Pathway Informatics 16th August, 2017 Ansuman Chattopadhyay, PhD Molecular Biology Information Services Health Sciences Library System University of Pittsburgh ansuman@pitt.edu

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

Software Search Gene Expression Databases: Correlation Engine Learn How to … Draw Pathway Diagram : ePath3D, Chem Office, Search PPI Databases: BioGrid, STRING Search Gene Expression Databases: Correlation Engine Find Statistically Overrepresented Attribute Linked to Differentially Expressed Genes: IPA, DAVID, 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

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

NCBI SRA Untreated Vs DEX

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

Download DEX vs UNT DEG Dataset http://files.hsls.pitt.edu/files/molbio/DEXvsUNT.xlsx

Software @ HSLS MolBio http://hsls.libguides.com/molbio/licensedtools/resources

GEO Correlated Studies IPA Enriched Pathways, Functions, Diseases, Upstream Regulators Correlation Engine GEO Correlated Studies +ve and -ve DEX vs UNT DEG

Pathway Drawing ePath3d http://www.epath3d.com/SignIn ChemOffice Professional http://technology.pitt.edu/software

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.1002375 http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1002375

Cellular Component Biological Process Molecular Function GO Annotation http://www.hsls.pitt.edu/molbio

Gene Ontology (GO) Levels of abstraction Khatri, P. et al. Bioinformatics 2005 21:3587-3595; doi:10.1093/bioinformatics/bti565 Copyright restrictions may apply.

Gene Lists Microarrays Protein arrays CHIP-chip SNP arrays RNA Seq Literature Search http://www.hsls.pitt.edu/molbio

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

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.1002375 http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1002375

IPA

Biological Pathways Metabolic Signaling http://www.hsls.pitt.edu/molbio

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

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

Retrieve Gene Lists http://www.hsls.pitt.edu/molbio

Gene Expression Databases NCBI Gene Expression Omnibus (GEO) EBI ArrayExpress http://www.hsls.pitt.edu/molbio

Gene Expression Database http://www.hsls.pitt.edu/molbio

Use of GEO Data http://goo.gl/yD2hR http://www.hsls.pitt.edu/molbio

Generate a gene list http://www.hsls.pitt.edu/molbio

Retrieve Gene Expression data NCBI GEO EBI ArrayExpress NextBio Research http://www.hsls.pitt.edu/molbio

Gene Expression Database http://www.hsls.pitt.edu/molbio

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

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

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

GEO2R http://www.hsls.pitt.edu/molbio

GEO2R – Experiment to Gene List http://www.hsls.pitt.edu/molbio

GEO2R – Experiment to Gene List http://www.hsls.pitt.edu/molbio

GEO2R – Experiment to Gene List http://www.hsls.pitt.edu/molbio

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

Literature to GeneList GEO Geo2R NextBio Gene List http://www.hsls.pitt.edu/molbio

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