Practical Bioinformatics Mark Voorhies 5/23/2019 Mark Voorhies - - PowerPoint PPT Presentation

▶
practical bioinformatics
SMART_READER_LITE
LIVE PREVIEW

Practical Bioinformatics Mark Voorhies 5/23/2019 Mark Voorhies - - PowerPoint PPT Presentation

Jan 09, 2023 198 likes •330 views

Practical Bioinformatics Mark Voorhies 5/23/2019 Mark Voorhies Practical Bioinformatics JavaTreeView link-out for ENSEMBL Mouse http://www.ensembl.org/Mus musculus/Gene/Summary?g=HEADER Mark Voorhies Practical Bioinformatics Science! Mark

slide-1
SLIDE 1

Practical Bioinformatics

Mark Voorhies 5/23/2019

Mark Voorhies Practical Bioinformatics

slide-2
SLIDE 2

JavaTreeView link-out for ENSEMBL Mouse

http://www.ensembl.org/Mus musculus/Gene/Summary?g=HEADER

Mark Voorhies Practical Bioinformatics

slide-3
SLIDE 3

Science!

Mark Voorhies Practical Bioinformatics

slide-4
SLIDE 4

Example Pipeline: Overview

Mark Voorhies Practical Bioinformatics

slide-5
SLIDE 5

Example Pipeline: Details

Mark Voorhies Practical Bioinformatics

slide-6
SLIDE 6

GSE88801 Pipelines

Mark Voorhies Practical Bioinformatics

slide-7
SLIDE 7

Linear Least Squares

Mark Voorhies Practical Bioinformatics

slide-8
SLIDE 8

Linear Least Squares

bi = yi σi

Mark Voorhies Practical Bioinformatics

slide-9
SLIDE 9

Linear Least Squares

Aij = fj(xi) σi

Mark Voorhies Practical Bioinformatics

slide-10
SLIDE 10

Linear Least Squares

χ2 = |A · a − b|2

Mark Voorhies Practical Bioinformatics

slide-11
SLIDE 11

Linear Least Squares

a =

M

  • i

Ui · b si

  • Vi

Mark Voorhies Practical Bioinformatics

slide-12
SLIDE 12

Multiple Hypothesis Testing

http://xkcd.com/882/ Mark Voorhies Practical Bioinformatics

slide-13
SLIDE 13

Homework

Explore today’s limma results for the

live uninfected |J77,24h comparison

(choose two or more):

1 Extract the gene names from

limma1.J774.Live.24-J774.uninfected.24.t0.csv and paste them into the selection window in JavaTreeView.

2 Filter yesterday’s heatmap to create a new CDT file for just

these differential genes.

3 Redo our PCA and clustering protocol for just these

differential genes.

4 Find the corresponding set of differential genes from the “J774

Live vs Uninfected” tab of S2 of the paper. Use python sets to find differential genes common to the two analysis pipelines.

5 Repeat the above for other interesting comparisons. Mark Voorhies Practical Bioinformatics