Lab 11: Simple genomic data analysis using R 1. UCSC genome
... type return as “gzip compressed”, then click “get output.” This will take a little time. Or you can access the file on the course website. The downloaded text file is a lit of human hg18 refseq genes. Open the file to take a quick look. Each row is for a gene. Columns are for properties of the genes ...
... type return as “gzip compressed”, then click “get output.” This will take a little time. Or you can access the file on the course website. The downloaded text file is a lit of human hg18 refseq genes. Open the file to take a quick look. Each row is for a gene. Columns are for properties of the genes ...
Talk2.stat.methods
... could be very small and hence it may result in inflated Type I errors and inflated false discovery rates. ...
... could be very small and hence it may result in inflated Type I errors and inflated false discovery rates. ...
Datamining Methods - ILRI Research Computing
... Sili = (bi-ai)/max(ai,bi) ai-average within cluster distance with respect to gene i bi-average between cluster distance with respect to gene i expvalues.sil = silhouette(expvalue.groups, expvalues.dist) ...
... Sili = (bi-ai)/max(ai,bi) ai-average within cluster distance with respect to gene i bi-average between cluster distance with respect to gene i expvalues.sil = silhouette(expvalue.groups, expvalues.dist) ...
Dr Ishtiaq Regulation of gene expression
... and is always expressed (constitutive). • Hinder production of β-galactosidase in the absence of lactose. • If lactose is missing from the growth medium, the repressor binds very tightly to a short DNA sequence called the lac operator. • The repressor binding to the operator interferes with binding ...
... and is always expressed (constitutive). • Hinder production of β-galactosidase in the absence of lactose. • If lactose is missing from the growth medium, the repressor binds very tightly to a short DNA sequence called the lac operator. • The repressor binding to the operator interferes with binding ...
GMO vs Selective breeding
... the process by which humans breed other animals and plants for particular traits. Typically, strains that are selectively bred are domesticated, and the breeding is normally done by a professional ...
... the process by which humans breed other animals and plants for particular traits. Typically, strains that are selectively bred are domesticated, and the breeding is normally done by a professional ...
Ph - SDU
... malformations in mucosa and in visceral organs. The most common symptom is epistaxis. However the disease may cause a wide variety of other serious symptoms as pulmonary arteriovenous malformations (PAVM), cerebrale arteriovenous malformations (CAVM) and gastrointestinal bleeding. HHT, as a disease, ...
... malformations in mucosa and in visceral organs. The most common symptom is epistaxis. However the disease may cause a wide variety of other serious symptoms as pulmonary arteriovenous malformations (PAVM), cerebrale arteriovenous malformations (CAVM) and gastrointestinal bleeding. HHT, as a disease, ...
Developing a new genetic system in bacteria
... – Fusing reporter gene with start codon (translational fusion) retains ribosome binding site from target organism – Fusing reporter gene with promoter usually replaces native ribosome binding site with that of reporter gene (due to proximity of ribosome binding site to start codon – need to add a go ...
... – Fusing reporter gene with start codon (translational fusion) retains ribosome binding site from target organism – Fusing reporter gene with promoter usually replaces native ribosome binding site with that of reporter gene (due to proximity of ribosome binding site to start codon – need to add a go ...
GENETIC ENGINEERING (ppt)
... • Genetically engineered Atlantic salmon has an added growth hormone from a Chinook salmon that allows the fish to produce growth hormone yearround. Scientists were able to keep the hormone active by using a gene from an eel-like fish called an ocean pout, which acts as an “on switch” for the hormon ...
... • Genetically engineered Atlantic salmon has an added growth hormone from a Chinook salmon that allows the fish to produce growth hormone yearround. Scientists were able to keep the hormone active by using a gene from an eel-like fish called an ocean pout, which acts as an “on switch” for the hormon ...
HOX genes (1)
... have a very broad binding specificity, which does not explain the refined specific regulation of target genes observed in vivo. So how can this be explained? ...
... have a very broad binding specificity, which does not explain the refined specific regulation of target genes observed in vivo. So how can this be explained? ...
Data Mining - functional statistical genetics/bioinformatics
... Expression (SAFE) Generalization and extension of GSEA method 2 stage permutation based approach to asses significant ...
... Expression (SAFE) Generalization and extension of GSEA method 2 stage permutation based approach to asses significant ...
Horizontal gene transfer of antimicrobial
... bacteria exchange AMR genes with other bacteria by horizontal gene transfer mechanisms – “bacterial sex”. Our recent studies have suggested that the important AMR pathogen methicillin-resistant Staphylococcus aureus (MRSA) acquires AMR genes at very high frequency as it colonizes the host, but also ...
... bacteria exchange AMR genes with other bacteria by horizontal gene transfer mechanisms – “bacterial sex”. Our recent studies have suggested that the important AMR pathogen methicillin-resistant Staphylococcus aureus (MRSA) acquires AMR genes at very high frequency as it colonizes the host, but also ...
Text S1.
... On the one hand, for expression values of the same mean, the higher the score, the less sparse the values are. It prioritizes the contrasts where genes’ expression values are more consistent. On the other hand, for expression values of the same standard deviation, the higher the score, the higher th ...
... On the one hand, for expression values of the same mean, the higher the score, the less sparse the values are. It prioritizes the contrasts where genes’ expression values are more consistent. On the other hand, for expression values of the same standard deviation, the higher the score, the higher th ...
OPERONS NOTES
... The lacI regulatory gene is called the lacI regulator gene. Regulatory genes are not necessarily close to the operons they affect. The general term for the product of a regulatory gene is a regulatory protein. -The Lac regulatory protein is called a repressor because it keeps RNA polymerase from tra ...
... The lacI regulatory gene is called the lacI regulator gene. Regulatory genes are not necessarily close to the operons they affect. The general term for the product of a regulatory gene is a regulatory protein. -The Lac regulatory protein is called a repressor because it keeps RNA polymerase from tra ...
Improved glutathione production by gene expression in
... Glutathione (GSH, or L - γ -glutamyl-L-γ -cysteinylglycine) exists widely in nature and protects cells againstoxidation (Meister 1994). Its antioxidation function is mainly due to its role in maintaining the normal redox environment of cells (Izawa et al. 1995). GSH is now widely used in pharmaceut ...
... Glutathione (GSH, or L - γ -glutamyl-L-γ -cysteinylglycine) exists widely in nature and protects cells againstoxidation (Meister 1994). Its antioxidation function is mainly due to its role in maintaining the normal redox environment of cells (Izawa et al. 1995). GSH is now widely used in pharmaceut ...
Genetics Unit 2 – Transmission Genetics
... A) Sickle Cell Anemia B) Familial Hypercholesterolemia 3. _______________________ – both alleles are expressed A) AB blood type 4. Epistasis – one _______________ or affects the expression of a different gene. A) Bombay phenotype – some people have Type ___ blood, but not genotype ___ due to __ and ...
... A) Sickle Cell Anemia B) Familial Hypercholesterolemia 3. _______________________ – both alleles are expressed A) AB blood type 4. Epistasis – one _______________ or affects the expression of a different gene. A) Bombay phenotype – some people have Type ___ blood, but not genotype ___ due to __ and ...
Heredity patterns of traits - WidgetsandWhatchamacallits
... • A chromosome stained in order to see the striping pattern of some of the genes. ...
... • A chromosome stained in order to see the striping pattern of some of the genes. ...
My Pediatric Endocrine Powerpoint
... of respirations (Kussmaul respirations: hyperventilation associated with metabolic acidosis) ...
... of respirations (Kussmaul respirations: hyperventilation associated with metabolic acidosis) ...
2. gene interactions
... genes plus the environment. SLIDE 2 Epistasis – Labrador colors We demonstrate the phenomenon of epistasis with the determination of hair color of Labrador dog breed. The dominant version of gene „B” (allele B) determines black color, while the recessive version (allele b) determines brown. Another ...
... genes plus the environment. SLIDE 2 Epistasis – Labrador colors We demonstrate the phenomenon of epistasis with the determination of hair color of Labrador dog breed. The dominant version of gene „B” (allele B) determines black color, while the recessive version (allele b) determines brown. Another ...
Identification of Coding Sequences
... use a data ‘training set’ to build rules that can make predictions or classifications on data sets. ...
... use a data ‘training set’ to build rules that can make predictions or classifications on data sets. ...
Maple Syrup Urine Disease
... encoding dihydrolipoyl transacylase (E2) component of human branched chain alpha-keto acid dehydrogenase and characterization of an E2 pseudogene. J. Biol. Chem. 267: 24090-24096,1992. 4. Mitsubuchi, H.; Nobukuni, Y.; Akaboshi, I.; Indo, Y.; Endo, F.; Matsuda, I.: Maple syrup urine disease caused by ...
... encoding dihydrolipoyl transacylase (E2) component of human branched chain alpha-keto acid dehydrogenase and characterization of an E2 pseudogene. J. Biol. Chem. 267: 24090-24096,1992. 4. Mitsubuchi, H.; Nobukuni, Y.; Akaboshi, I.; Indo, Y.; Endo, F.; Matsuda, I.: Maple syrup urine disease caused by ...
Document
... Yeast two-hybrid system: a genetic assay for detecting protein-protein interactions Regulation of gene expression in yeast ...
... Yeast two-hybrid system: a genetic assay for detecting protein-protein interactions Regulation of gene expression in yeast ...
Microsoft Word
... The candidate genes: CAMK4, TNP1 & 2, PRM1, 2 & 3, UBE2B, UGT2B17, ESR2 and APOB, were selected because studies on mouse and human have shown their roles in spermatogenesis. However, this is for the first time, the CAMK4, UBE2B, UGT2B17 and ESR2 were analyzed for their role in male infertility. Anal ...
... The candidate genes: CAMK4, TNP1 & 2, PRM1, 2 & 3, UBE2B, UGT2B17, ESR2 and APOB, were selected because studies on mouse and human have shown their roles in spermatogenesis. However, this is for the first time, the CAMK4, UBE2B, UGT2B17 and ESR2 were analyzed for their role in male infertility. Anal ...
Genetic Engineering of Late Blight Resistance in Potato
... Sanwen Huang, Dongyu Qu, Jianfei Xu, Zhiqi Jia, Cuihua Xin, Ying Li, Zhonghua Zhang ...
... Sanwen Huang, Dongyu Qu, Jianfei Xu, Zhiqi Jia, Cuihua Xin, Ying Li, Zhonghua Zhang ...
Document
... Figure S4 33Pi uptake in OsPT1-Ox, OsPT1-Ri and wild-type plants. OsPT1-Ox, OsPT1-Ri and wild-type plants were grown for 7d and then transferred into Pi-sufficient (300 µM Pi) medium for 3 d. The Pi uptake of these 10-d-old seedlings was monitored over a 12h period. ...
... Figure S4 33Pi uptake in OsPT1-Ox, OsPT1-Ri and wild-type plants. OsPT1-Ox, OsPT1-Ri and wild-type plants were grown for 7d and then transferred into Pi-sufficient (300 µM Pi) medium for 3 d. The Pi uptake of these 10-d-old seedlings was monitored over a 12h period. ...
Complications to the relationship between genotype to phenotype
... Rb− allele from the other parent. A single mutagenic event in a heterozygous somatic retinal cell that inactivates the normal allele will result in a cell homozygous for two mutant Rb− alleles. (b) In sporadic retinoblastoma, a child receives two normal Rb+ alleles. Two separate somatic mutations, i ...
... Rb− allele from the other parent. A single mutagenic event in a heterozygous somatic retinal cell that inactivates the normal allele will result in a cell homozygous for two mutant Rb− alleles. (b) In sporadic retinoblastoma, a child receives two normal Rb+ alleles. Two separate somatic mutations, i ...