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Pathway Informatics 16th August, 2017
Ansuman Chattopadhyay, PhD Molecular Biology Information Services Health Sciences Library System University of Pittsburgh
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Biological Pathway Map
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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,
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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
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RNA-seq Study
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NCBI SRA Untreated Vs DEX
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RNA-Seq Workshop FASTq Reads CLC Genomics WorkBench
RNA-Seq Analysis Pipeline Dex vs UNT DEG
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Download DEX vs UNT DEG Dataset
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HSLS MolBio
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GEO Correlated Studies
IPA Enriched Pathways, Functions, Diseases, Upstream Regulators Correlation Engine GEO Correlated Studies +ve and -ve DEX vs UNT DEG
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Pathway Drawing ePath3d http://www.epath3d.com/SignIn
ChemOffice Professional
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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): e
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Cellular Component Biological Process Molecular Function GO Annotation
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Gene Ontology (GO) Levels of abstraction
Khatri, P. et al. Bioinformatics : ; doi: /bioinformatics/bti565 Copyright restrictions may apply.
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Gene Lists Microarrays Protein arrays CHIP-chip SNP arrays RNA Seq
Literature Search
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DAVID Bioinformatics Resources
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DAVID Tools Functional Annotation Clustering Chart – Term centric
Table – Gene centric
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DAVID
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NIH DAVID
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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): e
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IPA
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Biological Pathways Metabolic Signaling
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Correlation Engine
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Correlation Engine
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Correlation Engine
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Pathway analysis in non human, mouse and rat
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Protein-Protein Interaction Database
Pathway Informatics List of Genes Protein-Protein Interaction Database Pathway Map
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PPI Databases BioGRID STRING
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Retrieve Gene Lists
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Gene Expression Databases
NCBI Gene Expression Omnibus (GEO) EBI ArrayExpress
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Gene Expression Database
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Use of GEO Data
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Generate a gene list
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Retrieve Gene Expression data
NCBI GEO EBI ArrayExpress NextBio Research
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Gene Expression Database
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Searching GEO
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Searching GEO
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Searching GEO
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GEO2R
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GEO2R – Experiment to Gene List
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GEO2R – Experiment to Gene List
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GEO2R – Experiment to Gene List
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Literature to GeneList
GEO Geo2R NextBio Gene List
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Thank you! Any questions?
Ansuman Chattopadhyay
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