Pathway Informatics 12 th - PowerPoint Presentation

Slide1

Pathway Informatics12th September, 2018

Ansuman Chattopadhyay, PhDMolecular Biology Information ServicesHealth Sciences Library SystemUniversity of Pittsburghansuman@pitt.eduSlide2

Workshop Pagehttp://hsls.libguides.com/pathwayinformaticshttp://

www.hsls.pitt.edu/molbioSlide3

Biological Pathway Map

http://www.hsls.pitt.edu/molbioSlide4

SoftwareLearn How to …Search Gene Expression Databases: Correlation EngineFind Statistically Overrepresented A

ttribute Linked to Differentially Expressed Genes: IPA, DAVID, Metacore,KPA

http://

www.hsls.pitt.edu/molbioSlide5

RNA-Seq Software @ HSLS MolBioRNA-Seq

Reads

CLC Genomics

Work Bench

CLC

BioMedical

Work Bench

Deferentially Expressed Genes

Variant Detection

Volcano Plot

Heat Map

Venn

Diagram

PCA Plot

Ingenuity

Pathway Analysis

Enrichment Analysis

Pathways

Functions

Diseases

Upstream Regulators

Down Stream Analysis

Key Pathway Advisor

Illumina

BaseSpace

Correlation Engine

Any Organism

Human, Mouse and Rat

Correlated Expression Studies

Ingenuity

Variant Analysis

Variant Annotation

and Prioritization

RNA-

Seq

AnalysisSlide6
Slide7

https://hsls.libguides.com/flowSlide8

Spotlight Series: Software Developed @ Pitt

Photo: www.flickr.com/photos/ky0ncheng/36928627722 FRED: A Versatile Framework for Modeling Infectious Diseases & Other Health Conditions

David Sinclair, PhD

Public Health Dynamics Lab

Thursday, September 20

th

, 2018

2 - 4 pm

Scaife Hall, Falk Library,

Upper

Floor Study Area

Wiki-PI & LENS:

Web Applications studying Genes to Functions, Pathways, & Drugs

Madhavi Ganapathiraju, PhD

Dept Biomedical Informatics

Thursday, October 25

th

, 2018

2 - 4 pm

Scaife Hall, Falk Library,

First

Floor Study Area

Register @

www.hsls.pitt.edu/calendar

Sessions begin with a 30-minute presentation of tool development & use cases, followed by instruction on software access/installation, discussion of parameters, & hands-on practice.  Slide9

Software Registrationhttp://hsls.libguides.com/molbio/licensedtools/resourcesSlide10

RNA-seq Studyhttp://journals.plos.org/plosone/article?id=10.1371/journal.pone.0099625Slide11
Slide12
Slide13

NCBI SRAUntreated Vs DEXSlide14

RNA-Seq WorkshopFASTq ReadsCLC Genomics

WorkBenchRNA-Seq Analysis PipelineDex vs UNT DEGSlide15
Slide16

Download DEX vs UNT DEG Datasethttp://files.hsls.pitt.edu/files/molbio/DEXvsUNT.xlsxSlide17

IPACorrelation Engine

DEX vs UNT DEGEnriched Pathways, Functions, Diseases, Upstream RegulatorsGEO Correlated Studies+ve and -veSlide18

Pathway DrawingePath3dhttp://www.epath3d.com/SignInChemOffice Professionalhttp://technology.pitt.edu/softwareSlide19

Figure 1. Overview of existing pathway analysis methods using gene expression data as an example.

Khatri P, Sirota M, Butte AJ (2012) Ten Years of Pathway Analysis: Current Approaches and Outstanding Challenges. PLOS Computational Biology 8(2): e1002375. https://doi.org/10.1371/journal.pcbi.1002375http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1002375Slide20

GO AnnotationCellular ComponentBiological ProcessMolecular Function

http://www.hsls.pitt.edu/molbioSlide21

Copyright restrictions may apply.

Khatri, P. et al. Bioinformatics 2005 21:3587-3595; doi:10.1093/bioinformatics/bti565Levels of abstractionGene Ontology (GO)Slide22

Gene ListsMicroarraysProtein arraysCHIP-chipSNP arraysRNA SeqLiterature Search

http://www.hsls.pitt.edu/molbioSlide23

DAVID Bioinformatics Resources  http://

www.hsls.pitt.edu/molbioSlide24

DAVID ToolsFunctional AnnotationClustering Chart – Term centricTable – Gene centric

http://www.hsls.pitt.edu/molbioSlide25

DAVIDhttp://www.nature.com/nprot/journal/v4/n1/fig_tab/nprot.2008.211_T1.html

http://www.hsls.pitt.edu/guides/geneticsSlide26

NIH DAVID

http://www.hsls.pitt.edu/molbioSlide27

http://

www.hsls.pitt.edu/molbioSlide28

Figure 1. Overview of existing pathway analysis methods using gene expression data as an example.

Khatri P, Sirota M, Butte AJ (2012) Ten Years of Pathway Analysis: Current Approaches and Outstanding Challenges. PLOS Computational Biology 8(2): e1002375. https://doi.org/10.1371/journal.pcbi.1002375http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1002375Slide29

IPASlide30

Biological PathwaysMetabolicSignaling

http://www.hsls.pitt.edu/molbioSlide31

Correlation Engine

http://www.hsls.pitt.edu/molbioSlide32
Slide33
Slide34
Slide35
Slide36

Correlation Engine

http://www.hsls.pitt.edu/molbioSlide37

Pathway analysis in non human, mouse and ratSlide38

Pathway Informatics

http://www.hsls.pitt.edu/molbioSlide39

PPI DatabasesBioGRIDSTRING

http://www.hsls.pitt.edu/molbioSlide40

Retrieve Gene Lists

http://www.hsls.pitt.edu/molbioSlide41

Gene Expression Databases

http://www.hsls.pitt.edu/molbioSlide42

Gene Expression Database

http://www.hsls.pitt.edu/molbioSlide43

Use of GEO Datahttp://goo.gl/yD2hR

http://www.hsls.pitt.edu/molbioSlide44

Generate a gene listhttp://

www.hsls.pitt.edu/molbioSlide45

Retrieve Gene Expression dataNCBI GEOEBI ArrayExpressNextBio Research

http://www.hsls.pitt.edu/molbioSlide46

Gene Expression Database

http://www.hsls.pitt.edu/molbioSlide47

Searching GEO

http://www.hsls.pitt.edu/molbioSlide48

Searching GEO

http://www.hsls.pitt.edu/molbioSlide49

Searching GEO

http://www.hsls.pitt.edu/molbioSlide50

GEO2R

http://www.hsls.pitt.edu/molbioSlide51

GEO2R – Experiment to Gene List

http://www.hsls.pitt.edu/molbioSlide52

GEO2R – Experiment to Gene List

http://www.hsls.pitt.edu/molbioSlide53

GEO2R – Experiment to Gene List

http://www.hsls.pitt.edu/molbioSlide54

http://

www.hsls.pitt.edu/molbioSlide55

Literature to GeneList

http://www.hsls.pitt.edu/molbioSlide56

Thank you!Any questions? Ansuman Chattopadhyay

ansuman@pitt.edu http://www.hsls.pitt.edu/molbio