Pathway Informatics December 5, 2018 Ansuman Chattopadhyay, PhD Asst Director, Molecular Biology information service Health sciences library system University of pittsburgh ansuman@pitt.edu

http://hsls.libguides.com/pathwayinformatics Workshop Page http://www.hsls.pitt.edu/molbio

Biological Pathway Map http://www.hsls.pitt.edu/molbio

Software Learn How to … Find Statistically Overrepresented Attribute Linked to Differentially Expressed Genes: IPA, DAVID, Reactome Identify correlated studies from public gene expression repository (GEO): BaseSpace Correlation Engine (Nextbio) http://www.hsls.pitt.edu/molbio

RNA-Seq Software @ HSLS MolBio Enrichment Analysis Deferentially Expressed Genes CLC Genomics Work Bench Ingenuity Pathway Analysis Functions Diseases Pathways RNA-Seq Reads Key Pathway Advisor Upstream Regulators Any Organism Volcano Plot PCA Plot Venn Diagram Heat Map Illumina BaseSpace Correlation Engine Correlated Expression Studies CLC BioMedical Work Bench Variant Detection Ingenuity Variant Analysis Human, Mouse and Rat Variant Annotation and Prioritization RNA-Seq Analysis Down Stream Analysis http://www.hsls.pitt.edu/molbio

RNA-seq Study http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0099625 http://www.hsls.pitt.edu/molbio

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

NCBI SRA Untreated Vs DEX

RNA-Seq Workshop FASTq Reads CLC Genomics WorkBench RNA-Seq Analysis Pipeline Dex vs UNT DEG

FDR p-value <0.05 Number of genes: 1161 Suggested Number of Genes: Dex vs. Unt CLCGx DEG Output FDR p-value <0.05 Number of genes: 1161 Suggested Number of Genes: Between 5% to 10% of the background http://files.hsls.pitt.edu/files/molbio/DEXvsUNT_CLCGx_IPA.xlsx

GraphPad Statistics Guide : https://www.graphpad.com/guides/prism/7/statistics/index.htm

Data Formatting

Software Registration http://hsls.libguides.com/molbio/licensedtools/resources

Data Formatting IPA One Excel spread sheet Row one: Column Headers

Correlation Engine Data Formatting One Excel spread sheet Column A should be gene names Column A Header: Gene

Reactome Data Formatting Save Excel Spread Sheet in a tab delimited text Column A header: #Gene; Column B header : # FoldChange etc

Pathway Drawing ePath3D https://hsls.libguides.com/MolBioWorkshops/PathViz

Seminal Paper http://www.pnas.org/content/102/43/15545

Input Datasets Gene List DEG with expression FC

Databases to Search Gene Ontology (GO) Broad Molecular Signature Database (mSigdb) Reactome Pathway WikiPathway Ingenuity Pathway database Metacore GeneGO Gene List Pathway Database Signaling Metabolic

https://journals. plos. org/ploscompbiol/article. id=10. 1371/journal https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1002375

Figure 1. Overview of existing pathway analysis methods using gene expression data as an example. NIH-DAVID GSEA IPA 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.1002375 http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1002375

DAVID Bioinformatics Resources http://www.hsls.pitt.edu/molbio

DAVID Tools Functional Annotation Clustering Chart – Term centric Table – Gene centric http://www.hsls.pitt.edu/molbio

DAVID http://www.nature.com/nprot/journal/v4/n1/fig_tab/nprot.2008.211_T1.html http://www.hsls.pitt.edu/guides/genetics

NIH DAVID http://www.hsls.pitt.edu/molbio

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

IPA

Correlation Engine http://www.hsls.pitt.edu/molbio

Correlation Engine http://www.hsls.pitt.edu/molbio

Pathway analysis in non human, mouse and rat

Protein-Protein Interaction Database Pathway Informatics List of Genes Protein-Protein Interaction Database Pathway Map http://www.hsls.pitt.edu/molbio

PPI Databases BioGRID STRING http://www.hsls.pitt.edu/molbio

Thank you! Any questions? Ansuman Chattopadhyay ansuman@pitt.edu http://www.hsls.pitt.edu/molbio