ZuoTi.Pro
Question

Generally, describe how the sequencing data was analyzed for differential gene expression. How was it determined that genes w
science   biology   
0 0
Add a comment Improve this question Transcribed image text
Next > < Previous
Sort answers by oldest

Homework Answers

Answer #1

Hi,

The answers for your questions are as follows.

2. DESeq is an R package to analyse count data from high-throughput sequencing assays such as RNA-Seq and test for differential expression analysis based on negative binomial distribution..

DESeq2 performs an internal normalization where geometric mean is calculated for each gene across all samples. The counts for a gene in each sample is then divided by this mean. DESeq2 detects automatically count outliers using Cooks's distance and removes these genes from analysis. This is how DESeq2 determines the differentially expressed genes.

3. COLLAPSE REPLICATES is the command that will change the number of differentially expressed genes. It works by Collapsing technical replicates in a Ranged Summarized Experiment or DESeqDataSet and thus reduces the numbers of differentially expressed genes.

Will be happy to receive a feedback.

All the best.

Regards,

Dr.VMK.

0 0
Add a comment
Know the answer?
Add Answer to:
Generally, describe how the sequencing data was analyzed for differential gene expression. How was it determined...
Your Answer:

Post as a guest

Your Name:

What's your source?

Earn Coins

Coins can be redeemed for fabulous gifts.

Log In

Sign Up

Not the answer you're looking for? Ask your own homework help question. Our experts will answer your question WITHIN MINUTES for Free.
Similar Homework Help Questions

  • In eukaryotic cells, there are specific transcription factors (activators) that regulate gene expression. Describe the organization...

    In eukaryotic cells, there are specific transcription factors (activators) that regulate gene expression. Describe the organization of eukaryotic genes (i.e. promoters/enhancers) and how transcription factors are able to control gene expression and enzyme activity. a) Throughout the course we discussed the enzyme lactase and how it is differently regulated (and therefore expressed) in different human populations. Describe how this gene is differently expressed in different populations and when this/these change(s) are predicted to have taken place. b) Differential gene expression...

  • Control of gene expression is thought to be achieved (in part) by establishing loops of chromatin...

    Control of gene expression is thought to be achieved (in part) by establishing loops of chromatin such that genes are influenced by DNA enhancers that lie within the same “loop” of DNA . Insulator elements define the boundaries between these distinct chromatin domains. Suppose cells have a region of the chromosome that looks like the following: Enhancer A’ helps drive expression of Gene A exclusively in the kidney. Enhancer B’ helps drive expression of gene B exclusively in the liver....

  • depaniak Bio 152-05 W17 Signed in as sama alsaady nze Homework scientific Thinking: Can Gene Expression...

    depaniak Bio 152-05 W17 Signed in as sama alsaady nze Homework scientific Thinking: Can Gene Expression Data Help Scientists Develop Persona 6 of 7 Part A Interpreting data Patients in Group I Patients in Group II In this activity, you will explore how DNA microarrays are being used as a tool forstudying-andpossibly treating-cancer. The data shown here were obtained from aDNA microarray study of gene expression pattems in 16 cancer patients. Although data for many more genes were obtained from...

  • please help table 1 , Question 1 and 10 procedure is done which is the color...

    please help table 1 , Question 1 and 10 procedure is done which is the color result taly Color in results from the slide microarray or attach a photo Label each gene appropriately O O o ооо Figure 1. Color Intensity chart Expression Ratios 16 1/4 1/8 1/16 Table 1 Gene 1 Gene 2 Gene 3 Gene 4 Gene 5 Gene 6 Expression Ratio Decimal Value Log2 Value Paper Microarray Exercise 1. Describe which genes were induced or repressed in...

  • What control elements regulate expression of the mPGES-1 gene? The promoter of a gene includes the...

    What control elements regulate expression of the mPGES-1 gene? The promoter of a gene includes the DNA immediately upstream of the transcription start site, but expression of the gene can also be affected by control elements. These can be thousands of base pairs upstream of the promoter, grouped in an enhancer. Because the distance and spacing of these control elements make them difficult to identify, scientists begin by deleting sections of DNA that contain possible control elements and measuring the...

  • Explain the following in terms a highschooler would understand (from article Expression of HoxD Genes in...

    Explain the following in terms a highschooler would understand (from article Expression of HoxD Genes in Developing and Regenerating Axolotl Limbs, 1998): DISCUSSION: Expression of HoxD genes in developing axolotl limb buds. We have examined the expression of Hoxd-8, Hoxd10, and Hoxd-11 genes in axolotl limb buds and find many similarities between the patterns of expression in axolotls and those described for other vertebrates. Similarities are most pronounced in phases I and II (Nelson et al., 1996; Shubin et al.,...

  • please answer all the question to get a like. Part III Dr. Hernandez sits down with...

    please answer all the question to get a like. Part III Dr. Hernandez sits down with Ann and her partner. The doctor is sorry to report that Ann has breast cancer; however, because it was caught early and responds to estrogen and progesterone, the prognosis is good. At this point it looks like the cancer is stage 1. However, as Ann is young, the doctor wants to perform a couple of tests. The first test is a genetic sequencing test...

  • Name 2ors L! You are inte finding protein are interested in understanding how Top5 expression is...

    Name 2ors L! You are inte finding protein are interested in understanding how Top5 expression is regulated. Top5 is a microtubule protein. You study a cell line where Top5 expression is controlled by a signal, Ligl. When hinds to and activates the membrane bound recentor it activates the Ras protein, which activates atein kinase called PKF, which then phosphorylates Grp4 on T224. Grp4 is a gene regulatory Wotein that can only enter the nucleus when phosphorylated: Thos is not expressed...

  • A quality engineer analyzed the paint job on the Lexus IS350 model at the Toyota plant...

    A quality engineer analyzed the paint job on the Lexus IS350 model at the Toyota plant in Woodstock. 250 cars were analyzed. The drying time (in hours) and colour of paint was recorded. dentify the variable(s) in the study, (ii) explain the type of data for each variable in the study (e.g., categorical and ordinal, continuous or discrete, etc.), (ii) identify the observational unit, and (iv) determine the sample size 1. For a list of positive numbers, is it possible...

  • 2. A dominant allele H reduces the number of body bristles that Drosophila flies have, giving...

    2. A dominant allele H reduces the number of body bristles that Drosophila flies have, giving rise to a “hairless” phenotype. In the homozygous condition, H is lethal. An independently assorting dominant allele S has no effect on bristle number except in the presence of H, in which case a single dose of S suppresses the hairless phenotype, thus restoring the "hairy" phenotype. However, S also is lethal in the homozygous (S/S) condition. What ratio of hairy to hairless flies...

ADVERTISEMENT
Free Homework Help App
Download From Google Play
Scan Your Homework
to Get Instant Free Answers
Need Online Homework Help?
Ask a Question
Get Answers For Free
Most questions answered within 3 hours.
ADVERTISEMENT
ADVERTISEMENT
ADVERTISEMENT