutionary models allow to estimate this risk, as we shall see. ...
... The claim that two sequences are homolog thus results from an inference, based on some evolutionary scenario (rate of mutation, level of similarity, !). The inference of homology is always attached to some risk of false positive. Evolutionary models allow to estimate this risk, as we shall see. ...
Functional Analysis of Drosophila melanogaster Gene Regulatory
... may be significant (Parsch et al. 1997). Gene replacement by homologous recombination is possible in Drosophila melanogaster (Rong and Golic 2000; Gong and Golic 2003), but this method is best applied when a particular gene or chromosomal region is targeted. When putative regulatory elements are bei ...
... may be significant (Parsch et al. 1997). Gene replacement by homologous recombination is possible in Drosophila melanogaster (Rong and Golic 2000; Gong and Golic 2003), but this method is best applied when a particular gene or chromosomal region is targeted. When putative regulatory elements are bei ...
Linkage and Recombination
... Note that the genes are linked; if they weren't, we would have 8 phenotypes and 8 gamete genotypes in approximately equal numbers. Arranged in pairs of equal numbers, in order of magnitude. Which are parental genotypes? Which are double crossover genotypes? ...
... Note that the genes are linked; if they weren't, we would have 8 phenotypes and 8 gamete genotypes in approximately equal numbers. Arranged in pairs of equal numbers, in order of magnitude. Which are parental genotypes? Which are double crossover genotypes? ...
iCLIP HeLa cells were UV crosslinked before lysing in lysis buffer
... proceeding to further analysis. (iii) Control file with random placement of iCLIP reads on corresponding genes was generated 100 times. Each 5’UTR, 3’ UTR, and each intron is its own region; all remaining parts of the gene are its own region (these will be all exononic sequences corresponding to OR ...
... proceeding to further analysis. (iii) Control file with random placement of iCLIP reads on corresponding genes was generated 100 times. Each 5’UTR, 3’ UTR, and each intron is its own region; all remaining parts of the gene are its own region (these will be all exononic sequences corresponding to OR ...
Probabilites on Pedigrees
... • Value greater than 3.0 considered to show linkage • (This is a 1 in 1000 chance–conservative but allows for multiple tests) • Value less than -2.0 shows non-linkage (100:1 against) ...
... • Value greater than 3.0 considered to show linkage • (This is a 1 in 1000 chance–conservative but allows for multiple tests) • Value less than -2.0 shows non-linkage (100:1 against) ...
Reconstruction of Amino Acid Biosynthesis Pathways from the
... During the pathway reconstruction process, we have noticed wide variations in the degree of annotation in different complete genome sequences. E. coli (Blattner et al. 1997) is the best annotated genome reflecting the fact that it is the best studied organism by biochemical, genetic, and other exper ...
... During the pathway reconstruction process, we have noticed wide variations in the degree of annotation in different complete genome sequences. E. coli (Blattner et al. 1997) is the best annotated genome reflecting the fact that it is the best studied organism by biochemical, genetic, and other exper ...
Molecular Biology Primer 3
... variation between individuals is quite small. • Out of 3 billion nucleotides, only roughly 3 million base pairs (0.1%) are different between individual genomes of humans. • Although there is a finite number of possible variations, the number is so high (43,000,000) that we can assume no two individu ...
... variation between individuals is quite small. • Out of 3 billion nucleotides, only roughly 3 million base pairs (0.1%) are different between individual genomes of humans. • Although there is a finite number of possible variations, the number is so high (43,000,000) that we can assume no two individu ...
Copy-number variation
Copy-number variations (CNVs)—a form of structural variation—are alterations of the DNA of a genome that results in the cell having an abnormal or, for certain genes, a normal variation in the number of copies of one or more sections of the DNA. CNVs correspond to relatively large regions of the genome that have been deleted (fewer than the normal number) or duplicated (more than the normal number) on certain chromosomes. For example, the chromosome that normally has sections in order as A-B-C-D might instead have sections A-B-C-C-D (a duplication of ""C"") or A-B-D (a deletion of ""C"").This variation accounts for roughly 13% of human genomic DNA and each variation may range from about one kilobase (1,000 nucleotide bases) to several megabases in size. CNVs contrast with single-nucleotide polymorphisms (SNPs), which affect only one single nucleotide base.