Term
| 2 methods to compare transcriptomes |
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Definition
Microarrays or RNA-seq
Microarrays are based on the genome sequence of one species. They can be used for closely-
related specie.DNA sequence divergence should not affect hybridization. |
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Term
| Genetic causes of different expression |
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Definition
a) cis – a change in the regulatory sequence
b) trans–a change in a different, unlinked gene(TFs) that affects expression of the target gene |
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Term
| How to distinguish between cis and trans? |
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Definition
| Made F1 hybrids,then compared expression level of genes in the two parents plus the hybrid offspring using pyrosequencing. If changes are trans, alleles should be expressed equally in hybrids (same pool of TFs). If changes are cis, the two alleles should be expressed differently in the hybrid and match the expression difference between the parents. |
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Term
| Cytochrome family's function in fly |
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Definition
| In D.melanogaster,Cyp6g1.Cytochrome P450’s are a large family of related genes (≈90) involved in the metabolism of many compounds. |
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Term
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Definition
| In DDT-R flies, there is a TE insertion at the 5’ end of the Cyp6g1.DDT-S flies (susceptible) don't have it. DDT-R flies have higher expression of Cyp6g1,than DDT-S flies. TE insertion increases gene expression and leads to DDT resistance |
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Term
| Population transcriptomics is |
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Definition
| The comparison of global gene expression levels among individuals from natural populations of a species. |
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Term
| M28 strain of yeast: characteristics |
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Definition
1.resistance to trifluoroleucine
2.resistance to copper sulfate
3.colony morphology (filigreed vs. smooth) |
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Term
| M28 strain of yeast:variation in transcriptome |
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Definition
| Compared M28 F progeny and S progeny using cDNA microarrays.378 genes had 2-fold or greater difference in expression between F and S (≈6% of genes). As a control, only 8 genes differed by 2-fold or more when different samples. |
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Term
| M28 strain of yeast:which genes are different |
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Definition
| Genes in F are involved in amino acid synthesis (12 of them for met).Two others are for sulfate transport. This is probably an important adaptation that leads to resistance to sulfates. |
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Term
| Factors,that affect transcriptome analysis |
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Definition
| quality of the data, the number of replicates, and the statistical method used to define differential expression |
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Term
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Definition
Expression quantitative trait loci, level of expression of a given gene is a phenotype that can be measured on a continuous scale, it can be treated like other quantitative
traits and one can look for associations between DNA sequence polymorphisms and expression level |
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Term
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Definition
If the SNP is on a different chromosome than the gene (or far away on the same chromosome), it can be considered trans-acting. If it is on the same chromosome and near the gene, it can be considered cis-acting. This will depend on the species and the amount of linkage disequilibrium(LD).
For humans it is 1 MB. |
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